Manganese in PDB 4gji: Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
All present enzymatic activity of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose:
5.3.1.14;
Protein crystallography data
The structure of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose, PDB code: 4gji
was solved by
H.Yoshida,
S.Kamitori,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.48 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.124,
104.917,
112.376,
90.00,
106.01,
90.00
|
R / Rfree (%)
|
17.5 /
19.5
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
(pdb code 4gji). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the
Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose, PDB code: 4gji:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 1 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1003
b:15.6
occ:1.00
|
OD1
|
A:ASP327
|
2.1
|
18.0
|
1.0
|
ND1
|
A:HIS281
|
2.2
|
16.0
|
1.0
|
OE2
|
A:GLU219
|
2.2
|
14.1
|
1.0
|
OD1
|
A:ASP254
|
2.2
|
11.2
|
1.0
|
O2
|
A:RNS1001
|
2.2
|
18.6
|
1.0
|
O3
|
A:RNS1001
|
2.4
|
18.5
|
1.0
|
CE1
|
A:HIS281
|
3.0
|
18.5
|
1.0
|
C2
|
A:RNS1001
|
3.1
|
19.8
|
1.0
|
CD
|
A:GLU219
|
3.1
|
13.4
|
1.0
|
CG
|
A:ASP327
|
3.2
|
16.1
|
1.0
|
C3
|
A:RNS1001
|
3.2
|
21.1
|
1.0
|
CG
|
A:HIS281
|
3.3
|
17.3
|
1.0
|
CG
|
A:ASP254
|
3.3
|
12.3
|
1.0
|
OE1
|
A:GLU219
|
3.4
|
12.9
|
1.0
|
CB
|
A:HIS281
|
3.7
|
16.0
|
1.0
|
CB
|
A:ASP327
|
3.8
|
13.8
|
1.0
|
CB
|
A:ASP254
|
3.8
|
12.1
|
1.0
|
O4
|
A:RNS1001
|
3.9
|
26.3
|
1.0
|
CE1
|
A:HIS257
|
3.9
|
12.6
|
1.0
|
MN
|
A:MN1004
|
4.1
|
20.2
|
1.0
|
C4
|
A:RNS1001
|
4.1
|
25.6
|
1.0
|
NE2
|
A:HIS281
|
4.2
|
18.8
|
1.0
|
NE2
|
A:HIS257
|
4.3
|
11.2
|
1.0
|
OD2
|
A:ASP327
|
4.3
|
14.3
|
1.0
|
CD2
|
A:HIS281
|
4.3
|
18.2
|
1.0
|
OD2
|
A:ASP254
|
4.4
|
13.3
|
1.0
|
O
|
A:HOH1110
|
4.4
|
15.4
|
1.0
|
C1
|
A:RNS1001
|
4.5
|
19.3
|
1.0
|
CG
|
A:GLU219
|
4.5
|
13.3
|
1.0
|
C5
|
A:RNS1001
|
4.8
|
25.4
|
1.0
|
ND1
|
A:HIS257
|
4.8
|
11.1
|
1.0
|
CD2
|
A:LEU252
|
4.9
|
17.7
|
1.0
|
O1
|
A:RNS1001
|
4.9
|
16.4
|
1.0
|
O
|
A:HOH1171
|
4.9
|
19.1
|
1.0
|
|
Manganese binding site 2 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 2 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1004
b:20.2
occ:1.00
|
O
|
A:HOH1110
|
1.9
|
15.4
|
1.0
|
O
|
A:HOH1171
|
2.1
|
19.1
|
1.0
|
O1
|
A:RNS1001
|
2.2
|
16.4
|
1.0
|
NE2
|
A:HIS257
|
2.2
|
11.2
|
1.0
|
O2
|
A:RNS1001
|
2.2
|
18.6
|
1.0
|
OD1
|
A:ASP289
|
2.3
|
18.6
|
1.0
|
C1
|
A:RNS1001
|
2.9
|
19.3
|
1.0
|
CE1
|
A:HIS257
|
3.0
|
12.6
|
1.0
|
C2
|
A:RNS1001
|
3.0
|
19.8
|
1.0
|
CG
|
A:ASP289
|
3.2
|
15.3
|
1.0
|
CD2
|
A:HIS257
|
3.3
|
14.0
|
1.0
|
OD2
|
A:ASP289
|
3.4
|
19.1
|
1.0
|
OD1
|
A:ASP254
|
3.8
|
11.2
|
1.0
|
NZ
|
A:LYS221
|
3.8
|
12.4
|
1.0
|
OD2
|
A:ASP291
|
4.0
|
19.2
|
1.0
|
OD1
|
A:ASP291
|
4.1
|
19.2
|
1.0
|
O4
|
A:RNS1001
|
4.1
|
26.3
|
1.0
|
MN
|
A:MN1003
|
4.1
|
15.6
|
1.0
|
CE
|
A:LYS221
|
4.1
|
12.7
|
1.0
|
ND1
|
A:HIS257
|
4.2
|
11.1
|
1.0
|
OD1
|
A:ASP327
|
4.2
|
18.0
|
1.0
|
C3
|
A:RNS1001
|
4.4
|
21.1
|
1.0
|
CG
|
A:HIS257
|
4.4
|
11.3
|
1.0
|
CG
|
A:ASP254
|
4.4
|
12.3
|
1.0
|
CD
|
A:LYS221
|
4.5
|
12.4
|
1.0
|
CG
|
A:ASP291
|
4.5
|
16.6
|
1.0
|
CB
|
A:ASP289
|
4.5
|
16.8
|
1.0
|
NH2
|
B:ARG65
|
4.6
|
14.4
|
1.0
|
OD2
|
A:ASP254
|
4.7
|
13.3
|
1.0
|
C4
|
A:RNS1001
|
4.7
|
25.6
|
1.0
|
OE2
|
A:GLU219
|
4.8
|
14.1
|
1.0
|
CZ
|
B:PHE66
|
4.9
|
17.9
|
1.0
|
O3
|
A:RNS1001
|
4.9
|
18.5
|
1.0
|
|
Manganese binding site 3 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 3 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn505
b:16.4
occ:1.00
|
OE2
|
B:GLU219
|
2.1
|
14.7
|
1.0
|
OD1
|
B:ASP327
|
2.1
|
18.7
|
1.0
|
ND1
|
B:HIS281
|
2.2
|
16.9
|
1.0
|
OD2
|
B:ASP254
|
2.2
|
12.2
|
1.0
|
O3
|
B:RM4501
|
2.3
|
17.8
|
0.5
|
O2
|
B:RM4501
|
2.3
|
18.5
|
0.5
|
O2
|
B:RNS502
|
2.4
|
14.9
|
0.5
|
O3
|
B:RNS502
|
2.4
|
16.3
|
0.5
|
CE1
|
B:HIS281
|
3.0
|
18.0
|
1.0
|
C2
|
B:RM4501
|
3.1
|
19.6
|
0.5
|
CD
|
B:GLU219
|
3.1
|
13.3
|
1.0
|
C2
|
B:RNS502
|
3.1
|
16.0
|
0.5
|
C3
|
B:RM4501
|
3.2
|
19.6
|
0.5
|
CG
|
B:HIS281
|
3.3
|
16.9
|
1.0
|
CG
|
B:ASP327
|
3.3
|
15.9
|
1.0
|
CG
|
B:ASP254
|
3.3
|
11.6
|
1.0
|
C3
|
B:RNS502
|
3.3
|
16.1
|
0.5
|
OE1
|
B:GLU219
|
3.4
|
15.1
|
1.0
|
CB
|
B:HIS281
|
3.7
|
15.4
|
1.0
|
CB
|
B:ASP254
|
3.8
|
11.9
|
1.0
|
CB
|
B:ASP327
|
3.8
|
13.7
|
1.0
|
C4
|
B:RM4501
|
3.9
|
20.5
|
0.5
|
CE1
|
B:HIS257
|
3.9
|
13.8
|
1.0
|
O4
|
B:RNS502
|
4.0
|
16.0
|
0.5
|
MN
|
B:MN506
|
4.1
|
21.9
|
1.0
|
NE2
|
B:HIS281
|
4.2
|
19.0
|
1.0
|
C4
|
B:RNS502
|
4.2
|
17.4
|
0.5
|
NE2
|
B:HIS257
|
4.3
|
13.8
|
1.0
|
OD2
|
B:ASP327
|
4.3
|
15.5
|
1.0
|
CD2
|
B:HIS281
|
4.3
|
17.2
|
1.0
|
OD1
|
B:ASP254
|
4.4
|
10.9
|
1.0
|
CG
|
B:GLU219
|
4.5
|
11.7
|
1.0
|
C1
|
B:RM4501
|
4.5
|
19.5
|
0.5
|
O
|
B:HOH601
|
4.5
|
14.7
|
1.0
|
C1
|
B:RNS502
|
4.6
|
15.1
|
0.5
|
O4
|
B:RM4501
|
4.7
|
21.4
|
0.5
|
ND1
|
B:HIS257
|
4.8
|
13.8
|
1.0
|
C5
|
B:RNS502
|
4.8
|
18.7
|
0.5
|
CD2
|
B:LEU252
|
4.9
|
20.5
|
1.0
|
O5
|
B:RM4501
|
4.9
|
20.8
|
0.5
|
O1
|
B:RM4501
|
5.0
|
19.3
|
0.5
|
|
Manganese binding site 4 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 4 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn506
b:21.9
occ:1.00
|
O
|
B:HOH601
|
1.9
|
14.7
|
1.0
|
O
|
B:HOH657
|
2.0
|
23.6
|
1.0
|
O1
|
B:RNS502
|
2.1
|
13.7
|
0.5
|
O2
|
B:RNS502
|
2.1
|
14.9
|
0.5
|
NE2
|
B:HIS257
|
2.2
|
13.8
|
1.0
|
O1
|
B:RM4501
|
2.3
|
19.3
|
0.5
|
O2
|
B:RM4501
|
2.3
|
18.5
|
0.5
|
OD2
|
B:ASP289
|
2.4
|
20.0
|
1.0
|
C1
|
B:RNS502
|
2.8
|
15.1
|
0.5
|
CE1
|
B:HIS257
|
2.9
|
13.8
|
1.0
|
C2
|
B:RNS502
|
2.9
|
16.0
|
0.5
|
C2
|
B:RM4501
|
3.2
|
19.6
|
0.5
|
C1
|
B:RM4501
|
3.2
|
19.5
|
0.5
|
CG
|
B:ASP289
|
3.2
|
16.1
|
1.0
|
CD2
|
B:HIS257
|
3.3
|
15.9
|
1.0
|
OD1
|
B:ASP289
|
3.4
|
19.4
|
1.0
|
O5
|
B:RM4501
|
3.7
|
20.8
|
0.5
|
NZ
|
B:LYS221
|
3.9
|
14.5
|
1.0
|
OD2
|
B:ASP254
|
3.9
|
12.2
|
1.0
|
CE
|
B:LYS221
|
3.9
|
13.8
|
1.0
|
O4
|
B:RNS502
|
4.0
|
16.0
|
0.5
|
OD2
|
B:ASP291
|
4.1
|
19.1
|
1.0
|
OD1
|
B:ASP291
|
4.1
|
19.6
|
1.0
|
ND1
|
B:HIS257
|
4.1
|
13.8
|
1.0
|
MN
|
B:MN505
|
4.1
|
16.4
|
1.0
|
C3
|
B:RNS502
|
4.3
|
16.1
|
0.5
|
O
|
B:HOH976
|
4.3
|
32.0
|
1.0
|
CG
|
B:HIS257
|
4.3
|
12.2
|
1.0
|
OD1
|
B:ASP327
|
4.3
|
18.7
|
1.0
|
CG
|
B:ASP254
|
4.4
|
11.6
|
1.0
|
CD
|
B:LYS221
|
4.4
|
12.9
|
1.0
|
CG
|
B:ASP291
|
4.5
|
19.6
|
1.0
|
C3
|
B:RM4501
|
4.5
|
19.6
|
0.5
|
OD1
|
B:ASP254
|
4.6
|
10.9
|
1.0
|
CB
|
B:ASP289
|
4.6
|
16.3
|
1.0
|
C4
|
B:RNS502
|
4.6
|
17.4
|
0.5
|
NH2
|
A:ARG65
|
4.8
|
16.6
|
1.0
|
OE2
|
B:GLU219
|
4.8
|
14.7
|
1.0
|
O3
|
B:RNS502
|
4.8
|
16.3
|
0.5
|
CZ
|
A:PHE66
|
4.8
|
15.2
|
1.0
|
C5
|
B:RM4501
|
4.9
|
19.7
|
0.5
|
C4
|
B:RM4501
|
5.0
|
20.5
|
0.5
|
|
Manganese binding site 5 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 5 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn503
b:20.6
occ:1.00
|
ND1
|
C:HIS281
|
2.0
|
22.4
|
1.0
|
OD1
|
C:ASP327
|
2.2
|
23.9
|
1.0
|
OD2
|
C:ASP254
|
2.2
|
14.8
|
1.0
|
OE2
|
C:GLU219
|
2.2
|
19.8
|
1.0
|
O2
|
C:RNS501
|
2.4
|
26.4
|
1.0
|
O3
|
C:RNS501
|
2.5
|
24.2
|
1.0
|
CE1
|
C:HIS281
|
2.9
|
26.3
|
1.0
|
CD
|
C:GLU219
|
3.1
|
19.4
|
1.0
|
CG
|
C:HIS281
|
3.2
|
23.1
|
1.0
|
C2
|
C:RNS501
|
3.2
|
25.6
|
1.0
|
CG
|
C:ASP327
|
3.3
|
22.2
|
1.0
|
CG
|
C:ASP254
|
3.3
|
16.0
|
1.0
|
C3
|
C:RNS501
|
3.4
|
27.5
|
1.0
|
OE1
|
C:GLU219
|
3.4
|
19.3
|
1.0
|
CB
|
C:HIS281
|
3.6
|
21.6
|
1.0
|
CB
|
C:ASP254
|
3.8
|
14.4
|
1.0
|
CB
|
C:ASP327
|
3.8
|
19.0
|
1.0
|
O4
|
C:RNS501
|
3.8
|
30.9
|
1.0
|
CE1
|
C:HIS257
|
3.9
|
15.6
|
1.0
|
NE2
|
C:HIS281
|
4.0
|
23.9
|
1.0
|
MN
|
C:MN504
|
4.2
|
26.8
|
1.0
|
C4
|
C:RNS501
|
4.2
|
29.8
|
1.0
|
CD2
|
C:HIS281
|
4.2
|
23.0
|
1.0
|
NE2
|
C:HIS257
|
4.3
|
14.9
|
1.0
|
OD2
|
C:ASP327
|
4.3
|
20.8
|
1.0
|
OD1
|
C:ASP254
|
4.4
|
14.4
|
1.0
|
O
|
C:HOH601
|
4.5
|
14.6
|
1.0
|
CG
|
C:GLU219
|
4.5
|
17.7
|
1.0
|
C1
|
C:RNS501
|
4.6
|
26.4
|
1.0
|
ND1
|
C:HIS257
|
4.8
|
15.9
|
1.0
|
C5
|
C:RNS501
|
4.9
|
31.3
|
1.0
|
|
Manganese binding site 6 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 6 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn504
b:26.8
occ:1.00
|
O
|
C:HOH601
|
1.9
|
14.6
|
1.0
|
O
|
C:HOH648
|
2.1
|
27.2
|
1.0
|
O1
|
C:RNS501
|
2.2
|
23.1
|
1.0
|
NE2
|
C:HIS257
|
2.2
|
14.9
|
1.0
|
O2
|
C:RNS501
|
2.2
|
26.4
|
1.0
|
OD1
|
C:ASP289
|
2.3
|
22.5
|
1.0
|
C1
|
C:RNS501
|
2.8
|
26.4
|
1.0
|
CE1
|
C:HIS257
|
3.0
|
15.6
|
1.0
|
C2
|
C:RNS501
|
3.0
|
25.6
|
1.0
|
CG
|
C:ASP289
|
3.2
|
18.4
|
1.0
|
OD2
|
C:ASP289
|
3.4
|
20.4
|
1.0
|
CD2
|
C:HIS257
|
3.4
|
15.9
|
1.0
|
NZ
|
C:LYS221
|
3.8
|
18.3
|
1.0
|
OD2
|
C:ASP254
|
3.9
|
14.8
|
1.0
|
OD1
|
C:ASP291
|
4.0
|
22.9
|
1.0
|
O4
|
C:RNS501
|
4.0
|
30.9
|
1.0
|
CE
|
C:LYS221
|
4.0
|
15.5
|
1.0
|
OD2
|
C:ASP291
|
4.1
|
21.2
|
1.0
|
ND1
|
C:HIS257
|
4.2
|
15.9
|
1.0
|
MN
|
C:MN503
|
4.2
|
20.6
|
1.0
|
C3
|
C:RNS501
|
4.3
|
27.5
|
1.0
|
CG
|
C:HIS257
|
4.4
|
15.4
|
1.0
|
OD1
|
C:ASP327
|
4.4
|
23.9
|
1.0
|
CD
|
C:LYS221
|
4.4
|
15.6
|
1.0
|
CG
|
C:ASP291
|
4.5
|
19.1
|
1.0
|
CG
|
C:ASP254
|
4.5
|
16.0
|
1.0
|
CB
|
C:ASP289
|
4.6
|
17.9
|
1.0
|
C4
|
C:RNS501
|
4.6
|
29.8
|
1.0
|
NH1
|
D:ARG65
|
4.7
|
20.1
|
1.0
|
OD1
|
C:ASP254
|
4.7
|
14.4
|
1.0
|
CZ
|
D:PHE66
|
4.8
|
20.3
|
1.0
|
O
|
C:HOH952
|
4.8
|
43.0
|
1.0
|
OE2
|
C:GLU219
|
4.9
|
19.8
|
1.0
|
O3
|
C:RNS501
|
4.9
|
24.2
|
1.0
|
|
Manganese binding site 7 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 7 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn505
b:31.3
occ:1.00
|
O
|
C:HOH917
|
1.7
|
14.6
|
1.0
|
O
|
C:HOH914
|
1.9
|
25.0
|
1.0
|
O
|
C:HOH916
|
2.3
|
17.4
|
1.0
|
OE2
|
B:GLU298
|
2.4
|
18.3
|
1.0
|
OE2
|
C:GLU298
|
2.4
|
18.1
|
1.0
|
O
|
C:HOH757
|
2.8
|
21.3
|
1.0
|
CD
|
C:GLU298
|
3.2
|
19.5
|
1.0
|
OE1
|
C:GLU298
|
3.3
|
18.6
|
1.0
|
CD
|
B:GLU298
|
3.4
|
19.4
|
1.0
|
O
|
B:HOH722
|
3.6
|
18.8
|
1.0
|
O
|
B:HOH829
|
3.6
|
29.9
|
1.0
|
O
|
C:HOH780
|
3.7
|
21.6
|
1.0
|
O
|
B:HOH965
|
3.9
|
20.7
|
1.0
|
OE1
|
B:GLU298
|
3.9
|
19.9
|
1.0
|
O
|
B:HOH852
|
4.0
|
19.1
|
1.0
|
O
|
B:HOH1006
|
4.1
|
39.2
|
1.0
|
O
|
C:HOH961
|
4.3
|
37.6
|
1.0
|
O
|
C:HOH737
|
4.3
|
19.4
|
1.0
|
CG
|
B:GLU298
|
4.5
|
15.9
|
1.0
|
NH1
|
C:ARG301
|
4.5
|
23.5
|
1.0
|
CG
|
C:GLU298
|
4.6
|
16.3
|
1.0
|
O
|
C:HOH918
|
4.7
|
24.8
|
1.0
|
O
|
B:HOH998
|
4.9
|
37.5
|
1.0
|
O
|
C:HOH929
|
4.9
|
31.0
|
1.0
|
OD1
|
C:ASN261
|
5.0
|
19.9
|
1.0
|
|
Manganese binding site 8 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 8 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn504
b:16.4
occ:1.00
|
ND1
|
D:HIS281
|
2.1
|
16.9
|
1.0
|
OE2
|
D:GLU219
|
2.2
|
15.3
|
1.0
|
OD1
|
D:ASP327
|
2.2
|
15.9
|
1.0
|
OD2
|
D:ASP254
|
2.2
|
13.7
|
1.0
|
O3
|
D:RM4501
|
2.3
|
13.2
|
0.5
|
O2
|
D:RM4501
|
2.3
|
14.1
|
0.5
|
O2
|
D:RNS502
|
2.4
|
26.0
|
0.5
|
O3
|
D:RNS502
|
2.5
|
26.3
|
0.5
|
CE1
|
D:HIS281
|
3.0
|
18.8
|
1.0
|
C2
|
D:RM4501
|
3.1
|
15.2
|
0.5
|
CD
|
D:GLU219
|
3.1
|
17.2
|
1.0
|
C2
|
D:RNS502
|
3.1
|
25.9
|
0.5
|
C3
|
D:RM4501
|
3.2
|
14.4
|
0.5
|
CG
|
D:HIS281
|
3.2
|
16.8
|
1.0
|
CG
|
D:ASP327
|
3.3
|
15.2
|
1.0
|
CG
|
D:ASP254
|
3.3
|
14.3
|
1.0
|
C3
|
D:RNS502
|
3.3
|
25.9
|
0.5
|
OE1
|
D:GLU219
|
3.4
|
15.7
|
1.0
|
CB
|
D:HIS281
|
3.7
|
15.1
|
1.0
|
CB
|
D:ASP327
|
3.8
|
14.2
|
1.0
|
CB
|
D:ASP254
|
3.8
|
13.2
|
1.0
|
O4
|
D:RNS502
|
3.9
|
26.6
|
0.5
|
CE1
|
D:HIS257
|
3.9
|
13.5
|
1.0
|
C4
|
D:RM4501
|
4.0
|
15.9
|
0.5
|
O
|
D:HOH602
|
4.0
|
15.4
|
1.0
|
MN
|
D:MN505
|
4.1
|
19.1
|
1.0
|
NE2
|
D:HIS281
|
4.2
|
18.5
|
1.0
|
C4
|
D:RNS502
|
4.2
|
26.9
|
0.5
|
NE2
|
D:HIS257
|
4.2
|
13.6
|
1.0
|
CD2
|
D:HIS281
|
4.3
|
17.2
|
1.0
|
OD2
|
D:ASP327
|
4.4
|
17.0
|
1.0
|
OD1
|
D:ASP254
|
4.4
|
12.3
|
1.0
|
CG
|
D:GLU219
|
4.5
|
13.7
|
1.0
|
C1
|
D:RM4501
|
4.5
|
14.3
|
0.5
|
C1
|
D:RNS502
|
4.6
|
24.9
|
0.5
|
O4
|
D:RM4501
|
4.8
|
19.3
|
0.5
|
ND1
|
D:HIS257
|
4.8
|
15.2
|
1.0
|
C5
|
D:RNS502
|
4.9
|
27.8
|
0.5
|
O1
|
D:RM4501
|
5.0
|
10.4
|
0.5
|
O5
|
D:RM4501
|
5.0
|
17.1
|
0.5
|
CD2
|
D:LEU252
|
5.0
|
16.8
|
1.0
|
|
Manganese binding site 9 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 9 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn505
b:19.1
occ:1.00
|
O
|
D:HOH602
|
2.1
|
15.4
|
1.0
|
O2
|
D:RNS502
|
2.1
|
26.0
|
0.5
|
O1
|
D:RNS502
|
2.2
|
21.6
|
0.5
|
O
|
D:HOH629
|
2.2
|
19.9
|
1.0
|
NE2
|
D:HIS257
|
2.2
|
13.6
|
1.0
|
O1
|
D:RM4501
|
2.2
|
10.4
|
0.5
|
O2
|
D:RM4501
|
2.2
|
14.1
|
0.5
|
OD1
|
D:ASP289
|
2.2
|
22.1
|
1.0
|
C1
|
D:RNS502
|
2.8
|
24.9
|
0.5
|
C2
|
D:RNS502
|
2.9
|
25.9
|
0.5
|
CE1
|
D:HIS257
|
3.0
|
13.5
|
1.0
|
C2
|
D:RM4501
|
3.1
|
15.2
|
0.5
|
C1
|
D:RM4501
|
3.1
|
14.3
|
0.5
|
CG
|
D:ASP289
|
3.2
|
18.1
|
1.0
|
CD2
|
D:HIS257
|
3.4
|
14.2
|
1.0
|
OD2
|
D:ASP289
|
3.4
|
20.2
|
1.0
|
O5
|
D:RM4501
|
3.6
|
17.1
|
0.5
|
OD2
|
D:ASP254
|
3.8
|
13.7
|
1.0
|
NZ
|
D:LYS221
|
4.0
|
15.3
|
1.0
|
O4
|
D:RNS502
|
4.0
|
26.6
|
0.5
|
OD2
|
D:ASP291
|
4.0
|
17.9
|
1.0
|
MN
|
D:MN504
|
4.1
|
16.4
|
1.0
|
CE
|
D:LYS221
|
4.1
|
11.7
|
1.0
|
OD1
|
D:ASP291
|
4.1
|
18.6
|
1.0
|
OD1
|
D:ASP327
|
4.2
|
15.9
|
1.0
|
ND1
|
D:HIS257
|
4.2
|
15.2
|
1.0
|
C3
|
D:RNS502
|
4.2
|
25.9
|
0.5
|
CG
|
D:ASP254
|
4.3
|
14.3
|
1.0
|
CG
|
D:HIS257
|
4.4
|
13.1
|
1.0
|
C3
|
D:RM4501
|
4.5
|
14.4
|
0.5
|
CG
|
D:ASP291
|
4.5
|
16.2
|
1.0
|
CD
|
D:LYS221
|
4.5
|
13.0
|
1.0
|
CB
|
D:ASP289
|
4.5
|
17.3
|
1.0
|
OD1
|
D:ASP254
|
4.6
|
12.3
|
1.0
|
C4
|
D:RNS502
|
4.6
|
26.9
|
0.5
|
NH2
|
C:ARG65
|
4.7
|
19.9
|
1.0
|
OE2
|
D:GLU219
|
4.7
|
15.3
|
1.0
|
O3
|
D:RNS502
|
4.8
|
26.3
|
0.5
|
C5
|
D:RM4501
|
4.9
|
15.9
|
0.5
|
C4
|
D:RM4501
|
4.9
|
15.9
|
0.5
|
CZ
|
C:PHE66
|
4.9
|
17.9
|
1.0
|
O3
|
D:RM4501
|
4.9
|
13.2
|
0.5
|
CG
|
D:ASP327
|
5.0
|
15.2
|
1.0
|
|
Manganese binding site 10 out
of 10 in 4gji
Go back to
Manganese Binding Sites List in 4gji
Manganese binding site 10 out
of 10 in the Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of Crystal Structure of Pseudomonas Stutzeri L-Rhamnose Isomerase Mutant H101N in Complex with L-Rhamnopyranose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn506
b:31.7
occ:1.00
|
O
|
A:HOH1465
|
1.7
|
11.9
|
1.0
|
O
|
D:HOH958
|
2.0
|
20.4
|
1.0
|
O
|
D:HOH961
|
2.2
|
16.3
|
1.0
|
OE2
|
A:GLU298
|
2.3
|
17.5
|
1.0
|
OE2
|
D:GLU298
|
2.4
|
20.8
|
1.0
|
O
|
D:HOH765
|
2.6
|
20.5
|
1.0
|
CD
|
D:GLU298
|
3.2
|
20.8
|
1.0
|
OE1
|
D:GLU298
|
3.2
|
18.9
|
1.0
|
CD
|
A:GLU298
|
3.3
|
17.9
|
1.0
|
O
|
A:HOH1313
|
3.5
|
17.7
|
1.0
|
O
|
A:HOH1333
|
3.6
|
28.4
|
1.0
|
O
|
D:HOH846
|
3.8
|
22.2
|
1.0
|
OE1
|
A:GLU298
|
3.9
|
18.1
|
1.0
|
O
|
D:HOH977
|
3.9
|
35.3
|
1.0
|
O
|
A:HOH1364
|
3.9
|
20.5
|
1.0
|
O
|
A:HOH1328
|
4.0
|
18.4
|
1.0
|
O
|
D:HOH774
|
4.3
|
17.4
|
1.0
|
O
|
A:HOH1481
|
4.3
|
27.9
|
1.0
|
CG
|
A:GLU298
|
4.4
|
15.6
|
1.0
|
O
|
D:HOH899
|
4.5
|
27.1
|
1.0
|
CG
|
D:GLU298
|
4.6
|
16.3
|
1.0
|
NH2
|
D:ARG301
|
4.6
|
19.6
|
1.0
|
O
|
D:HOH876
|
4.8
|
31.6
|
1.0
|
O
|
A:HOH1502
|
5.0
|
42.8
|
1.0
|
OD1
|
D:ASN261
|
5.0
|
22.7
|
1.0
|
|
Reference:
H.Yoshida,
A.Yoshihara,
M.Teraoka,
S.Yamashita,
K.Izumori,
S.Kamitori.
Structure of L-Rhamnose Isomerase in Complex with L-Rhamnopyranose Demonstrates the Sugar-Ring Opening Mechanism and the Role of A Substrate Sub-Binding Site. Febs Open Bio V. 3 35 2013.
ISSN: ESSN 2211-5463
PubMed: 23772372
DOI: 10.1016/J.FOB.2012.11.008
Page generated: Sat Oct 5 19:32:46 2024
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