Manganese in PDB 4r1p: Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
Enzymatic activity of Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
All present enzymatic activity of Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+:
5.3.1.4;
Protein crystallography data
The structure of Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+, PDB code: 4r1p
was solved by
J.M.Choi,
Y.J.Lee,
D.W.Lee,
S.H.Lee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.69 /
2.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
223.659,
153.120,
91.239,
90.00,
103.85,
90.00
|
R / Rfree (%)
|
15.5 /
21.2
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
(pdb code 4r1p). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+, PDB code: 4r1p:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 4r1p
Go back to
Manganese Binding Sites List in 4r1p
Manganese binding site 1 out
of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:12.5
occ:1.00
|
OE1
|
A:GLU332
|
2.1
|
15.4
|
1.0
|
NE2
|
A:HIS448
|
2.2
|
12.1
|
1.0
|
O
|
A:HOH770
|
2.3
|
22.2
|
1.0
|
OE1
|
A:GLU307
|
2.3
|
18.1
|
1.0
|
NE2
|
A:HIS349
|
2.4
|
9.6
|
1.0
|
O
|
A:HOH768
|
2.8
|
16.1
|
1.0
|
CE1
|
A:HIS448
|
3.1
|
10.2
|
1.0
|
CD
|
A:GLU332
|
3.2
|
24.9
|
1.0
|
CD
|
A:GLU307
|
3.2
|
17.8
|
1.0
|
CD2
|
A:HIS349
|
3.3
|
10.5
|
1.0
|
CD2
|
A:HIS448
|
3.3
|
9.7
|
1.0
|
OE2
|
A:GLU307
|
3.4
|
22.6
|
1.0
|
CE1
|
A:HIS349
|
3.5
|
10.4
|
1.0
|
OE2
|
A:GLU332
|
3.6
|
31.8
|
1.0
|
O
|
A:HOH732
|
4.1
|
13.1
|
1.0
|
O
|
A:HOH652
|
4.1
|
17.5
|
1.0
|
NE2
|
A:HIS447
|
4.2
|
14.4
|
1.0
|
ND1
|
A:HIS448
|
4.3
|
9.8
|
1.0
|
CD2
|
A:HIS447
|
4.3
|
15.3
|
1.0
|
CG
|
A:HIS448
|
4.4
|
15.4
|
1.0
|
CG
|
A:HIS349
|
4.5
|
11.7
|
1.0
|
CG
|
A:GLU332
|
4.5
|
16.0
|
1.0
|
ND1
|
A:HIS349
|
4.5
|
14.4
|
1.0
|
CG
|
A:GLU307
|
4.6
|
10.6
|
1.0
|
O
|
B:HOH813
|
4.7
|
22.7
|
1.0
|
CZ
|
A:PHE330
|
4.7
|
6.8
|
1.0
|
CB
|
A:GLU332
|
4.8
|
7.7
|
1.0
|
|
Manganese binding site 2 out
of 6 in 4r1p
Go back to
Manganese Binding Sites List in 4r1p
Manganese binding site 2 out
of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:12.7
occ:1.00
|
NE2
|
B:HIS448
|
2.1
|
14.6
|
1.0
|
OE1
|
B:GLU307
|
2.3
|
18.2
|
1.0
|
NE2
|
B:HIS349
|
2.6
|
9.9
|
1.0
|
O
|
B:HOH610
|
2.6
|
11.2
|
1.0
|
OE1
|
B:GLU332
|
2.6
|
20.4
|
1.0
|
O
|
B:HOH714
|
2.8
|
12.2
|
1.0
|
CE1
|
B:HIS448
|
3.1
|
8.9
|
1.0
|
CD2
|
B:HIS448
|
3.1
|
8.7
|
1.0
|
CD
|
B:GLU332
|
3.2
|
20.2
|
1.0
|
CD
|
B:GLU307
|
3.3
|
15.3
|
1.0
|
OE2
|
B:GLU332
|
3.3
|
30.4
|
1.0
|
CD2
|
B:HIS349
|
3.3
|
9.1
|
1.0
|
OE2
|
B:GLU307
|
3.6
|
20.5
|
1.0
|
CE1
|
B:HIS349
|
3.7
|
18.8
|
1.0
|
ND1
|
B:HIS448
|
4.2
|
8.9
|
1.0
|
O
|
B:HOH737
|
4.2
|
17.7
|
1.0
|
CG
|
B:HIS448
|
4.2
|
7.2
|
1.0
|
CD2
|
B:HIS447
|
4.3
|
10.9
|
1.0
|
NE2
|
B:HIS447
|
4.3
|
12.1
|
1.0
|
O
|
B:HOH783
|
4.3
|
24.6
|
1.0
|
O
|
E:HOH608
|
4.4
|
15.2
|
1.0
|
CG
|
B:HIS349
|
4.5
|
17.0
|
1.0
|
CG
|
B:GLU332
|
4.6
|
12.8
|
1.0
|
CG
|
B:GLU307
|
4.6
|
15.5
|
1.0
|
CZ
|
B:PHE330
|
4.6
|
8.2
|
1.0
|
ND1
|
B:HIS349
|
4.7
|
16.9
|
1.0
|
CB
|
B:GLU332
|
4.9
|
11.9
|
1.0
|
|
Manganese binding site 3 out
of 6 in 4r1p
Go back to
Manganese Binding Sites List in 4r1p
Manganese binding site 3 out
of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn501
b:14.7
occ:1.00
|
NE2
|
C:HIS448
|
2.2
|
15.0
|
1.0
|
OE1
|
C:GLU307
|
2.3
|
19.8
|
1.0
|
NE2
|
C:HIS349
|
2.4
|
16.0
|
1.0
|
O
|
C:HOH610
|
2.5
|
14.3
|
1.0
|
OE2
|
C:GLU332
|
2.5
|
26.3
|
1.0
|
O
|
C:HOH708
|
2.6
|
13.9
|
1.0
|
CE1
|
C:HIS448
|
3.1
|
13.5
|
1.0
|
CD
|
C:GLU332
|
3.1
|
19.6
|
1.0
|
CD
|
C:GLU307
|
3.2
|
20.3
|
1.0
|
OE1
|
C:GLU332
|
3.2
|
27.5
|
1.0
|
CD2
|
C:HIS448
|
3.2
|
9.3
|
1.0
|
CD2
|
C:HIS349
|
3.3
|
17.9
|
1.0
|
CE1
|
C:HIS349
|
3.4
|
15.8
|
1.0
|
OE2
|
C:GLU307
|
3.4
|
24.0
|
1.0
|
O
|
C:HOH624
|
4.1
|
16.9
|
1.0
|
O
|
C:HOH637
|
4.2
|
6.9
|
1.0
|
ND1
|
C:HIS448
|
4.3
|
11.4
|
1.0
|
CD2
|
C:HIS447
|
4.3
|
15.8
|
1.0
|
NE2
|
C:HIS447
|
4.3
|
16.9
|
1.0
|
CG
|
C:HIS448
|
4.4
|
10.1
|
1.0
|
CG
|
C:GLU332
|
4.4
|
19.1
|
1.0
|
CG
|
C:HIS349
|
4.5
|
15.3
|
1.0
|
ND1
|
C:HIS349
|
4.5
|
17.2
|
1.0
|
CG
|
C:GLU307
|
4.6
|
13.2
|
1.0
|
CZ
|
C:PHE330
|
4.8
|
12.1
|
1.0
|
CB
|
C:GLU332
|
4.9
|
17.6
|
1.0
|
|
Manganese binding site 4 out
of 6 in 4r1p
Go back to
Manganese Binding Sites List in 4r1p
Manganese binding site 4 out
of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn501
b:11.8
occ:1.00
|
NE2
|
D:HIS349
|
2.1
|
8.6
|
1.0
|
OE2
|
D:GLU307
|
2.2
|
16.5
|
1.0
|
NE2
|
D:HIS448
|
2.3
|
7.9
|
1.0
|
OE1
|
D:GLU332
|
2.3
|
18.7
|
1.0
|
O
|
D:HOH796
|
2.3
|
12.2
|
1.0
|
CD
|
D:GLU307
|
3.0
|
11.7
|
1.0
|
CE1
|
D:HIS349
|
3.0
|
11.8
|
1.0
|
OE1
|
D:GLU307
|
3.1
|
23.1
|
1.0
|
CE1
|
D:HIS448
|
3.1
|
6.1
|
1.0
|
CD2
|
D:HIS349
|
3.2
|
12.8
|
1.0
|
CD2
|
D:HIS448
|
3.4
|
5.8
|
1.0
|
O
|
D:HOH795
|
3.4
|
27.9
|
1.0
|
CD
|
D:GLU332
|
3.5
|
22.6
|
1.0
|
O
|
D:HOH794
|
3.8
|
30.5
|
1.0
|
OE2
|
D:GLU332
|
4.1
|
37.4
|
1.0
|
ND1
|
D:HIS349
|
4.1
|
13.5
|
1.0
|
CG
|
D:HIS349
|
4.3
|
15.5
|
1.0
|
NE2
|
D:HIS447
|
4.3
|
16.3
|
1.0
|
ND1
|
D:HIS448
|
4.3
|
5.1
|
1.0
|
O
|
D:HOH688
|
4.3
|
13.2
|
1.0
|
CG
|
D:GLU307
|
4.4
|
10.0
|
1.0
|
CG
|
D:HIS448
|
4.4
|
5.6
|
1.0
|
CD2
|
D:HIS447
|
4.5
|
13.6
|
1.0
|
CG
|
D:GLU332
|
4.6
|
12.7
|
1.0
|
CZ
|
D:PHE330
|
4.8
|
9.5
|
1.0
|
CB
|
D:GLU307
|
5.0
|
8.9
|
1.0
|
|
Manganese binding site 5 out
of 6 in 4r1p
Go back to
Manganese Binding Sites List in 4r1p
Manganese binding site 5 out
of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn501
b:13.9
occ:1.00
|
NE2
|
E:HIS448
|
2.2
|
11.7
|
1.0
|
OE1
|
E:GLU332
|
2.3
|
10.9
|
1.0
|
OE1
|
E:GLU307
|
2.4
|
9.5
|
1.0
|
NE2
|
E:HIS349
|
2.5
|
16.4
|
1.0
|
O
|
E:HOH794
|
2.8
|
22.9
|
1.0
|
CE1
|
E:HIS448
|
3.1
|
10.1
|
1.0
|
CD2
|
E:HIS448
|
3.2
|
9.8
|
1.0
|
CD
|
E:GLU332
|
3.2
|
18.3
|
1.0
|
CD
|
E:GLU307
|
3.3
|
13.5
|
1.0
|
CD2
|
E:HIS349
|
3.3
|
14.2
|
1.0
|
OE2
|
E:GLU307
|
3.5
|
24.0
|
1.0
|
OE2
|
E:GLU332
|
3.5
|
30.0
|
1.0
|
CE1
|
E:HIS349
|
3.6
|
19.3
|
1.0
|
CE1
|
E:HIS447
|
3.9
|
18.2
|
1.0
|
O
|
E:HOH671
|
4.0
|
10.9
|
1.0
|
O
|
E:HOH795
|
4.2
|
21.7
|
1.0
|
ND1
|
E:HIS448
|
4.2
|
11.7
|
1.0
|
ND1
|
E:HIS447
|
4.3
|
12.8
|
1.0
|
CG
|
E:HIS448
|
4.3
|
12.1
|
1.0
|
CG
|
E:HIS349
|
4.5
|
16.6
|
1.0
|
CG
|
E:GLU332
|
4.6
|
11.8
|
1.0
|
O
|
A:HOH803
|
4.6
|
13.2
|
1.0
|
ND1
|
E:HIS349
|
4.6
|
17.8
|
1.0
|
CG
|
E:GLU307
|
4.6
|
10.3
|
1.0
|
CZ
|
E:PHE330
|
4.8
|
11.1
|
1.0
|
CB
|
E:GLU332
|
4.8
|
9.0
|
1.0
|
|
Manganese binding site 6 out
of 6 in 4r1p
Go back to
Manganese Binding Sites List in 4r1p
Manganese binding site 6 out
of 6 in the Crystal Structure of Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+
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 Thermophilic Geobacillus Kaustophilus L-Arabinose Isomerase with MN2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn501
b:13.9
occ:1.00
|
NE2
|
F:HIS448
|
2.2
|
14.8
|
1.0
|
OE2
|
F:GLU307
|
2.3
|
21.2
|
1.0
|
O
|
F:HOH624
|
2.3
|
17.9
|
1.0
|
NE2
|
F:HIS349
|
2.4
|
16.7
|
1.0
|
OE1
|
F:GLU332
|
2.4
|
23.3
|
1.0
|
O
|
F:HOH740
|
2.7
|
14.5
|
1.0
|
CD
|
F:GLU307
|
3.0
|
22.8
|
1.0
|
OE1
|
F:GLU307
|
3.0
|
42.9
|
1.0
|
CE1
|
F:HIS448
|
3.1
|
14.4
|
1.0
|
CD
|
F:GLU332
|
3.1
|
22.9
|
1.0
|
CD2
|
F:HIS448
|
3.2
|
11.1
|
1.0
|
CD2
|
F:HIS349
|
3.2
|
19.9
|
1.0
|
OE2
|
F:GLU332
|
3.3
|
32.1
|
1.0
|
CE1
|
F:HIS349
|
3.4
|
17.5
|
1.0
|
O
|
F:HOH689
|
3.8
|
25.0
|
1.0
|
NE2
|
F:HIS447
|
4.1
|
16.5
|
1.0
|
ND1
|
F:HIS448
|
4.2
|
10.3
|
1.0
|
O
|
F:HOH695
|
4.3
|
15.1
|
1.0
|
CD2
|
F:HIS447
|
4.3
|
16.8
|
1.0
|
CG
|
F:HIS448
|
4.3
|
9.1
|
1.0
|
CG
|
F:HIS349
|
4.4
|
21.6
|
1.0
|
CG
|
F:GLU332
|
4.5
|
15.1
|
1.0
|
ND1
|
F:HIS349
|
4.5
|
25.1
|
1.0
|
CG
|
F:GLU307
|
4.5
|
17.8
|
1.0
|
CZ
|
F:PHE330
|
4.7
|
14.7
|
1.0
|
CB
|
F:GLU332
|
4.8
|
16.0
|
1.0
|
|
Reference:
J.M.Choi,
Y.J.Lee,
D.W.Lee,
S.H.Lee.
Crystal Structure of Thermophilic L-Arabinose with MN2+ From Geobacillus Kaustophilus To Be Published.
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