Manganese in PDB 4ug4: Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
Protein crystallography data
The structure of Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti, PDB code: 4ug4
was solved by
E.Valkov,
B.Van Loo,
F.Hollfelder,
M.Hyvonen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
88.550 /
2.79
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.556,
163.248,
177.625,
90.00,
94.40,
90.00
|
R / Rfree (%)
|
21.88 /
25.35
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
(pdb code 4ug4). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti, PDB code: 4ug4:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 1 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1513
b:96.8
occ:1.00
|
SG
|
A:CYS54
|
2.2
|
80.8
|
1.0
|
OD2
|
A:ASP296
|
2.4
|
25.7
|
1.0
|
NE2
|
A:HIS297
|
2.4
|
28.6
|
1.0
|
OD1
|
A:ASP14
|
2.5
|
35.8
|
1.0
|
OD2
|
A:ASP14
|
2.9
|
35.0
|
1.0
|
CB
|
A:CYS54
|
3.0
|
24.1
|
1.0
|
CG
|
A:ASP14
|
3.0
|
34.8
|
1.0
|
CA
|
A:CYS54
|
3.3
|
23.9
|
1.0
|
CD2
|
A:HIS297
|
3.3
|
27.9
|
1.0
|
CE1
|
A:HIS297
|
3.3
|
28.3
|
1.0
|
CG
|
A:ASP296
|
3.5
|
25.9
|
1.0
|
N
|
A:CYS54
|
3.7
|
24.1
|
1.0
|
CD2
|
A:HIS201
|
4.0
|
23.6
|
1.0
|
OD1
|
A:ASP296
|
4.1
|
25.9
|
1.0
|
NZ
|
A:LYS102
|
4.2
|
33.6
|
1.0
|
ND1
|
A:HIS297
|
4.4
|
28.3
|
1.0
|
CG
|
A:HIS297
|
4.4
|
27.1
|
1.0
|
NE
|
A:ARG58
|
4.5
|
24.4
|
1.0
|
CB
|
A:ASP14
|
4.5
|
32.2
|
1.0
|
NE2
|
A:HIS201
|
4.6
|
23.6
|
1.0
|
CE
|
A:LYS102
|
4.6
|
32.9
|
1.0
|
NH2
|
A:ARG58
|
4.6
|
24.6
|
1.0
|
C
|
A:CYS54
|
4.6
|
25.3
|
1.0
|
CE
|
A:LYS309
|
4.7
|
28.8
|
1.0
|
CB
|
A:ASP296
|
4.7
|
26.2
|
1.0
|
C
|
A:LEU53
|
4.7
|
22.7
|
1.0
|
OE1
|
A:GLN15
|
4.9
|
28.2
|
1.0
|
N
|
A:GLN15
|
4.9
|
28.4
|
1.0
|
CD
|
A:LYS309
|
4.9
|
30.8
|
1.0
|
|
Manganese binding site 2 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 2 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1513
b:49.9
occ:1.00
|
OD2
|
B:ASP296
|
2.1
|
13.9
|
1.0
|
OD1
|
B:ASP14
|
2.3
|
20.9
|
1.0
|
NE2
|
B:HIS297
|
2.6
|
15.2
|
1.0
|
OD2
|
B:ASP14
|
2.8
|
21.0
|
1.0
|
SG
|
B:CYS54
|
2.8
|
56.0
|
1.0
|
CG
|
B:ASP14
|
2.9
|
20.1
|
1.0
|
CG
|
B:ASP296
|
3.2
|
21.2
|
1.0
|
CE1
|
B:HIS297
|
3.3
|
14.3
|
1.0
|
CB
|
B:CYS54
|
3.4
|
19.1
|
1.0
|
CD2
|
B:HIS297
|
3.4
|
13.7
|
1.0
|
CA
|
B:CYS54
|
3.5
|
13.6
|
1.0
|
OD1
|
B:ASP296
|
3.6
|
22.9
|
1.0
|
NZ
|
B:LYS102
|
4.1
|
21.4
|
1.0
|
CD2
|
B:HIS201
|
4.1
|
13.1
|
1.0
|
N
|
B:CYS54
|
4.1
|
13.5
|
1.0
|
ND1
|
B:HIS297
|
4.3
|
13.9
|
1.0
|
NH2
|
B:ARG58
|
4.3
|
14.0
|
1.0
|
NE
|
B:ARG58
|
4.3
|
21.5
|
1.0
|
CB
|
B:ASP14
|
4.3
|
18.4
|
1.0
|
CG
|
B:HIS297
|
4.4
|
13.8
|
1.0
|
N
|
B:GLN15
|
4.5
|
18.9
|
1.0
|
CB
|
B:ASP296
|
4.5
|
14.2
|
1.0
|
CE
|
B:LYS102
|
4.5
|
21.5
|
1.0
|
CZ
|
B:ARG58
|
4.8
|
22.2
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
12.9
|
1.0
|
CA
|
B:ASP14
|
4.8
|
18.1
|
1.0
|
C
|
B:CYS54
|
4.8
|
13.7
|
1.0
|
C
|
B:ASP14
|
4.9
|
20.2
|
1.0
|
NZ
|
B:LYS309
|
5.0
|
22.1
|
1.0
|
CB
|
B:GLN15
|
5.0
|
17.1
|
1.0
|
C
|
B:LEU53
|
5.0
|
13.6
|
1.0
|
|
Manganese binding site 3 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 3 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn1513
b:67.4
occ:1.00
|
OD2
|
C:ASP296
|
1.8
|
21.2
|
1.0
|
NE2
|
C:HIS297
|
2.4
|
22.9
|
1.0
|
OD1
|
C:ASP14
|
2.5
|
31.0
|
1.0
|
OD2
|
C:ASP14
|
2.6
|
29.5
|
1.0
|
CG
|
C:ASP14
|
2.8
|
29.1
|
1.0
|
CG
|
C:ASP296
|
2.9
|
21.3
|
1.0
|
CD2
|
C:HIS297
|
3.0
|
23.0
|
1.0
|
SG
|
C:CYS54
|
3.1
|
49.1
|
1.0
|
CE1
|
C:HIS297
|
3.2
|
23.6
|
1.0
|
OD1
|
C:ASP296
|
3.4
|
21.9
|
1.0
|
CA
|
C:CYS54
|
3.5
|
26.4
|
1.0
|
CB
|
C:CYS54
|
3.6
|
24.6
|
1.0
|
CG
|
C:HIS297
|
4.0
|
23.0
|
1.0
|
ND1
|
C:HIS297
|
4.1
|
23.4
|
1.0
|
N
|
C:CYS54
|
4.1
|
27.1
|
1.0
|
CB
|
C:ASP296
|
4.2
|
23.4
|
1.0
|
CB
|
C:ASP14
|
4.3
|
25.5
|
1.0
|
NE
|
C:ARG58
|
4.3
|
25.7
|
1.0
|
N
|
C:GLN15
|
4.4
|
22.8
|
1.0
|
CD2
|
C:HIS201
|
4.5
|
30.9
|
1.0
|
NZ
|
C:LYS102
|
4.5
|
29.1
|
1.0
|
NH2
|
C:ARG58
|
4.5
|
31.3
|
1.0
|
CA
|
C:ASP14
|
4.8
|
23.6
|
1.0
|
C
|
C:CYS54
|
4.8
|
27.8
|
1.0
|
C
|
C:LEU53
|
4.8
|
26.8
|
1.0
|
CE
|
C:LYS102
|
4.9
|
29.8
|
1.0
|
C
|
C:ASP14
|
4.9
|
23.5
|
1.0
|
CZ
|
C:ARG58
|
4.9
|
30.3
|
1.0
|
CB
|
C:GLN15
|
5.0
|
23.1
|
1.0
|
|
Manganese binding site 4 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 4 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn1513
b:71.0
occ:1.00
|
SG
|
D:CYS54
|
2.3
|
74.6
|
1.0
|
OD2
|
D:ASP296
|
2.4
|
17.9
|
1.0
|
OD2
|
D:ASP14
|
2.4
|
25.2
|
1.0
|
OD1
|
D:ASP14
|
2.7
|
23.3
|
1.0
|
CB
|
D:CYS54
|
2.8
|
24.3
|
1.0
|
CG
|
D:ASP14
|
2.9
|
22.8
|
1.0
|
NE2
|
D:HIS297
|
2.9
|
35.7
|
1.0
|
CA
|
D:CYS54
|
3.1
|
25.3
|
1.0
|
NZ
|
D:LYS102
|
3.5
|
25.6
|
1.0
|
CG
|
D:ASP296
|
3.6
|
19.2
|
1.0
|
CD2
|
D:HIS297
|
3.7
|
34.4
|
1.0
|
CE1
|
D:HIS297
|
3.8
|
35.9
|
1.0
|
N
|
D:CYS54
|
3.9
|
25.9
|
1.0
|
CE
|
D:LYS102
|
4.0
|
24.9
|
1.0
|
CD2
|
D:HIS201
|
4.1
|
13.0
|
1.0
|
OD1
|
D:ASP296
|
4.2
|
18.9
|
1.0
|
NE
|
D:ARG58
|
4.3
|
19.9
|
1.0
|
C
|
D:CYS54
|
4.4
|
28.1
|
1.0
|
CB
|
D:ASP14
|
4.4
|
19.9
|
1.0
|
NE2
|
D:HIS201
|
4.6
|
12.8
|
1.0
|
CB
|
D:ASP296
|
4.7
|
20.8
|
1.0
|
CG
|
D:HIS297
|
4.8
|
33.2
|
1.0
|
ND1
|
D:HIS297
|
4.8
|
34.9
|
1.0
|
NH2
|
D:ARG58
|
4.8
|
21.2
|
1.0
|
O
|
D:CYS54
|
4.8
|
27.2
|
1.0
|
C
|
D:LEU53
|
4.9
|
24.8
|
1.0
|
|
Manganese binding site 5 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 5 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn1513
b:56.1
occ:1.00
|
OD2
|
E:ASP296
|
2.1
|
17.3
|
1.0
|
OD1
|
E:ASP14
|
2.4
|
26.5
|
1.0
|
NE2
|
E:HIS297
|
2.6
|
26.0
|
1.0
|
OD2
|
E:ASP14
|
2.6
|
26.7
|
1.0
|
CG
|
E:ASP14
|
2.8
|
26.1
|
1.0
|
SG
|
E:CYS54
|
2.9
|
47.7
|
1.0
|
CG
|
E:ASP296
|
3.2
|
17.2
|
1.0
|
CB
|
E:CYS54
|
3.3
|
22.9
|
1.0
|
CA
|
E:CYS54
|
3.4
|
22.7
|
1.0
|
CD2
|
E:HIS297
|
3.4
|
24.3
|
1.0
|
CE1
|
E:HIS297
|
3.4
|
25.1
|
1.0
|
OD1
|
E:ASP296
|
3.8
|
18.2
|
1.0
|
N
|
E:CYS54
|
4.0
|
23.8
|
1.0
|
NZ
|
E:LYS102
|
4.0
|
25.2
|
1.0
|
CD2
|
E:HIS201
|
4.1
|
15.6
|
1.0
|
NE
|
E:ARG58
|
4.3
|
14.5
|
1.0
|
CB
|
E:ASP14
|
4.3
|
24.6
|
1.0
|
ND1
|
E:HIS297
|
4.4
|
24.0
|
1.0
|
CG
|
E:HIS297
|
4.4
|
22.9
|
1.0
|
CB
|
E:ASP296
|
4.5
|
15.8
|
1.0
|
CE
|
E:LYS102
|
4.5
|
22.5
|
1.0
|
N
|
E:GLN15
|
4.5
|
21.8
|
1.0
|
NH2
|
E:ARG58
|
4.6
|
15.8
|
1.0
|
C
|
E:CYS54
|
4.6
|
22.5
|
1.0
|
NE2
|
E:HIS201
|
4.8
|
16.9
|
1.0
|
C
|
E:LEU53
|
4.8
|
23.3
|
1.0
|
OE1
|
E:GLN15
|
4.8
|
28.2
|
1.0
|
CA
|
E:ASP14
|
4.9
|
22.1
|
1.0
|
CZ
|
E:ARG58
|
4.9
|
17.4
|
1.0
|
CB
|
E:GLN15
|
4.9
|
22.5
|
1.0
|
O
|
E:CYS54
|
5.0
|
21.7
|
1.0
|
C
|
E:ASP14
|
5.0
|
22.1
|
1.0
|
|
Manganese binding site 6 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 6 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn1513
b:67.6
occ:1.00
|
OD2
|
F:ASP296
|
2.3
|
31.2
|
1.0
|
SG
|
F:CYS54
|
2.4
|
80.1
|
1.0
|
OD1
|
F:ASP14
|
2.5
|
29.1
|
1.0
|
NE2
|
F:HIS297
|
2.5
|
36.4
|
1.0
|
OD2
|
F:ASP14
|
2.6
|
30.8
|
1.0
|
CG
|
F:ASP14
|
2.9
|
29.3
|
1.0
|
CB
|
F:CYS54
|
3.0
|
25.6
|
1.0
|
CA
|
F:CYS54
|
3.3
|
25.1
|
1.0
|
CD2
|
F:HIS297
|
3.3
|
35.1
|
1.0
|
CG
|
F:ASP296
|
3.4
|
32.0
|
1.0
|
CE1
|
F:HIS297
|
3.5
|
35.6
|
1.0
|
NZ
|
F:LYS102
|
3.7
|
42.4
|
1.0
|
N
|
F:CYS54
|
3.8
|
26.0
|
1.0
|
OD1
|
F:ASP296
|
3.9
|
33.4
|
1.0
|
CD2
|
F:HIS201
|
4.1
|
32.1
|
1.0
|
CB
|
F:ASP14
|
4.4
|
28.0
|
1.0
|
CG
|
F:HIS297
|
4.4
|
33.4
|
1.0
|
CE
|
F:LYS102
|
4.4
|
41.9
|
1.0
|
ND1
|
F:HIS297
|
4.4
|
34.1
|
1.0
|
NE
|
F:ARG58
|
4.5
|
26.9
|
1.0
|
C
|
F:CYS54
|
4.6
|
25.8
|
1.0
|
CB
|
F:ASP296
|
4.7
|
31.4
|
1.0
|
C
|
F:LEU53
|
4.8
|
26.5
|
1.0
|
N
|
F:GLN15
|
4.8
|
30.4
|
1.0
|
NE2
|
F:HIS201
|
4.8
|
32.3
|
1.0
|
CE
|
F:LYS309
|
4.9
|
36.0
|
1.0
|
NH2
|
F:ARG58
|
5.0
|
28.4
|
1.0
|
|
Manganese binding site 7 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 7 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn1513
b:94.6
occ:1.00
|
OD2
|
G:ASP296
|
2.2
|
31.4
|
1.0
|
OD2
|
G:ASP14
|
2.6
|
35.8
|
1.0
|
SG
|
G:CYS54
|
2.8
|
53.4
|
1.0
|
CB
|
G:CYS54
|
2.8
|
32.8
|
1.0
|
OD1
|
G:ASP14
|
2.9
|
34.5
|
1.0
|
CA
|
G:CYS54
|
2.9
|
33.0
|
1.0
|
NE2
|
G:HIS297
|
2.9
|
35.0
|
1.0
|
CG
|
G:ASP14
|
3.1
|
34.5
|
1.0
|
CG
|
G:ASP296
|
3.4
|
30.9
|
1.0
|
CD2
|
G:HIS297
|
3.6
|
34.1
|
1.0
|
N
|
G:CYS54
|
3.7
|
33.1
|
1.0
|
NE
|
G:ARG58
|
3.8
|
23.9
|
1.0
|
NZ
|
G:LYS102
|
3.8
|
29.6
|
1.0
|
CE1
|
G:HIS297
|
3.9
|
35.2
|
1.0
|
C
|
G:CYS54
|
4.0
|
35.0
|
1.0
|
CE
|
G:LYS102
|
4.1
|
28.3
|
1.0
|
OD1
|
G:ASP296
|
4.2
|
30.2
|
1.0
|
O
|
G:CYS54
|
4.3
|
35.3
|
1.0
|
CB
|
G:ASP296
|
4.4
|
30.4
|
1.0
|
NH2
|
G:ARG58
|
4.5
|
24.2
|
1.0
|
CB
|
G:ASP14
|
4.5
|
32.3
|
1.0
|
CD
|
G:ARG58
|
4.6
|
23.0
|
1.0
|
CZ
|
G:ARG58
|
4.6
|
25.1
|
1.0
|
C
|
G:LEU53
|
4.6
|
31.9
|
1.0
|
CD2
|
G:HIS201
|
4.7
|
33.5
|
1.0
|
CG
|
G:HIS297
|
4.7
|
33.3
|
1.0
|
ND1
|
G:HIS297
|
4.8
|
34.3
|
1.0
|
|
Manganese binding site 8 out
of 8 in 4ug4
Go back to
Manganese Binding Sites List in 4ug4
Manganese binding site 8 out
of 8 in the Crystal Structure of A Choline Sulfatase From Sinorhizobium Melliloti
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 A Choline Sulfatase From Sinorhizobium Melliloti within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn1513
b:56.6
occ:1.00
|
OD2
|
H:ASP296
|
1.9
|
15.7
|
1.0
|
NE2
|
H:HIS297
|
2.4
|
20.2
|
1.0
|
OD2
|
H:ASP14
|
2.5
|
27.1
|
1.0
|
OD1
|
H:ASP14
|
2.6
|
23.8
|
1.0
|
SG
|
H:CYS54
|
2.8
|
47.2
|
1.0
|
CG
|
H:ASP14
|
2.9
|
25.1
|
1.0
|
CG
|
H:ASP296
|
3.0
|
22.3
|
1.0
|
CD2
|
H:HIS297
|
3.2
|
19.3
|
1.0
|
CB
|
H:CYS54
|
3.3
|
15.8
|
1.0
|
CE1
|
H:HIS297
|
3.3
|
19.9
|
1.0
|
CA
|
H:CYS54
|
3.4
|
17.9
|
1.0
|
OD1
|
H:ASP296
|
3.6
|
23.2
|
1.0
|
NZ
|
H:LYS102
|
3.9
|
24.2
|
1.0
|
N
|
H:CYS54
|
4.0
|
18.6
|
1.0
|
NE
|
H:ARG58
|
4.1
|
15.3
|
1.0
|
CG
|
H:HIS297
|
4.2
|
19.6
|
1.0
|
CB
|
H:ASP296
|
4.2
|
21.6
|
1.0
|
ND1
|
H:HIS297
|
4.2
|
19.9
|
1.0
|
NH2
|
H:ARG58
|
4.3
|
33.7
|
1.0
|
CB
|
H:ASP14
|
4.3
|
21.6
|
1.0
|
CE
|
H:LYS102
|
4.5
|
23.6
|
1.0
|
CD2
|
H:HIS201
|
4.6
|
16.2
|
1.0
|
C
|
H:CYS54
|
4.6
|
18.7
|
1.0
|
N
|
H:GLN15
|
4.7
|
21.7
|
1.0
|
CZ
|
H:ARG58
|
4.7
|
34.9
|
1.0
|
C
|
H:LEU53
|
4.8
|
18.6
|
1.0
|
CA
|
H:ASP14
|
4.9
|
19.1
|
1.0
|
O
|
H:CYS54
|
4.9
|
17.2
|
1.0
|
|
Reference:
B.Van Loo,
M.Schober,
E.Valkov,
M.Heberlein,
K.Faber,
M.Hyvonen,
F.Hollfelder.
Structural and Mechanistic Analysis of the Choline Sulfatase From Sinorhizobium Melliloti: A Class I Sulfatase Specific For An Alkyl Sulfate Ester To Be Published.
Page generated: Tue Dec 15 04:29:46 2020
|