Manganese in PDB 7o93: Dimn-Sulerythrin
Protein crystallography data
The structure of Dimn-Sulerythrin, PDB code: 7o93
was solved by
J.-H.Jeoung,
H.Dobbek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.96 /
1.17
|
Space group
|
P 63
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.611,
72.611,
99.272,
90,
90,
120
|
R / Rfree (%)
|
12.5 /
14.4
|
Other elements in 7o93:
The structure of Dimn-Sulerythrin also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Dimn-Sulerythrin
(pdb code 7o93). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Dimn-Sulerythrin, PDB code: 7o93:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 7o93
Go back to
Manganese Binding Sites List in 7o93
Manganese binding site 1 out
of 4 in the Dimn-Sulerythrin
![](/pictures/MN/pdb/o9/7o93-MN-sphere_01.jpg) Mono view
![](/pictures/MN/pdb/o9/7o93-MN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Dimn-Sulerythrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn202
b:9.1
occ:0.89
|
OE2
|
B:GLU53
|
2.1
|
9.6
|
1.0
|
OE2
|
A:GLU126
|
2.1
|
9.9
|
1.0
|
ND1
|
A:HIS129
|
2.2
|
9.2
|
1.0
|
OE2
|
A:GLU92
|
2.2
|
10.5
|
1.0
|
O1
|
A:PEO204
|
2.2
|
12.6
|
0.8
|
OE1
|
A:GLU92
|
2.3
|
10.8
|
1.0
|
CD
|
A:GLU92
|
2.6
|
10.2
|
1.0
|
CD
|
B:GLU53
|
3.0
|
9.0
|
1.0
|
CE1
|
A:HIS129
|
3.1
|
9.7
|
1.0
|
CD
|
A:GLU126
|
3.1
|
9.2
|
1.0
|
O2
|
A:PEO204
|
3.2
|
11.9
|
0.8
|
OE1
|
B:GLU53
|
3.2
|
9.4
|
1.0
|
CG
|
A:HIS129
|
3.3
|
8.9
|
1.0
|
CB
|
A:HIS129
|
3.7
|
9.3
|
1.0
|
MN
|
B:MN201
|
3.8
|
8.6
|
0.9
|
OE1
|
A:GLU126
|
3.8
|
11.2
|
1.0
|
OE1
|
A:GLU95
|
4.1
|
16.4
|
1.0
|
CG
|
A:GLU92
|
4.1
|
10.6
|
1.0
|
CG
|
A:GLU126
|
4.1
|
9.8
|
1.0
|
CA
|
A:GLU126
|
4.2
|
9.2
|
1.0
|
CB
|
A:GLU126
|
4.3
|
9.0
|
1.0
|
NE2
|
A:HIS129
|
4.3
|
9.8
|
1.0
|
CG
|
B:GLU53
|
4.4
|
8.5
|
1.0
|
CD2
|
A:HIS129
|
4.4
|
9.4
|
1.0
|
CG2
|
B:ILE49
|
4.4
|
9.1
|
1.0
|
OH
|
B:TYR27
|
4.5
|
11.4
|
1.0
|
CE2
|
B:TYR27
|
4.5
|
9.6
|
1.0
|
O
|
A:HOH407
|
4.7
|
18.9
|
1.0
|
CB
|
A:GLU92
|
4.9
|
10.5
|
1.0
|
|
Manganese binding site 2 out
of 4 in 7o93
Go back to
Manganese Binding Sites List in 7o93
Manganese binding site 2 out
of 4 in the Dimn-Sulerythrin
![](/pictures/MN/pdb/o9/7o93-MN-sphere_02.jpg) Mono view
![](/pictures/MN/pdb/o9/7o93-MN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Dimn-Sulerythrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn203
b:12.2
occ:0.94
|
OE1
|
B:GLU126
|
2.1
|
14.6
|
1.0
|
OE1
|
A:GLU53
|
2.1
|
12.4
|
1.0
|
OE2
|
A:GLU20
|
2.2
|
12.9
|
1.0
|
ND1
|
A:HIS56
|
2.2
|
13.1
|
1.0
|
O1
|
B:PEO203
|
2.3
|
14.6
|
0.8
|
OE1
|
A:GLU20
|
2.3
|
13.3
|
1.0
|
CD
|
A:GLU20
|
2.6
|
12.2
|
1.0
|
CD
|
B:GLU126
|
2.9
|
13.9
|
1.0
|
OE2
|
B:GLU126
|
3.1
|
14.4
|
1.0
|
CD
|
A:GLU53
|
3.1
|
12.0
|
1.0
|
CE1
|
A:HIS56
|
3.1
|
13.1
|
1.0
|
O2
|
B:PEO203
|
3.3
|
15.9
|
0.8
|
CG
|
A:HIS56
|
3.3
|
12.6
|
1.0
|
CB
|
A:HIS56
|
3.7
|
12.0
|
1.0
|
OE2
|
A:GLU53
|
3.7
|
13.3
|
1.0
|
MN
|
B:MN202
|
3.8
|
13.1
|
0.9
|
CG
|
A:GLU20
|
4.1
|
11.7
|
1.0
|
CA
|
A:GLU53
|
4.2
|
11.4
|
1.0
|
CG
|
A:GLU53
|
4.2
|
11.1
|
1.0
|
O
|
B:HOH302
|
4.3
|
24.1
|
1.0
|
CG
|
B:GLU126
|
4.3
|
14.1
|
1.0
|
NE2
|
A:HIS56
|
4.3
|
13.3
|
1.0
|
CB
|
A:GLU53
|
4.3
|
10.7
|
1.0
|
OE1
|
B:GLU95
|
4.4
|
19.2
|
0.5
|
OE2
|
B:GLU95
|
4.4
|
21.4
|
0.5
|
CD2
|
A:HIS56
|
4.4
|
12.8
|
1.0
|
OE1
|
B:GLU95
|
4.5
|
19.2
|
0.5
|
OH
|
B:TYR100
|
4.7
|
14.4
|
1.0
|
CD
|
B:GLU95
|
4.7
|
17.9
|
0.5
|
CE2
|
B:TYR100
|
4.8
|
13.8
|
1.0
|
CE1
|
B:HIS129
|
4.8
|
13.3
|
1.0
|
N
|
A:GLU53
|
4.9
|
11.0
|
1.0
|
CB
|
A:GLU20
|
4.9
|
11.2
|
1.0
|
O
|
A:GLY52
|
4.9
|
12.2
|
1.0
|
ND1
|
B:HIS129
|
5.0
|
13.4
|
1.0
|
|
Manganese binding site 3 out
of 4 in 7o93
Go back to
Manganese Binding Sites List in 7o93
Manganese binding site 3 out
of 4 in the Dimn-Sulerythrin
![](/pictures/MN/pdb/o9/7o93-MN-sphere_03.jpg) Mono view
![](/pictures/MN/pdb/o9/7o93-MN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Dimn-Sulerythrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn201
b:8.6
occ:0.87
|
OE1
|
A:GLU126
|
2.1
|
11.2
|
1.0
|
OE1
|
B:GLU53
|
2.1
|
9.4
|
1.0
|
OE2
|
B:GLU20
|
2.2
|
10.1
|
1.0
|
ND1
|
B:HIS56
|
2.2
|
8.8
|
1.0
|
O2
|
A:PEO204
|
2.2
|
11.9
|
0.8
|
OE1
|
B:GLU20
|
2.3
|
10.5
|
1.0
|
CD
|
B:GLU20
|
2.6
|
9.5
|
1.0
|
CD
|
A:GLU126
|
2.9
|
9.2
|
1.0
|
OE2
|
A:GLU126
|
3.1
|
9.9
|
1.0
|
CE1
|
B:HIS56
|
3.1
|
9.5
|
1.0
|
CD
|
B:GLU53
|
3.1
|
9.0
|
1.0
|
CG
|
B:HIS56
|
3.3
|
8.8
|
1.0
|
O1
|
A:PEO204
|
3.3
|
12.6
|
0.8
|
CB
|
B:HIS56
|
3.7
|
9.2
|
1.0
|
OE2
|
B:GLU53
|
3.8
|
9.6
|
1.0
|
MN
|
A:MN202
|
3.8
|
9.1
|
0.9
|
CG
|
B:GLU20
|
4.1
|
9.9
|
1.0
|
CA
|
B:GLU53
|
4.2
|
8.3
|
1.0
|
CG
|
B:GLU53
|
4.2
|
8.5
|
1.0
|
O
|
A:HOH329
|
4.3
|
19.5
|
1.0
|
CG
|
A:GLU126
|
4.3
|
9.8
|
1.0
|
NE2
|
B:HIS56
|
4.3
|
9.7
|
1.0
|
CB
|
B:GLU53
|
4.3
|
8.4
|
1.0
|
CD2
|
B:HIS56
|
4.4
|
9.4
|
1.0
|
OE1
|
A:GLU95
|
4.6
|
16.4
|
1.0
|
OH
|
A:TYR100
|
4.7
|
11.0
|
1.0
|
CE2
|
A:TYR100
|
4.8
|
10.2
|
1.0
|
CE1
|
A:HIS129
|
4.8
|
9.7
|
1.0
|
N
|
B:GLU53
|
4.9
|
8.3
|
1.0
|
CB
|
B:GLU20
|
4.9
|
9.8
|
1.0
|
O
|
B:GLY52
|
5.0
|
9.3
|
1.0
|
ND1
|
A:HIS129
|
5.0
|
9.2
|
1.0
|
|
Manganese binding site 4 out
of 4 in 7o93
Go back to
Manganese Binding Sites List in 7o93
Manganese binding site 4 out
of 4 in the Dimn-Sulerythrin
![](/pictures/MN/pdb/o9/7o93-MN-sphere_04.jpg) Mono view
![](/pictures/MN/pdb/o9/7o93-MN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Dimn-Sulerythrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn202
b:13.1
occ:0.92
|
OE2
|
A:GLU53
|
2.1
|
13.3
|
1.0
|
OE2
|
B:GLU126
|
2.1
|
14.4
|
1.0
|
ND1
|
B:HIS129
|
2.2
|
13.4
|
1.0
|
OE2
|
B:GLU92
|
2.2
|
14.4
|
1.0
|
O2
|
B:PEO203
|
2.2
|
15.9
|
0.8
|
OE1
|
B:GLU92
|
2.3
|
13.9
|
1.0
|
CD
|
B:GLU92
|
2.6
|
13.5
|
1.0
|
CD
|
A:GLU53
|
3.0
|
12.0
|
1.0
|
CE1
|
B:HIS129
|
3.1
|
13.3
|
1.0
|
CD
|
B:GLU126
|
3.1
|
13.9
|
1.0
|
OE1
|
A:GLU53
|
3.2
|
12.4
|
1.0
|
O1
|
B:PEO203
|
3.2
|
14.6
|
0.8
|
CG
|
B:HIS129
|
3.3
|
13.7
|
1.0
|
CB
|
B:HIS129
|
3.7
|
14.0
|
1.0
|
MN
|
A:MN203
|
3.8
|
12.2
|
0.9
|
OE1
|
B:GLU126
|
3.8
|
14.6
|
1.0
|
OE1
|
B:GLU95
|
3.8
|
19.2
|
0.5
|
CG
|
B:GLU92
|
4.1
|
14.3
|
1.0
|
CG
|
B:GLU126
|
4.2
|
14.1
|
1.0
|
CA
|
B:GLU126
|
4.2
|
15.0
|
1.0
|
OE1
|
B:GLU95
|
4.2
|
19.2
|
0.5
|
NE2
|
B:HIS129
|
4.3
|
13.8
|
1.0
|
CB
|
B:GLU126
|
4.3
|
14.4
|
1.0
|
CG
|
A:GLU53
|
4.4
|
11.1
|
1.0
|
CD2
|
B:HIS129
|
4.4
|
14.0
|
1.0
|
CG2
|
A:ILE49
|
4.4
|
12.3
|
1.0
|
OH
|
A:TYR27
|
4.5
|
15.1
|
1.0
|
CE2
|
A:TYR27
|
4.6
|
12.8
|
1.0
|
CD
|
B:GLU95
|
4.9
|
17.9
|
0.5
|
O
|
B:HOH389
|
4.9
|
27.3
|
1.0
|
CB
|
B:GLU92
|
4.9
|
14.8
|
1.0
|
|
Reference:
J.H.Jeoung,
S.Runger,
M.Haumann,
B.Neumann,
F.Klemke,
V.Davis,
A.Fischer,
H.Dau,
U.Wollenberger,
H.Dobbek.
Bimetallic Mn, Fe, Co, and Ni Sites in A Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation. Inorg.Chem. 2021.
ISSN: ISSN 0020-1669
PubMed: 34757735
DOI: 10.1021/ACS.INORGCHEM.1C01919
Page generated: Fri Dec 17 11:06:45 2021
|