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:

Chlorine (Cl) 2 atoms

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


Mono view


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


Mono view


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


Mono view


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


Mono view


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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy