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Manganese in PDB 7o91: Dimn-Sulerythrin

Protein crystallography data

The structure of Dimn-Sulerythrin, PDB code: 7o91 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) 43.74 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.62, 87.48, 59.757, 90, 115.04, 90
R / Rfree (%) 13.6 / 16.4

Other elements in 7o91:

The structure of Dimn-Sulerythrin also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dimn-Sulerythrin (pdb code 7o91). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dimn-Sulerythrin, PDB code: 7o91:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7o91

Go back to Manganese Binding Sites List in 7o91
Manganese binding site 1 out of 6 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:8.7
occ:1.00
 OE1 A:GLU53 2.1 9.0 1.0
ND1 A:HIS56 2.2 8.8 1.0
OE2 A:GLU20 2.2 9.3 1.0
OE1 A:GLU20 2.3 9.6 1.0
CD A:GLU20 2.5 8.0 1.0
CE1 A:HIS56 3.1 10.0 1.0
CD A:GLU53 3.1 8.0 1.0
CG A:HIS56 3.3 7.6 1.0
CB A:HIS56 3.7 7.9 1.0
OE2 A:GLU53 3.7 9.4 1.0
CG A:GLU20 4.1 8.3 1.0
CA A:GLU53 4.2 8.2 1.0
CG A:GLU53 4.2 7.6 1.0
NE2 A:HIS56 4.3 8.5 1.0
CD2 A:HIS56 4.4 8.4 1.0
CB A:GLU53 4.4 7.8 1.0
N A:GLU53 4.9 7.3 1.0
CB A:GLU20 4.9 8.1 1.0
O A:GLY52 4.9 8.7 1.0

Manganese binding site 2 out of 6 in 7o91

Go back to Manganese Binding Sites List in 7o91
Manganese binding site 2 out of 6 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:9.0
occ:1.00
 OE2 A:GLU126 2.1 9.8 1.0
OE2 A:GLU92 2.2 9.6 1.0
ND1 A:HIS129 2.2 8.6 1.0
OE1 A:GLU92 2.3 10.6 1.0
O A:HOH324 2.4 10.9 1.0
CD A:GLU92 2.6 9.4 1.0
CE1 A:HIS129 3.1 9.3 1.0
CD A:GLU126 3.1 8.6 1.0
CG A:HIS129 3.4 7.8 1.0
CB A:HIS129 3.7 8.9 1.0
OE1 A:GLU126 3.7 10.7 1.0
CG A:GLU92 4.1 9.0 1.0
CG A:GLU126 4.1 8.4 1.0
OE1 A:GLU95 4.2 14.4 1.0
CA A:GLU126 4.2 8.6 1.0
CB A:GLU126 4.3 8.5 1.0
NE2 A:HIS129 4.3 9.1 1.0
CD2 A:HIS129 4.4 8.9 1.0
CB A:GLU92 4.9 8.9 1.0
O A:HOH321 5.0 15.4 1.0
N A:GLU126 5.0 8.5 1.0

Manganese binding site 3 out of 6 in 7o91

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Manganese binding site 3 out of 6 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:9.2
occ:1.00
 OE2 B:GLU126 2.1 9.8 1.0
OE2 C:GLU53 2.1 9.0 1.0
OE2 B:GLU92 2.2 8.9 1.0
ND1 B:HIS129 2.2 8.8 1.0
OE1 B:GLU92 2.3 10.4 1.0
O B:HOH312 2.5 13.5 1.0
CD B:GLU92 2.6 8.3 1.0
CD C:GLU53 2.9 8.0 1.0
CD B:GLU126 3.1 8.8 1.0
CE1 B:HIS129 3.1 8.3 1.0
OE1 C:GLU53 3.1 8.1 1.0
CG B:HIS129 3.3 8.4 1.0
MN C:MN201 3.6 8.7 1.0
CB B:HIS129 3.7 8.2 1.0
OE1 B:GLU126 3.8 9.6 1.0
OE1 B:GLU95 4.0 13.3 0.4
CG B:GLU92 4.1 8.6 1.0
CG B:GLU126 4.1 8.9 1.0
CA B:GLU126 4.3 7.9 1.0
CB B:GLU126 4.3 8.4 1.0
NE2 B:HIS129 4.3 8.4 1.0
OE1 B:GLU95 4.3 10.6 0.6
CG C:GLU53 4.3 7.7 1.0
CD2 B:HIS129 4.4 8.8 1.0
CG2 C:ILE49 4.5 8.8 1.0
OH C:TYR27 4.5 9.2 1.0
CE1 C:TYR27 4.6 8.4 1.0
CB B:GLU92 4.9 8.6 1.0

Manganese binding site 4 out of 6 in 7o91

Go back to Manganese Binding Sites List in 7o91
Manganese binding site 4 out of 6 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:Mn203

b:9.4
occ:1.00
 OE1 C:GLU126 2.1 11.5 1.0
OE1 B:GLU53 2.1 9.3 1.0
ND1 B:HIS56 2.2 9.2 1.0
OE2 B:GLU20 2.2 9.5 1.0
OE1 B:GLU20 2.3 10.7 1.0
O C:HOH314 2.3 14.1 1.0
CD B:GLU20 2.6 10.2 1.0
CD C:GLU126 2.9 9.9 1.0
OE2 C:GLU126 3.0 10.1 1.0
CE1 B:HIS56 3.1 9.2 1.0
CD B:GLU53 3.1 8.4 1.0
CG B:HIS56 3.3 8.5 1.0
MN C:MN202 3.6 9.9 1.0
CB B:HIS56 3.7 9.4 1.0
OE2 B:GLU53 3.7 9.2 1.0
OE1 C:GLU95 4.0 17.9 0.5
CG B:GLU20 4.1 9.1 1.0
O C:HOH311 4.1 18.0 1.0
CA B:GLU53 4.2 8.0 1.0
OE1 C:GLU95 4.2 14.7 0.5
CG B:GLU53 4.2 8.9 1.0
NE2 B:HIS56 4.3 9.0 1.0
CG C:GLU126 4.3 9.2 1.0
CB B:GLU53 4.4 8.6 1.0
CD2 B:HIS56 4.4 9.2 1.0
OH C:TYR100 4.7 11.5 1.0
OE2 C:GLU95 4.7 14.1 0.5
CE1 C:TYR100 4.8 11.0 1.0
CE1 C:HIS129 4.8 9.7 1.0
CD C:GLU95 4.8 12.2 0.5
N B:GLU53 4.9 8.1 1.0
ND1 C:HIS129 4.9 9.4 1.0
CB B:GLU20 4.9 8.6 1.0
O B:GLY52 4.9 9.2 1.0

Manganese binding site 5 out of 6 in 7o91

Go back to Manganese Binding Sites List in 7o91
Manganese binding site 5 out of 6 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dimn-Sulerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn201

b:8.7
occ:1.00
 OE1 B:GLU126 2.1 9.6 1.0
OE1 C:GLU53 2.1 8.1 1.0
OE2 C:GLU20 2.2 8.8 1.0
ND1 C:HIS56 2.2 8.2 1.0
OE1 C:GLU20 2.3 10.1 1.0
O B:HOH312 2.4 13.5 1.0
CD C:GLU20 2.6 8.5 1.0
CD B:GLU126 2.9 8.8 1.0
OE2 B:GLU126 3.0 9.8 1.0
CE1 C:HIS56 3.1 9.0 1.0
CD C:GLU53 3.1 8.0 1.0
CG C:HIS56 3.3 8.1 1.0
MN B:MN201 3.6 9.2 1.0
OE2 C:GLU53 3.7 9.0 1.0
CB C:HIS56 3.7 8.0 1.0
CG C:GLU20 4.1 8.5 1.0
OE1 B:GLU95 4.1 10.6 0.6
O B:HOH306 4.2 28.2 1.0
CG C:GLU53 4.2 7.7 1.0
CA C:GLU53 4.3 7.9 1.0
OE1 B:GLU95 4.3 13.3 0.4
CG B:GLU126 4.3 8.9 1.0
NE2 C:HIS56 4.3 8.7 1.0
CD2 C:HIS56 4.4 8.1 1.0
CB C:GLU53 4.4 7.6 1.0
OH B:TYR100 4.7 9.4 1.0
CE1 B:TYR100 4.7 8.0 1.0
CE1 B:HIS129 4.7 8.3 1.0
ND1 B:HIS129 4.8 8.8 1.0
N C:GLU53 4.9 7.4 1.0
CD B:GLU95 4.9 10.2 0.4
OE2 B:GLU95 4.9 12.1 0.4
CB C:GLU20 5.0 8.2 1.0
O C:GLY52 5.0 8.2 1.0

Manganese binding site 6 out of 6 in 7o91

Go back to Manganese Binding Sites List in 7o91
Manganese binding site 6 out of 6 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dimn-Sulerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn202

b:9.9
occ:1.00
 OE2 C:GLU126 2.1 10.1 1.0
OE2 B:GLU53 2.1 9.2 1.0
OE2 C:GLU92 2.2 11.2 1.0
OE1 C:GLU92 2.2 11.9 1.0
ND1 C:HIS129 2.2 9.4 1.0
O C:HOH314 2.4 14.1 1.0
CD C:GLU92 2.6 10.1 1.0
CD B:GLU53 2.9 8.4 1.0
CE1 C:HIS129 3.1 9.7 1.0
OE1 B:GLU53 3.1 9.3 1.0
CD C:GLU126 3.1 9.9 1.0
CG C:HIS129 3.3 9.4 1.0
MN B:MN203 3.6 9.4 1.0
CB C:HIS129 3.7 9.8 1.0
OE1 C:GLU126 3.8 11.5 1.0
CG C:GLU92 4.1 10.0 1.0
OE1 C:GLU95 4.1 14.7 0.5
CG C:GLU126 4.1 9.2 1.0
OE1 C:GLU95 4.2 17.9 0.5
CA C:GLU126 4.2 9.8 1.0
CB C:GLU126 4.2 9.4 1.0
NE2 C:HIS129 4.3 9.2 1.0
CG B:GLU53 4.3 8.9 1.0
CD2 C:HIS129 4.4 9.6 1.0
CG2 B:ILE49 4.5 8.4 1.0
OH B:TYR27 4.6 10.5 1.0
CE1 B:TYR27 4.6 9.6 1.0
CB C:GLU92 4.9 10.1 1.0
N C:GLU126 5.0 9.1 1.0
O C:HOH311 5.0 18.0 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: Sun Oct 6 10:19:11 2024

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