Chlorine in PDB 7o9d: Peroxide-Bound Dico-Sulerythrin

Protein crystallography data

The structure of Peroxide-Bound Dico-Sulerythrin, PDB code: 7o9d 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) 38.86 / 1.28
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 72.539, 72.539, 98.912, 90, 90, 120
R / Rfree (%) 13.6 / 17.4

Other elements in 7o9d:

The structure of Peroxide-Bound Dico-Sulerythrin also contains other interesting chemical elements:

Cobalt (Co) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Peroxide-Bound Dico-Sulerythrin (pdb code 7o9d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Peroxide-Bound Dico-Sulerythrin, PDB code: 7o9d:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7o9d

Go back to Chlorine Binding Sites List in 7o9d
Chlorine binding site 1 out of 2 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:32.8
occ:1.00
CA A:TYR39 3.2 15.4 1.0
N A:GLU41 3.2 14.9 1.0
C A:TYR39 3.2 13.7 1.0
O A:HOH326 3.2 21.7 1.0
CB A:GLU41 3.3 17.2 0.3
CB A:TYR39 3.4 16.2 1.0
CB A:GLU41 3.5 15.4 0.7
N A:ILE42 3.5 15.2 1.0
NE2 B:GLN139 3.5 62.8 1.0
N A:PRO40 3.5 14.5 1.0
O A:TYR39 3.7 14.9 1.0
CA A:GLU41 3.7 15.1 0.3
CA A:GLU41 3.7 14.4 0.7
CD1 A:TYR39 3.7 18.9 1.0
CG1 A:ILE42 3.8 16.9 1.0
CG A:GLU41 4.0 16.1 0.7
CG A:TYR39 4.0 15.8 1.0
CD A:PRO40 4.1 16.6 1.0
C A:GLU41 4.1 14.4 1.0
OE1 A:GLU41 4.2 23.5 0.7
C A:PRO40 4.2 14.1 1.0
CD1 A:ILE42 4.3 19.3 1.0
CD A:GLU41 4.4 20.4 0.7
CB A:ILE42 4.4 15.5 1.0
CA A:PRO40 4.5 14.5 1.0
CG A:GLU41 4.5 18.9 0.3
CA A:ILE42 4.5 14.9 1.0
N A:TYR39 4.6 14.7 1.0
CG A:PRO40 4.6 15.5 1.0
O A:GLY38 4.8 18.2 1.0
CE1 A:TYR39 4.9 21.1 1.0
CD B:GLN139 4.9 84.8 1.0

Chlorine binding site 2 out of 2 in 7o9d

Go back to Chlorine Binding Sites List in 7o9d
Chlorine binding site 2 out of 2 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:31.5
occ:1.00
O B:HOH349 2.8 15.2 1.0
O B:HOH380 2.9 24.9 1.0
N B:GLU41 3.0 10.3 1.0
C B:TYR39 3.3 9.9 1.0
CA B:TYR39 3.3 10.3 1.0
N B:PRO40 3.4 10.0 1.0
CB B:GLU41 3.4 11.8 1.0
CD B:PRO40 3.6 11.0 1.0
CG B:GLU41 3.7 14.6 1.0
CA B:GLU41 3.7 10.1 1.0
N B:ILE42 3.8 10.3 1.0
CB B:TYR39 3.8 10.6 1.0
O B:TYR39 3.8 10.4 1.0
C B:PRO40 4.0 10.0 1.0
CD B:GLU41 4.1 17.1 1.0
OE2 B:GLU41 4.1 20.8 1.0
CG B:PRO40 4.1 10.8 1.0
CD1 B:TYR39 4.2 12.6 1.0
CA B:PRO40 4.2 9.8 1.0
C B:GLU41 4.3 10.5 1.0
CG1 B:ILE42 4.5 11.9 1.0
CG B:TYR39 4.5 11.1 1.0
N B:TYR39 4.6 11.1 1.0
O B:GLY38 4.6 11.9 1.0
OE1 B:GLU41 4.8 20.8 1.0
CB B:PRO40 4.9 10.6 1.0
CB B:ILE42 4.9 11.2 1.0
CD1 B:ILE42 5.0 14.2 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 08:53:54 2021

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