Nickel in PDB 7o9e: Dini-Sulerythrin

The structure of Dini-Sulerythrin, PDB code: 7o9e 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)	38.93 / 1.25
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.831, 72.831, 98.976, 90, 90, 120
R / Rfree (%)	12.5 / 15.4

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

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the Dini-Sulerythrin (pdb code 7o9e). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Dini-Sulerythrin, PDB code: 7o9e:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Dini-Sulerythrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Dini-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:10.9 occ:0.90 OE1 B:GLU126 2.0 12.7 1.0 OE1 A:GLU53 2.0 12.2 1.0 ND1 A:HIS56 2.1 10.6 1.0 O A:HOH372 2.1 13.7 1.0 OE2 A:GLU20 2.1 11.3 1.0 OE1 A:GLU20 2.1 12.6 1.0 CD A:GLU20 2.4 11.8 1.0 CD B:GLU126 2.9 11.4 1.0 CE1 A:HIS56 3.0 10.3 1.0 CD A:GLU53 3.1 9.9 1.0 CG A:HIS56 3.2 11.2 1.0 OE2 B:GLU126 3.2 12.8 1.0 CB A:HIS56 3.6 10.5 1.0 OE2 A:GLU53 3.8 11.5 1.0 CG A:GLU20 3.9 10.9 1.0 O B:HOH307 4.0 13.7 1.0 CA A:GLU53 4.1 9.8 1.0 NI B:NI201 4.2 11.9 0.9 CG A:GLU53 4.2 10.7 1.0 NE2 A:HIS56 4.2 11.4 1.0 CB A:GLU53 4.2 10.4 1.0 CG B:GLU126 4.3 12.6 1.0 CD2 A:HIS56 4.3 12.0 1.0 OH B:TYR100 4.6 13.7 1.0 OE2 B:GLU95 4.6 27.8 1.0 CE2 B:TYR100 4.7 10.7 1.0 OE1 B:GLU95 4.8 18.1 1.0 CB A:GLU20 4.8 11.2 1.0 N A:GLU53 4.8 10.3 1.0 CD B:GLU95 4.9 19.3 1.0 O A:GLY52 4.9 10.6 1.0 CE1 B:HIS129 5.0 11.6 1.0

Nickel binding site 2 out of 5 in the Dini-Sulerythrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Dini-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:9.0 occ:0.90 OE2 B:GLU53 2.0 10.2 1.0 OE2 A:GLU126 2.0 9.9 1.0 ND1 A:HIS129 2.1 8.6 1.0 OE2 A:GLU92 2.1 9.2 1.0 O A:HOH317 2.1 10.9 1.0 OE1 A:GLU92 2.2 10.0 1.0 CD A:GLU92 2.5 9.7 1.0 CE1 A:HIS129 3.0 8.8 1.0 CD B:GLU53 3.0 8.8 1.0 CD A:GLU126 3.1 9.2 1.0 CG A:HIS129 3.2 8.5 1.0 OE1 B:GLU53 3.3 9.3 1.0 CB A:HIS129 3.6 9.0 1.0 OE1 A:GLU126 3.8 9.8 1.0 O B:HOH364 3.9 12.6 1.0 CG A:GLU92 4.0 9.7 1.0 OE1 A:GLU95 4.0 16.0 1.0 CG A:GLU126 4.1 8.9 1.0 CA A:GLU126 4.1 8.9 1.0 NI B:NI202 4.2 8.8 0.9 NE2 A:HIS129 4.2 8.5 1.0 CB A:GLU126 4.2 9.0 1.0 CD2 A:HIS129 4.3 8.3 1.0 OH B:TYR27 4.3 10.9 1.0 CG B:GLU53 4.3 8.1 1.0 CG2 B:ILE49 4.4 9.2 1.0 CE2 B:TYR27 4.4 9.4 1.0 CB A:GLU92 4.8 9.6 1.0 CZ B:TYR27 4.8 9.2 1.0 O A:GLU126 4.9 9.5 1.0 N A:GLU126 5.0 8.5 1.0

Nickel binding site 3 out of 5 in the Dini-Sulerythrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Dini-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:11.9 occ:0.90 OE2 A:GLU53 2.0 11.5 1.0 OE2 B:GLU126 2.0 12.8 1.0 ND1 B:HIS129 2.1 12.5 1.0 OE2 B:GLU92 2.1 12.3 1.0 O B:HOH307 2.2 13.7 1.0 OE1 B:GLU92 2.2 12.7 1.0 CD B:GLU92 2.5 12.6 1.0 CE1 B:HIS129 3.0 11.6 1.0 CD A:GLU53 3.0 9.9 1.0 CD B:GLU126 3.1 11.4 1.0 CG B:HIS129 3.2 13.5 1.0 OE1 A:GLU53 3.3 12.2 1.0 CB B:HIS129 3.6 11.2 1.0 OE1 B:GLU126 3.8 12.7 1.0 O A:HOH372 3.9 13.7 1.0 CG B:GLU92 4.0 13.1 1.0 OE1 B:GLU95 4.0 18.1 1.0 CG B:GLU126 4.1 12.6 1.0 CA B:GLU126 4.1 13.1 1.0 NI A:NI202 4.2 10.9 0.9 NE2 B:HIS129 4.2 12.1 1.0 CB B:GLU126 4.2 12.8 1.0 OH A:TYR27 4.3 13.8 1.0 CD2 B:HIS129 4.3 12.6 1.0 CG A:GLU53 4.3 10.7 1.0 CG2 A:ILE49 4.3 11.2 1.0 CE2 A:TYR27 4.4 11.2 1.0 CB B:GLU92 4.8 12.9 1.0 CZ A:TYR27 4.9 12.0 1.0 O B:GLU126 4.9 14.1 1.0 N B:GLU126 5.0 12.3 1.0

Nickel binding site 4 out of 5 in the Dini-Sulerythrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Dini-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:8.8 occ:0.90 OE1 A:GLU126 2.0 9.8 1.0 OE1 B:GLU53 2.0 9.3 1.0 ND1 B:HIS56 2.1 8.5 1.0 OE2 B:GLU20 2.1 9.1 1.0 O B:HOH364 2.1 12.6 1.0 OE1 B:GLU20 2.2 9.7 1.0 CD B:GLU20 2.5 9.0 1.0 CD A:GLU126 2.9 9.2 1.0 CE1 B:HIS56 3.0 8.9 1.0 CD B:GLU53 3.1 8.8 1.0 CG B:HIS56 3.2 8.0 1.0 OE2 A:GLU126 3.3 9.9 1.0 CB B:HIS56 3.6 7.4 1.0 OE2 B:GLU53 3.8 10.2 1.0 CG B:GLU20 4.0 9.3 1.0 O A:HOH317 4.0 10.9 1.0 CA B:GLU53 4.1 8.6 1.0 CG B:GLU53 4.1 8.1 1.0 NI A:NI203 4.2 9.0 0.9 NE2 B:HIS56 4.2 9.2 1.0 CB B:GLU53 4.2 8.2 1.0 CG A:GLU126 4.3 8.9 1.0 CD2 B:HIS56 4.3 8.7 1.0 O A:HOH309 4.5 34.0 1.0 OH A:TYR100 4.6 10.4 1.0 CE2 A:TYR100 4.7 9.8 1.0 OE1 A:GLU95 4.8 16.0 1.0 CB B:GLU20 4.8 8.7 1.0 N B:GLU53 4.8 7.8 1.0 O B:GLY52 4.9 8.6 1.0 CE1 A:HIS129 4.9 8.8 1.0 OE2 A:GLU95 5.0 29.2 1.0

Nickel binding site 5 out of 5 in the Dini-Sulerythrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Dini-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:11.6 occ:0.53 O B:HOH402 2.0 31.3 1.0 ND1 B:HIS0 2.0 21.6 1.0 N B:HIS0 2.1 19.0 1.0 N B:GLY-1 2.1 21.9 1.0 C B:GLY-1 2.9 18.5 1.0 CA B:GLY-1 3.0 18.6 1.0 CE1 B:HIS0 3.0 20.3 1.0 CG B:HIS0 3.1 22.3 1.0 CA B:HIS0 3.2 18.0 1.0 CB B:HIS0 3.4 19.9 1.0 N B:MET1 3.8 16.6 1.0 C B:HIS0 4.0 17.3 1.0 O B:HOH447 4.1 46.4 1.0 O B:GLY-1 4.1 18.7 1.0 NE2 B:HIS0 4.2 23.6 1.0 CD2 B:HIS0 4.2 25.2 1.0 O B:HOH483 4.3 27.8 1.0 CG B:MET1 4.9 22.2 1.0

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