Nickel in PDB 7o9c: Dini-Sulerythrin Treated By Hydrogen Perxoide

The structure of Dini-Sulerythrin Treated By Hydrogen Perxoide, PDB code: 7o9c 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)	29.30 / 1.60
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.991, 72.991, 99.199, 90, 90, 120
R / Rfree (%)	14.8 / 18.1

The structure of Dini-Sulerythrin Treated By Hydrogen Perxoide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the Dini-Sulerythrin Treated By Hydrogen Perxoide (pdb code 7o9c). 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 Treated By Hydrogen Perxoide, PDB code: 7o9c:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Dini-Sulerythrin Treated By Hydrogen Perxoide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Dini-Sulerythrin Treated By Hydrogen Perxoide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:16.7 occ:1.00 OE2 B:GLU53 2.0 15.1 1.0 OE1 A:GLU126 2.0 17.4 1.0 ND1 A:HIS129 2.1 13.7 1.0 O A:HOH310 2.2 20.0 1.0 OE2 A:GLU92 2.2 16.1 1.0 OE1 A:GLU92 2.2 15.7 1.0 CD A:GLU92 2.5 16.4 1.0 CE1 A:HIS129 2.9 13.9 1.0 CD B:GLU53 3.0 14.6 1.0 HE1 A:HIS129 3.0 16.7 1.0 CD A:GLU126 3.1 18.1 1.0 CG A:HIS129 3.2 13.7 1.0 OE1 B:GLU53 3.3 15.1 1.0 HA A:GLU126 3.3 16.9 1.0 HB2 A:HIS129 3.4 17.0 1.0 O B:HOH380 3.4 20.5 1.0 HB3 A:HIS129 3.6 17.0 1.0 HH B:TYR27 3.6 21.1 1.0 HE2 B:TYR27 3.6 18.4 1.0 CB A:HIS129 3.6 14.2 1.0 HB3 A:GLU126 3.7 18.2 1.0 NI B:NI201 3.8 17.0 1.0 OE2 A:GLU126 3.8 16.4 1.0 OE1 A:GLU95 3.9 23.4 1.0 CG A:GLU92 4.0 14.9 1.0 HG23 B:ILE49 4.0 16.7 1.0 NE2 A:HIS129 4.1 15.2 1.0 CA A:GLU126 4.1 14.1 1.0 CB A:GLU126 4.1 15.2 1.0 CG A:GLU126 4.2 16.3 1.0 HG21 B:ILE49 4.2 16.7 1.0 CD2 A:HIS129 4.3 14.6 1.0 HE1 B:HIS56 4.3 18.6 1.0 CG B:GLU53 4.3 12.7 1.0 HG2 A:GLU92 4.4 17.9 1.0 HG3 A:GLU92 4.4 17.9 1.0 OH B:TYR27 4.4 17.6 1.0 CG2 B:ILE49 4.4 13.9 1.0 HG3 B:GLU53 4.5 15.3 1.0 CE2 B:TYR27 4.5 15.3 1.0 HG22 B:ILE49 4.5 16.7 1.0 HA A:GLU92 4.5 20.8 1.0 HB3 A:GLU92 4.6 18.2 1.0 HG2 B:GLU53 4.6 15.3 1.0 HG3 A:GLU126 4.7 19.5 1.0 HE2 A:PHE133 4.7 18.2 1.0 CB A:GLU92 4.8 15.2 1.0 HG2 A:GLU126 4.8 19.5 1.0 HE2 A:HIS129 4.9 18.2 1.0 CZ B:TYR27 5.0 15.2 1.0 HB1 B:ALA23 5.0 18.4 1.0 O A:GLU126 5.0 16.8 1.0 N A:GLU126 5.0 15.1 1.0

Nickel binding site 2 out of 5 in the Dini-Sulerythrin Treated By Hydrogen Perxoide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Dini-Sulerythrin Treated By Hydrogen Perxoide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:19.3 occ:0.90 OE2 B:GLU126 2.0 19.5 1.0 OE1 A:GLU53 2.0 23.1 1.0 ND1 A:HIS56 2.2 21.0 1.0 OE1 A:GLU20 2.2 24.4 1.0 OE2 A:GLU20 2.2 31.1 1.0 O B:HOH387 2.3 22.1 0.8 CD A:GLU20 2.6 21.2 1.0 CD B:GLU126 2.7 20.8 1.0 OE1 B:GLU126 2.8 26.4 1.0 CE1 A:HIS56 3.0 19.2 1.0 CD A:GLU53 3.0 22.2 1.0 HE1 A:HIS56 3.1 23.0 1.0 CG A:HIS56 3.3 19.5 1.0 O B:HOH312 3.4 23.1 1.0 HB2 A:HIS56 3.4 20.8 1.0 HA A:GLU53 3.4 19.6 1.0 OE2 A:GLU53 3.5 16.5 1.0 HB3 A:HIS56 3.6 20.8 1.0 CB A:HIS56 3.7 17.4 1.0 NI B:NI203 3.7 20.0 0.9 HE1 B:HIS129 3.9 24.7 1.0 HB3 A:GLU53 4.0 24.4 1.0 HH B:TYR100 4.0 26.8 1.0 HE2 B:TYR100 4.0 24.3 1.0 CG A:GLU20 4.1 19.9 1.0 CG B:GLU126 4.2 20.8 1.0 NE2 A:HIS56 4.2 19.6 1.0 CG A:GLU53 4.2 16.8 1.0 CA A:GLU53 4.3 16.4 1.0 CB A:GLU53 4.3 20.3 1.0 CD2 A:HIS56 4.3 21.3 1.0 HG3 B:GLU126 4.4 24.9 1.0 HG2 B:GLU126 4.4 24.9 1.0 HG B:LEU122 4.5 28.8 1.0 HG3 A:GLU20 4.5 23.9 1.0 HA A:GLU20 4.5 19.2 1.0 HG2 A:GLU20 4.5 23.9 1.0 OE1 B:GLU95 4.5 26.0 1.0 CE1 B:HIS129 4.6 20.6 1.0 HG3 A:GLU53 4.6 20.2 1.0 OH B:TYR100 4.8 22.4 1.0 HB3 A:GLU20 4.8 20.5 1.0 CE2 B:TYR100 4.8 20.3 1.0 ND1 B:HIS129 4.8 20.1 1.0 HG2 A:GLU53 4.9 20.2 1.0 N A:GLU53 4.9 19.8 1.0 CB A:GLU20 4.9 17.1 1.0 HE2 A:HIS56 4.9 23.5 1.0 OE2 B:GLU95 5.0 40.0 1.0

Nickel binding site 3 out of 5 in the Dini-Sulerythrin Treated By Hydrogen Perxoide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Dini-Sulerythrin Treated By Hydrogen Perxoide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:17.0 occ:1.00 OE1 B:GLU53 2.0 15.1 1.0 OE2 A:GLU126 2.0 16.4 1.0 OE1 B:GLU20 2.1 18.4 1.0 O B:HOH380 2.1 20.5 1.0 ND1 B:HIS56 2.2 14.9 1.0 OE2 B:GLU20 2.3 22.5 1.0 CD B:GLU20 2.5 18.7 1.0 CD A:GLU126 2.8 18.1 1.0 CE1 B:HIS56 3.0 15.5 1.0 OE1 A:GLU126 3.0 17.4 1.0 CD B:GLU53 3.1 14.6 1.0 HE1 B:HIS56 3.1 18.6 1.0 CG B:HIS56 3.2 17.0 1.0 HA B:GLU53 3.3 17.1 1.0 HB2 B:HIS56 3.4 16.3 1.0 O A:HOH310 3.6 20.0 1.0 OE2 B:GLU53 3.6 15.1 1.0 HB3 B:HIS56 3.6 16.3 1.0 CB B:HIS56 3.7 13.5 1.0 NI A:NI202 3.8 16.7 1.0 HB3 B:GLU53 3.9 15.2 1.0 HE2 A:TYR100 4.0 20.6 1.0 HH A:TYR100 4.0 20.8 1.0 HE1 A:HIS129 4.0 16.7 1.0 CG B:GLU20 4.1 15.5 1.0 NE2 B:HIS56 4.2 14.8 1.0 CA B:GLU53 4.2 14.2 1.0 CG B:GLU53 4.2 12.7 1.0 CG A:GLU126 4.2 16.3 1.0 O A:HOH356 4.3 39.4 1.0 CB B:GLU53 4.3 12.6 1.0 CD2 B:HIS56 4.3 15.8 1.0 HA B:GLU20 4.4 16.6 1.0 HG3 A:GLU126 4.4 19.5 1.0 HG3 B:GLU20 4.4 18.6 1.0 HG2 B:GLU20 4.5 18.6 1.0 HG A:LEU122 4.5 21.8 1.0 HG2 A:GLU126 4.5 19.5 1.0 OE1 A:GLU95 4.6 23.4 1.0 HB3 B:GLU20 4.6 18.1 1.0 HG3 B:GLU53 4.7 15.3 1.0 CE1 A:HIS129 4.7 13.9 1.0 OH A:TYR100 4.7 17.3 1.0 CE2 A:TYR100 4.8 17.1 1.0 CB B:GLU20 4.8 15.1 1.0 HG2 B:GLU53 4.9 15.3 1.0 N B:GLU53 4.9 15.0 1.0 HE2 B:HIS56 4.9 17.8 1.0 ND1 A:HIS129 5.0 13.7 1.0 O B:GLY52 5.0 15.1 1.0 HB3 B:ALA23 5.0 18.4 1.0

Nickel binding site 4 out of 5 in the Dini-Sulerythrin Treated By Hydrogen Perxoide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Dini-Sulerythrin Treated By Hydrogen Perxoide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:27.3 occ:0.43 O B:HOH302 1.6 18.1 1.0 H3 B:GLY-1 1.7 52.8 1.0 N B:HIS0 1.8 51.7 1.0 HD1 B:HIS0 1.8 86.9 1.0 H2 B:GLY-1 2.0 52.8 1.0 O A:HOH311 2.1 48.3 1.0 N B:GLY-1 2.2 44.0 1.0 HB3 B:HIS0 2.5 76.4 1.0 ND1 B:HIS0 2.5 72.4 1.0 C B:GLY-1 2.7 38.2 1.0 CA B:HIS0 2.8 62.0 1.0 CB B:HIS0 2.8 63.7 1.0 CA B:GLY-1 2.9 40.4 1.0 H1 B:GLY-1 2.9 52.8 1.0 CG B:HIS0 3.0 71.6 1.0 HA B:HIS0 3.2 74.4 1.0 HA2 B:GLY-1 3.4 48.4 1.0 HA3 B:GLY-1 3.6 48.4 1.0 H B:MET1 3.7 49.5 1.0 CE1 B:HIS0 3.7 79.9 1.0 O B:GLY-1 3.8 37.4 1.0 HB2 B:HIS0 3.8 76.4 1.0 OE1 A:GLU114 3.9 35.3 1.0 C B:HIS0 4.0 52.0 1.0 OE2 A:GLU114 4.1 37.2 1.0 HE1 B:HIS0 4.1 95.9 1.0 N B:MET1 4.2 41.2 1.0 CD2 B:HIS0 4.3 69.2 1.0 CD A:GLU114 4.4 48.3 1.0 NE2 B:HIS0 4.7 77.5 1.0

Nickel binding site 5 out of 5 in the Dini-Sulerythrin Treated By Hydrogen Perxoide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Dini-Sulerythrin Treated By Hydrogen Perxoide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:20.0 occ:0.88 OE1 B:GLU126 1.9 26.4 1.0 OE2 A:GLU53 2.0 16.5 1.0 O B:HOH312 2.1 23.1 1.0 ND1 B:HIS129 2.1 20.1 1.0 OE2 B:GLU92 2.1 23.4 1.0 OE1 B:GLU92 2.2 19.2 1.0 CD B:GLU92 2.5 21.7 1.0 CE1 B:HIS129 2.9 20.6 1.0 HE1 B:HIS129 3.0 24.7 1.0 CD B:GLU126 3.0 20.8 1.0 CD A:GLU53 3.0 22.2 1.0 CG B:HIS129 3.2 21.1 1.0 HA B:GLU126 3.3 26.4 1.0 OE1 A:GLU53 3.4 23.1 1.0 O B:HOH387 3.4 22.1 0.8 HB2 B:HIS129 3.4 25.5 1.0 HB3 B:HIS129 3.5 25.5 1.0 HH A:TYR27 3.6 26.9 1.0 CB B:HIS129 3.6 21.3 1.0 HE2 A:TYR27 3.6 21.8 1.0 HB3 B:GLU126 3.7 25.8 1.0 NI A:NI203 3.7 19.3 0.9 OE2 B:GLU126 3.8 19.5 1.0 OE1 B:GLU95 3.9 26.0 1.0 CG B:GLU92 4.0 21.6 1.0 HG23 A:ILE49 4.1 21.3 1.0 NE2 B:HIS129 4.1 20.7 1.0 CG B:GLU126 4.1 20.8 1.0 HG21 A:ILE49 4.1 21.3 1.0 CB B:GLU126 4.1 21.6 1.0 CA B:GLU126 4.2 22.0 1.0 CD2 B:HIS129 4.2 21.2 1.0 CG A:GLU53 4.3 16.8 1.0 HE1 A:HIS56 4.3 23.0 1.0 HG2 B:GLU92 4.4 25.9 1.0 OH A:TYR27 4.4 22.4 1.0 HG3 A:GLU53 4.4 20.2 1.0 CG2 A:ILE49 4.4 17.7 1.0 HG3 B:GLU92 4.4 25.9 1.0 HG22 A:ILE49 4.4 21.3 1.0 CE2 A:TYR27 4.5 18.2 1.0 HA B:GLU92 4.5 27.1 1.0 HG2 A:GLU53 4.6 20.2 1.0 HB3 B:GLU92 4.6 29.8 1.0 HG3 B:GLU126 4.7 24.9 1.0 HG2 B:GLU126 4.7 24.9 1.0 HE2 B:PHE133 4.8 25.2 1.0 CB B:GLU92 4.8 24.8 1.0 HE2 B:HIS129 4.8 24.7 1.0 CZ A:TYR27 5.0 18.4 1.0 CE1 A:HIS56 5.0 19.2 1.0 N B:GLU126 5.0 22.4 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