Zinc in PDB 6qwo: Zinc-Reconstituted Odp From T. Maritima

The structure of Zinc-Reconstituted Odp From T. Maritima, PDB code: 6qwo was solved by A.R.Muok, B.R.Crane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.22 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.433, 121.709, 159.531, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.9

The binding sites of Zinc atom in the Zinc-Reconstituted Odp From T. Maritima (pdb code 6qwo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc-Reconstituted Odp From T. Maritima, PDB code: 6qwo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zinc-Reconstituted Odp From T. Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Reconstituted Odp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.1 occ:1.00 O A:HOH444 1.9 21.3 1.0 NE2 A:HIS75 2.1 18.2 1.0 OD2 A:ASP77 2.1 19.7 1.0 NE2 A:HIS144 2.1 21.9 1.0 OD2 A:ASP163 2.2 21.6 1.0 CE1 A:HIS75 3.0 17.0 1.0 CG A:ASP77 3.0 18.6 1.0 CE1 A:HIS144 3.1 22.3 1.0 CD2 A:HIS75 3.1 18.9 1.0 CD2 A:HIS144 3.1 20.5 1.0 CG A:ASP163 3.3 21.8 1.0 ZN A:ZN302 3.6 21.7 1.0 CB A:ASP77 3.6 20.6 1.0 O A:HOH484 3.7 19.9 1.0 OD1 A:ASP163 3.7 16.6 1.0 OD1 A:ASP77 4.0 20.8 1.0 ND1 A:HIS75 4.1 17.7 1.0 ND1 A:HIS144 4.2 22.5 1.0 CG A:HIS75 4.2 19.1 1.0 CG A:HIS144 4.2 22.8 1.0 OD1 A:ASP79 4.3 18.1 1.0 CB A:ASP163 4.5 18.4 1.0 CE2 B:PHE105 4.8 19.0 1.0 CZ3 B:TRP102 4.9 20.2 1.0 OD2 A:ASP79 4.9 17.4 1.0

Zinc binding site 2 out of 4 in the Zinc-Reconstituted Odp From T. Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Reconstituted Odp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:21.7 occ:1.00 O A:HOH444 2.1 21.3 1.0 OE1 A:GLN220 2.1 18.1 1.0 NE2 A:HIS221 2.1 18.7 1.0 OD1 A:ASP163 2.2 16.6 1.0 OD2 A:ASP79 2.3 17.4 1.0 CD2 A:HIS221 3.1 19.4 1.0 CE1 A:HIS221 3.1 21.3 1.0 CD A:GLN220 3.1 18.9 1.0 CG A:ASP163 3.1 21.8 1.0 CG A:ASP79 3.3 20.3 1.0 OD2 A:ASP163 3.4 21.6 1.0 OD1 A:ASP79 3.5 18.1 1.0 NE2 A:GLN220 3.5 18.4 1.0 ZN A:ZN301 3.6 22.1 1.0 O A:HOH456 4.0 18.2 1.0 CE1 A:HIS75 4.2 17.0 1.0 ND1 A:HIS221 4.2 18.3 1.0 CG A:HIS221 4.2 21.3 1.0 CE2 B:PHE105 4.2 19.0 1.0 NE2 A:HIS75 4.4 18.2 1.0 CG2 A:VAL80 4.4 17.2 1.0 CG A:GLN220 4.4 18.9 1.0 CB A:ASP163 4.5 18.4 1.0 CB A:ASP79 4.6 18.6 1.0 CB A:GLN220 4.7 19.0 1.0 CA A:ASP163 4.9 21.2 1.0 OD2 A:ASP77 5.0 19.7 1.0 CZ B:PHE105 5.0 24.7 1.0

Zinc binding site 3 out of 4 in the Zinc-Reconstituted Odp From T. Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Reconstituted Odp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:20.8 occ:1.00 O B:HOH475 1.9 19.4 1.0 OD2 B:ASP77 2.1 19.1 1.0 NE2 B:HIS75 2.1 18.8 1.0 NE2 B:HIS144 2.1 19.4 1.0 OD2 B:ASP163 2.2 18.9 1.0 CG B:ASP77 3.0 19.7 1.0 CE1 B:HIS75 3.0 19.5 1.0 CD2 B:HIS144 3.1 21.2 1.0 CE1 B:HIS144 3.1 17.6 1.0 CD2 B:HIS75 3.1 19.3 1.0 CG B:ASP163 3.3 19.4 1.0 CB B:ASP77 3.5 19.7 1.0 ZN B:ZN302 3.6 20.8 1.0 OD1 B:ASP163 3.7 16.9 1.0 O B:HOH468 3.7 20.9 1.0 OD1 B:ASP77 4.0 19.6 1.0 ND1 B:HIS75 4.1 17.8 1.0 ND1 B:HIS144 4.2 18.9 1.0 CG B:HIS144 4.2 19.6 1.0 CG B:HIS75 4.2 19.7 1.0 OD1 B:ASP79 4.3 18.3 1.0 CB B:ASP163 4.5 18.0 1.0 CE2 A:PHE105 4.7 20.9 1.0 OD2 B:ASP79 4.9 19.5 1.0 CZ3 A:TRP102 4.9 19.8 1.0 CA B:ASP77 5.0 19.2 1.0

Zinc binding site 4 out of 4 in the Zinc-Reconstituted Odp From T. Maritima


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Reconstituted Odp From T. Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.8 occ:1.00 O B:HOH475 2.0 19.4 1.0 NE2 B:HIS221 2.1 20.5 1.0 OE1 B:GLN220 2.1 17.8 1.0 OD1 B:ASP163 2.1 16.9 1.0 OD2 B:ASP79 2.3 19.5 1.0 CD2 B:HIS221 3.0 18.3 1.0 CE1 B:HIS221 3.0 21.5 1.0 CG B:ASP163 3.1 19.4 1.0 CD B:GLN220 3.2 20.4 1.0 CG B:ASP79 3.2 21.4 1.0 OD2 B:ASP163 3.4 18.9 1.0 OD1 B:ASP79 3.5 18.3 1.0 ZN B:ZN301 3.6 20.8 1.0 NE2 B:GLN220 3.7 17.9 1.0 O B:HOH428 3.8 20.3 1.0 ND1 B:HIS221 4.1 17.9 1.0 CG B:HIS221 4.1 18.4 1.0 CE1 B:HIS75 4.2 19.5 1.0 CE2 A:PHE105 4.2 20.9 1.0 CG2 B:VAL80 4.3 19.2 1.0 NE2 B:HIS75 4.4 18.8 1.0 CB B:ASP163 4.4 18.0 1.0 CG B:GLN220 4.5 19.9 1.0 CB B:ASP79 4.6 19.8 1.0 CB B:GLN220 4.7 19.2 1.0 CA B:ASP163 4.9 19.1 1.0 CZ A:PHE105 5.0 21.7 1.0

A.R.Muok, Y.Deng, V.M.Gumerov, J.E.Chong, J.R.Derosa, K.Kurniyati, R.E.Coleman, K.M.Lancaster, C.Li, I.B.Zhulin, B.R.Crane. A Di-Iron Protein Recruited As An Fe[II] and Oxygen Sensor For Bacterial Chemotaxis Functions By Stabilizing An Iron-Peroxy Species. Proc.Natl.Acad.Sci.Usa V. 116 14955 2019.
ISSN: ESSN 1091-6490
PubMed: 31270241
DOI: 10.1073/PNAS.1904234116