Zinc in PDB 7p5h: Tmhydabc- D2 Map

All present enzymatic activity of Tmhydabc- D2 Map:
1.12.1.4;

The structure of Tmhydabc- D2 Map also contains other interesting chemical elements:

Iron

(Fe)

104 atoms

The binding sites of Zinc atom in the Tmhydabc- D2 Map (pdb code 7p5h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Tmhydabc- D2 Map, PDB code: 7p5h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Tmhydabc- D2 Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tmhydabc- D2 Map within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn704 b:63.8 occ:1.00 NE2 B:HIS555 2.0 28.9 1.0 SG B:CYS565 2.3 37.2 1.0 SG B:CYS468 2.3 31.6 1.0 SG B:CYS560 2.3 39.0 1.0 CE1 B:HIS555 2.7 28.9 1.0 HB2 B:CYS565 2.8 37.2 1.0 HE1 B:HIS555 2.8 28.9 1.0 HB2 B:CYS468 2.8 31.6 1.0 CB B:CYS468 3.0 31.6 1.0 HB3 B:CYS468 3.1 31.6 1.0 CB B:CYS565 3.1 37.2 1.0 CD2 B:HIS555 3.2 28.9 1.0 HD2 B:HIS555 3.5 28.9 1.0 HB2 B:CYS560 3.5 39.0 1.0 CB B:CYS560 3.6 39.0 1.0 H B:CYS565 3.7 37.2 1.0 HB3 B:CYS565 3.7 37.2 1.0 HB B:VAL470 3.8 24.5 1.0 ND1 B:HIS555 3.9 28.9 1.0 HA B:CYS560 4.1 39.0 1.0 CG B:HIS555 4.2 28.9 1.0 N B:CYS565 4.3 37.2 1.0 CA B:CYS565 4.3 37.2 1.0 HG3 B:MET564 4.3 37.3 1.0 HB3 B:CYS560 4.3 39.0 1.0 H B:GLU471 4.4 23.8 1.0 HD2 B:PRO561 4.4 37.6 1.0 CA B:CYS468 4.4 31.6 1.0 HB2 B:GLU471 4.5 23.8 1.0 CA B:CYS560 4.5 39.0 1.0 HG B:SER562 4.7 37.0 1.0 HD1 B:HIS555 4.7 28.9 1.0 HA B:CYS565 4.7 37.2 1.0 HA B:CYS468 4.7 31.6 1.0 CB B:VAL470 4.8 24.5 1.0 HA B:THR506 4.8 22.6 1.0 OG B:SER562 4.8 37.0 1.0 HG23 B:VAL470 4.9 24.5 1.0 HG22 B:THR506 4.9 22.6 1.0 H B:VAL470 4.9 24.5 1.0 N B:GLU471 5.0 23.8 1.0

Zinc binding site 2 out of 4 in the Tmhydabc- D2 Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tmhydabc- D2 Map within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn704 b:65.6 occ:1.00 NE2 E:HIS555 2.0 28.9 1.0 SG E:CYS565 2.3 37.4 1.0 SG E:CYS468 2.3 31.7 1.0 SG E:CYS560 2.3 39.3 1.0 CE1 E:HIS555 2.7 28.9 1.0 HB2 E:CYS565 2.8 37.4 1.0 HE1 E:HIS555 2.8 28.9 1.0 HB2 E:CYS468 2.8 31.7 1.0 CB E:CYS468 3.0 31.7 1.0 HB3 E:CYS468 3.1 31.7 1.0 CB E:CYS565 3.1 37.4 1.0 CD2 E:HIS555 3.2 28.9 1.0 HD2 E:HIS555 3.5 28.9 1.0 HB2 E:CYS560 3.5 39.3 1.0 CB E:CYS560 3.6 39.3 1.0 H E:CYS565 3.7 37.4 1.0 HB3 E:CYS565 3.7 37.4 1.0 HB E:VAL470 3.8 24.5 1.0 ND1 E:HIS555 3.9 28.9 1.0 HA E:CYS560 4.1 39.3 1.0 CG E:HIS555 4.2 28.9 1.0 N E:CYS565 4.3 37.4 1.0 CA E:CYS565 4.3 37.4 1.0 HG3 E:MET564 4.3 37.5 1.0 HB3 E:CYS560 4.3 39.3 1.0 H E:GLU471 4.3 23.9 1.0 HD2 E:PRO561 4.4 37.7 1.0 CA E:CYS468 4.4 31.7 1.0 HB2 E:GLU471 4.5 23.9 1.0 CA E:CYS560 4.5 39.3 1.0 HG E:SER562 4.7 37.3 1.0 HD1 E:HIS555 4.7 28.9 1.0 HA E:CYS565 4.7 37.4 1.0 HA E:CYS468 4.7 31.7 1.0 CB E:VAL470 4.7 24.5 1.0 OG E:SER562 4.8 37.3 1.0 HA E:THR506 4.8 22.6 1.0 HG23 E:VAL470 4.9 24.5 1.0 HG22 E:THR506 4.9 22.6 1.0 H E:VAL470 4.9 24.5 1.0 N E:GLU471 5.0 23.9 1.0

Zinc binding site 3 out of 4 in the Tmhydabc- D2 Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tmhydabc- D2 Map within 5.0Å range: probe atom residue distance (Å) B Occ b:Zn704 b:66.0 occ:1.00 NE2 b:HIS555 2.0 28.9 1.0 SG b:CYS565 2.3 37.6 1.0 SG b:CYS468 2.3 31.7 1.0 SG b:CYS560 2.3 39.3 1.0 CE1 b:HIS555 2.7 28.9 1.0 HB2 b:CYS565 2.8 37.6 1.0 HE1 b:HIS555 2.8 28.9 1.0 HB2 b:CYS468 2.8 31.7 1.0 CB b:CYS468 3.0 31.7 1.0 HB3 b:CYS468 3.1 31.7 1.0 CB b:CYS565 3.1 37.6 1.0 CD2 b:HIS555 3.2 28.9 1.0 HD2 b:HIS555 3.5 28.9 1.0 HB2 b:CYS560 3.5 39.3 1.0 CB b:CYS560 3.6 39.3 1.0 H b:CYS565 3.7 37.6 1.0 HB3 b:CYS565 3.7 37.6 1.0 HB b:VAL470 3.8 24.4 1.0 ND1 b:HIS555 4.0 28.9 1.0 HA b:CYS560 4.1 39.3 1.0 CG b:HIS555 4.2 28.9 1.0 N b:CYS565 4.3 37.6 1.0 CA b:CYS565 4.3 37.6 1.0 HG3 b:MET564 4.3 37.5 1.0 HB3 b:CYS560 4.3 39.3 1.0 H b:GLU471 4.3 23.7 1.0 HD2 b:PRO561 4.4 37.7 1.0 CA b:CYS468 4.4 31.7 1.0 HB2 b:GLU471 4.5 23.7 1.0 CA b:CYS560 4.5 39.3 1.0 HG b:SER562 4.7 37.3 1.0 HD1 b:HIS555 4.7 28.9 1.0 HA b:CYS565 4.7 37.6 1.0 HA b:CYS468 4.7 31.7 1.0 CB b:VAL470 4.7 24.4 1.0 OG b:SER562 4.8 37.3 1.0 HA b:THR506 4.8 22.6 1.0 HG23 b:VAL470 4.9 24.4 1.0 HG22 b:THR506 4.9 22.6 1.0 H b:VAL470 4.9 24.4 1.0 N b:GLU471 5.0 23.7 1.0

Zinc binding site 4 out of 4 in the Tmhydabc- D2 Map


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tmhydabc- D2 Map within 5.0Å range: probe atom residue distance (Å) B Occ e:Zn704 b:64.0 occ:1.00 NE2 e:HIS555 2.0 28.9 1.0 SG e:CYS565 2.3 37.4 1.0 SG e:CYS468 2.3 31.6 1.0 SG e:CYS560 2.3 39.2 1.0 CE1 e:HIS555 2.7 28.9 1.0 HB2 e:CYS565 2.8 37.4 1.0 HE1 e:HIS555 2.8 28.9 1.0 HB2 e:CYS468 2.8 31.6 1.0 CB e:CYS468 3.0 31.6 1.0 HB3 e:CYS468 3.1 31.6 1.0 CB e:CYS565 3.1 37.4 1.0 CD2 e:HIS555 3.2 28.9 1.0 HD2 e:HIS555 3.5 28.9 1.0 HB2 e:CYS560 3.6 39.2 1.0 CB e:CYS560 3.6 39.2 1.0 H e:CYS565 3.7 37.4 1.0 HB3 e:CYS565 3.7 37.4 1.0 HB e:VAL470 3.8 24.4 1.0 ND1 e:HIS555 4.0 28.9 1.0 HA e:CYS560 4.1 39.2 1.0 CG e:HIS555 4.2 28.9 1.0 N e:CYS565 4.3 37.4 1.0 CA e:CYS565 4.3 37.4 1.0 HG3 e:MET564 4.3 37.2 1.0 HB3 e:CYS560 4.3 39.2 1.0 H e:GLU471 4.3 23.8 1.0 HD2 e:PRO561 4.4 37.6 1.0 CA e:CYS468 4.4 31.6 1.0 HB2 e:GLU471 4.5 23.8 1.0 CA e:CYS560 4.5 39.2 1.0 HG e:SER562 4.7 37.1 1.0 HD1 e:HIS555 4.7 28.9 1.0 HA e:CYS565 4.7 37.4 1.0 HA e:CYS468 4.7 31.6 1.0 CB e:VAL470 4.7 24.4 1.0 OG e:SER562 4.8 37.1 1.0 HA e:THR506 4.8 22.6 1.0 HG23 e:VAL470 4.9 24.4 1.0 HG22 e:THR506 4.9 22.6 1.0 H e:VAL470 4.9 24.4 1.0 N e:GLU471 5.0 23.8 1.0

C.Furlan, N.Chongdar, P.Gupta, W.Lubitz, H.Ogata, J.N.Blaza, J.A.Birrell. Structural Insight on the Mechanism of An Electron-Bifurcating [Fefe] Hydrogenase. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36018003
DOI: 10.7554/ELIFE.79361