Zinc in PDB 9f47: Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii

The structure of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f47 was solved by J.Duan, A.Rutz, E.Hofmann, T.Happe, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.26 / 2.90
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	169, 169, 127, 90, 90, 90
R / Rfree (%)	24.2 / 29.8

The structure of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii also contains other interesting chemical elements:

Chlorine	(Cl)	10 atoms
Iron	(Fe)	28 atoms

The binding sites of Zinc atom in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii (pdb code 9f47). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f47:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn705 b:76.8 occ:1.00 NE2 A:HIS199 2.0 82.9 1.0 SG A:CYS113 2.3 71.3 1.0 SG A:CYS205 2.3 61.3 1.0 SG A:CYS210 2.3 97.1 1.0 HB2 A:CYS205 2.6 72.9 1.0 CD2 A:HIS199 2.9 79.5 1.0 HD2 A:HIS199 2.9 95.4 1.0 CB A:CYS205 3.0 60.7 1.0 HB2 A:CYS113 3.1 83.6 1.0 CE1 A:HIS199 3.1 79.7 1.0 HE21 A:GLN116 3.3 98.9 1.0 CB A:CYS113 3.3 69.6 1.0 HE1 A:HIS199 3.4 95.7 1.0 HB3 A:CYS205 3.6 72.9 1.0 HB2 A:CYS210 3.7 97.8 1.0 HB A:ILE115 3.7 100.3 1.0 CB A:CYS210 3.7 81.5 1.0 H A:CYS210 3.7 89.3 1.0 HB3 A:CYS113 3.7 83.6 1.0 HA A:CYS205 3.8 104.4 1.0 HG2 A:GLN116 3.8 91.1 1.0 HG12 A:ILE115 4.0 84.0 1.0 CA A:CYS205 4.0 87.0 1.0 CG A:HIS199 4.1 72.8 1.0 NE2 A:GLN116 4.1 82.4 1.0 ND1 A:HIS199 4.2 85.7 1.0 HB2 A:GLN209 4.2 87.5 1.0 HD12 A:LEU213 4.2 91.2 1.0 N A:CYS210 4.2 74.4 1.0 HB3 A:CYS210 4.4 97.8 1.0 H A:GLN116 4.4 85.8 1.0 HG13 A:ILE115 4.5 84.0 1.0 H A:GLN209 4.5 74.3 1.0 CB A:ILE115 4.5 83.6 1.0 CG1 A:ILE115 4.5 70.0 1.0 CA A:CYS210 4.5 80.3 1.0 CA A:CYS113 4.6 75.3 1.0 HE22 A:GLN116 4.6 98.9 1.0 HA A:CYS113 4.6 90.4 1.0 H A:ILE115 4.6 82.0 1.0 CG A:GLN116 4.6 75.9 1.0 OG1 A:THR207 4.6 92.4 1.0 HG1 A:THR207 4.7 110.9 1.0 HG3 A:GLN116 4.7 91.1 1.0 HA A:CYS210 4.8 96.4 1.0 CD A:GLN116 4.9 81.2 1.0 C A:CYS205 5.0 80.7 1.0 HD1 A:HIS199 5.0 102.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn705 b:95.8 occ:1.00 NE2 B:HIS199 2.1 84.5 1.0 SG B:CYS205 2.3 60.7 1.0 SG B:CYS113 2.3 85.5 1.0 SG B:CYS210 2.3 76.0 1.0 HB2 B:CYS205 2.8 98.3 1.0 CD2 B:HIS199 2.9 72.0 1.0 HD2 B:HIS199 2.9 86.3 1.0 HB2 B:CYS113 3.1 99.1 1.0 CB B:CYS205 3.2 81.9 1.0 CE1 B:HIS199 3.2 94.4 1.0 CB B:CYS113 3.3 82.6 1.0 HB B:ILE115 3.4 88.4 1.0 HG12 B:ILE115 3.5 90.5 1.0 HE1 B:HIS199 3.5 113.3 1.0 HB2 B:CYS210 3.5 92.0 1.0 CB B:CYS210 3.6 76.6 1.0 H B:CYS210 3.7 88.3 1.0 HB3 B:CYS113 3.7 99.1 1.0 HG2 B:GLN116 3.8 98.6 1.0 HB3 B:CYS205 3.8 98.3 1.0 HA B:CYS205 4.0 92.7 1.0 HG13 B:ILE115 4.0 90.5 1.0 CG1 B:ILE115 4.1 75.4 1.0 CG B:HIS199 4.1 70.8 1.0 HB2 B:GLN209 4.1 90.4 1.0 HE21 B:GLN116 4.2 100.4 1.0 N B:CYS210 4.2 73.6 1.0 ND1 B:HIS199 4.2 78.1 1.0 CA B:CYS205 4.2 77.3 1.0 CB B:ILE115 4.2 73.7 1.0 H B:ILE115 4.2 85.5 1.0 HB3 B:CYS210 4.3 92.0 1.0 HD12 B:LEU213 4.3 93.7 1.0 HG1 B:THR207 4.4 98.7 1.0 H B:GLN116 4.4 93.2 1.0 CA B:CYS210 4.5 84.5 1.0 H B:GLN209 4.5 84.2 1.0 CA B:CYS113 4.7 79.1 1.0 CG B:GLN116 4.7 82.2 1.0 HA B:CYS113 4.7 95.0 1.0 HA B:CYS210 4.8 101.5 1.0 HG3 B:GLN116 4.8 98.6 1.0 N B:ILE115 4.9 71.2 1.0 CB B:GLN209 5.0 75.3 1.0 NE2 B:GLN116 5.0 83.7 1.0 OG1 B:THR207 5.0 82.3 1.0 HD1 B:HIS199 5.0 93.7 1.0

J.Duan, A.Rutz, A.Kawamoto, S.Naskar, K.Edenharter, S.Leimkuehler, E.Hofmann, T.Happe, G.Kurisu. A Zinc Binding Four-Helix Domain Stabilizes the Dimeric Structure of O2-Stable [Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii To Be Published.