Zinc in PDB 9f46: Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii

The structure of Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f46 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)	48.89 / 2.45
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	167.9, 167.9, 125.38, 90, 90, 90
R / Rfree (%)	23.9 / 28.9

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

Chlorine	(Cl)	12 atoms
Iron	(Fe)	24 atoms

The binding sites of Zinc atom in the Crystal Structure of Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii (pdb code 9f46). 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 Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii, PDB code: 9f46:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Apo-[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 Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn704 b:70.0 occ:1.00 NE2 A:HIS199 2.1 76.6 1.0 SG A:CYS205 2.3 63.6 1.0 SG A:CYS113 2.3 68.9 1.0 SG A:CYS210 2.3 70.9 1.0 HB2 A:CYS205 2.9 76.3 1.0 CD2 A:HIS199 3.0 66.8 1.0 HB2 A:CYS113 3.0 78.5 1.0 HD2 A:HIS199 3.1 80.3 1.0 CE1 A:HIS199 3.2 72.2 1.0 HB2 A:CYS210 3.2 84.9 1.0 CB A:CYS205 3.2 63.4 1.0 CB A:CYS113 3.3 65.2 1.0 HB A:ILE115 3.3 82.4 1.0 CB A:CYS210 3.4 70.5 1.0 HE1 A:HIS199 3.4 86.9 1.0 H A:CYS210 3.5 78.3 1.0 HG2 A:GLN116 3.5 67.7 1.0 HB3 A:CYS113 3.6 78.5 1.0 HB3 A:CYS205 3.9 76.3 1.0 HA A:CYS205 3.9 85.1 1.0 N A:CYS210 4.0 65.0 1.0 HE21 A:GLN116 4.0 79.2 1.0 HB3 A:CYS210 4.1 84.9 1.0 CA A:CYS205 4.1 70.7 1.0 H A:GLN116 4.1 76.9 1.0 CG A:HIS199 4.2 69.7 1.0 HD12 A:LEU213 4.2 78.6 1.0 HG13 A:ILE115 4.2 89.3 1.0 CB A:ILE115 4.2 68.5 1.0 ND1 A:HIS199 4.2 75.9 1.0 CA A:CYS210 4.3 65.0 1.0 HB2 A:GLN209 4.3 76.4 1.0 H A:ILE115 4.4 72.6 1.0 CG A:GLN116 4.4 56.2 1.0 HG12 A:ILE115 4.4 89.3 1.0 HG1 A:THR207 4.4 90.9 1.0 HG3 A:GLN116 4.5 67.7 1.0 CG1 A:ILE115 4.5 74.2 1.0 H A:GLN209 4.6 64.9 1.0 HA A:CYS210 4.6 78.2 1.0 CA A:CYS113 4.6 73.3 1.0 HA A:CYS113 4.7 88.2 1.0 NE2 A:GLN116 4.8 65.8 1.0 N A:GLN116 4.9 63.9 1.0 C A:GLN209 4.9 67.3 1.0 HG22 A:ILE115 4.9 83.8 1.0 HA A:SER155 5.0 68.1 1.0 N A:ILE115 5.0 60.3 1.0 HG21 A:ILE115 5.0 83.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Apo-[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 Apo-[Fefe]-Hydrogenase CBA5H From Clostridium Beijerinckii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn704 b:69.2 occ:1.00 NE2 B:HIS199 2.1 69.4 1.0 SG B:CYS205 2.3 64.2 1.0 SG B:CYS113 2.3 59.0 1.0 SG B:CYS210 2.3 65.3 1.0 HB2 B:CYS205 2.7 71.8 1.0 CD2 B:HIS199 3.0 69.6 1.0 CB B:CYS205 3.1 59.7 1.0 HD2 B:HIS199 3.1 83.7 1.0 CE1 B:HIS199 3.1 79.2 1.0 HB2 B:CYS113 3.2 83.5 1.0 HB2 B:CYS210 3.3 85.3 1.0 HB B:ILE115 3.3 68.3 1.0 HE1 B:HIS199 3.4 95.2 1.0 CB B:CYS113 3.4 69.4 1.0 CB B:CYS210 3.4 70.9 1.0 H B:CYS210 3.5 67.5 1.0 HG2 B:GLN116 3.6 88.2 1.0 HB3 B:CYS113 3.8 83.5 1.0 HB3 B:CYS205 3.8 71.8 1.0 HA B:CYS205 3.8 80.3 1.0 N B:CYS210 4.0 56.1 1.0 CA B:CYS205 4.1 66.7 1.0 CG B:HIS199 4.1 74.7 1.0 HB2 B:GLN209 4.2 82.1 1.0 H B:GLN116 4.2 83.4 1.0 HB3 B:CYS210 4.2 85.3 1.0 ND1 B:HIS199 4.2 71.7 1.0 HG13 B:ILE115 4.2 79.0 1.0 CB B:ILE115 4.2 56.8 1.0 CA B:CYS210 4.3 63.9 1.0 HD12 B:LEU213 4.3 76.3 1.0 HE21 B:GLN116 4.3 106.0 1.0 HG12 B:ILE115 4.3 79.0 1.0 H B:ILE115 4.4 77.1 1.0 HG3 B:GLN116 4.4 88.2 1.0 CG B:GLN116 4.4 73.3 1.0 HG1 B:THR207 4.4 83.4 1.0 CG1 B:ILE115 4.5 65.6 1.0 H B:GLN209 4.5 74.9 1.0 HA B:CYS210 4.6 76.9 1.0 CA B:CYS113 4.7 66.4 1.0 HA B:CYS113 4.8 80.0 1.0 C B:GLN209 4.9 61.7 1.0 N B:GLN116 4.9 69.3 1.0 HG21 B:ILE115 4.9 72.5 1.0 HG22 B:ILE115 4.9 72.5 1.0 HA B:SER155 4.9 66.6 1.0 CB B:GLN209 5.0 68.2 1.0 HD1 B:HIS199 5.0 86.3 1.0 CG2 B:ILE115 5.0 60.2 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.