Zinc in PDB 1xa8: Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa)

The structure of Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa), PDB code: 1xa8 was solved by A.M.Neculai, D.Neculai, C.Griesinger, J.A.Vorholt, S.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.16 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.910, 120.620, 97.140, 90.00, 97.68, 90.00
R / Rfree (%)	19.5 / 24.8

The binding sites of Zinc atom in the Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa) (pdb code 1xa8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa), PDB code: 1xa8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:26.2 occ:1.00 SG A:CYS35 2.4 29.5 1.0 SG A:CYS101 2.4 22.3 1.0 SG A:CYS33 2.4 25.0 1.0 SG A:CYS104 2.4 24.1 1.0 CB A:CYS101 3.2 23.0 1.0 CB A:CYS104 3.3 26.0 1.0 CB A:CYS33 3.4 26.4 1.0 CB A:CYS35 3.4 30.0 1.0 N A:CYS35 3.7 30.4 1.0 N A:CYS104 3.8 26.6 1.0 CA A:CYS35 4.1 30.8 1.0 CA A:CYS104 4.1 25.5 1.0 N A:LYS34 4.2 27.6 1.0 CE A:LYS86 4.3 24.9 1.0 NZ A:LYS86 4.5 27.1 1.0 C A:LYS34 4.6 29.1 1.0 C A:CYS33 4.6 26.7 1.0 CA A:CYS33 4.6 26.0 1.0 CA A:CYS101 4.6 23.6 1.0 C A:ASP103 4.7 27.7 1.0 CB A:ASP103 4.8 28.9 1.0 CA A:LYS34 4.9 28.4 1.0 N A:ASP103 4.9 28.2 1.0 N A:VAL40 4.9 26.1 1.0 CA A:ASP103 5.0 28.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:24.2 occ:1.00 SG B:CYS101 2.3 22.8 1.0 SG B:CYS104 2.3 21.6 1.0 SG B:CYS35 2.4 26.2 1.0 SG B:CYS33 2.4 21.9 1.0 CB B:CYS101 3.2 24.0 1.0 CB B:CYS33 3.5 24.0 1.0 CB B:CYS104 3.5 22.3 1.0 CB B:CYS35 3.5 30.7 1.0 N B:CYS104 3.7 23.7 1.0 N B:CYS35 3.7 30.6 1.0 CA B:CYS35 4.2 31.2 1.0 CA B:CYS104 4.2 22.2 1.0 N B:LYS34 4.2 26.2 1.0 CE B:LYS86 4.4 28.5 1.0 CB B:ASP103 4.6 24.3 1.0 CA B:CYS101 4.6 24.3 1.0 C B:ASP103 4.7 24.6 1.0 C B:LYS34 4.7 28.9 1.0 NZ B:LYS86 4.7 31.2 1.0 CA B:CYS33 4.7 23.9 1.0 C B:CYS33 4.7 25.2 1.0 N B:ASP103 4.9 24.9 1.0 CA B:ASP103 4.9 24.4 1.0 CG2 B:VAL40 4.9 26.4 1.0 CA B:LYS34 4.9 27.6 1.0 C B:CYS101 5.0 24.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn200 b:50.9 occ:1.00 SG C:CYS33 2.3 50.0 1.0 SG C:CYS101 2.3 49.1 1.0 SG C:CYS104 2.4 47.5 1.0 SG C:CYS35 2.4 55.8 1.0 CB C:CYS33 3.2 48.7 1.0 CB C:CYS101 3.2 49.1 1.0 CB C:CYS104 3.5 47.7 1.0 CB C:CYS35 3.6 53.6 1.0 N C:CYS104 3.7 48.1 1.0 N C:CYS35 3.8 52.6 1.0 NZ C:LYS86 4.0 42.6 1.0 N C:LYS34 4.1 50.1 1.0 CA C:CYS104 4.2 47.5 1.0 CA C:CYS35 4.3 53.6 1.0 CA C:CYS33 4.4 48.5 1.0 C C:CYS33 4.5 49.0 1.0 CG2 C:VAL40 4.6 51.7 1.0 C C:LYS34 4.6 51.8 1.0 CE C:LYS86 4.7 43.7 1.0 CB C:ASP103 4.7 47.7 1.0 CA C:CYS101 4.7 48.7 1.0 C C:ASP103 4.8 48.1 1.0 CA C:LYS34 4.9 51.1 1.0 C C:CYS104 5.0 47.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Glutathione-Dependent Formaldehyde- Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn200 b:45.3 occ:1.00 SG D:CYS33 2.3 41.0 1.0 SG D:CYS104 2.3 43.9 1.0 SG D:CYS101 2.3 46.5 1.0 SG D:CYS35 2.4 49.8 1.0 CB D:CYS101 3.3 46.5 1.0 CB D:CYS33 3.3 40.7 1.0 CB D:CYS104 3.4 43.6 1.0 CB D:CYS35 3.5 46.8 1.0 N D:CYS104 3.5 44.6 1.0 N D:CYS35 3.8 45.8 1.0 CA D:CYS104 4.0 43.5 1.0 CA D:CYS35 4.1 47.5 1.0 N D:LYS34 4.3 42.7 1.0 NZ D:LYS86 4.4 38.8 1.0 CA D:CYS33 4.6 40.6 1.0 CB D:ASP103 4.6 44.5 1.0 C D:LYS34 4.6 44.8 1.0 C D:ASP103 4.6 45.2 1.0 C D:CYS33 4.6 41.8 1.0 CE D:LYS86 4.7 43.1 1.0 CA D:CYS101 4.7 46.6 1.0 C D:CYS104 4.8 43.1 1.0 N D:GLY105 4.9 42.1 1.0 CA D:ASP103 4.9 45.0 1.0 CG2 D:VAL40 4.9 41.3 1.0 N D:ASP103 4.9 46.4 1.0

A.M.Neculai, D.Neculai, C.Griesinger, J.A.Vorholt, S.Becker. A Dynamic Zinc Redox Switch J.Biol.Chem. V. 280 2826 2005.
ISSN: ISSN 0021-9258
PubMed: 15548539
DOI: 10.1074/JBC.C400517200