Zinc in PDB 1x6m: Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa)

The structure of Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa), PDB code: 1x6m was solved by A.M.Neculai, D.Neculai, J.A.Vorholt, S.Becker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.29 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.360, 118.860, 95.990, 90.00, 97.48, 90.00
R / Rfree (%)	18.9 / 25

The binding sites of Zinc atom in the Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) (pdb code 1x6m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa), PDB code: 1x6m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the 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 of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:33.7 occ:1.00 SG A:CYS35 2.3 36.1 1.0 SG A:CYS101 2.3 31.7 1.0 SG A:CYS104 2.4 33.6 1.0 SG A:CYS33 2.4 32.2 1.0 CB A:CYS101 3.2 31.4 1.0 CB A:CYS104 3.3 33.4 1.0 CB A:CYS35 3.3 40.2 1.0 CB A:CYS33 3.4 33.2 1.0 N A:CYS104 3.5 34.7 1.0 N A:CYS35 3.6 40.1 1.0 CA A:CYS35 4.0 40.8 1.0 NZ A:LYS86 4.0 39.3 1.0 CA A:CYS104 4.0 33.3 1.0 N A:LYS34 4.1 36.4 1.0 C A:ASP103 4.5 37.0 1.0 C A:LYS34 4.5 39.1 1.0 CA A:CYS33 4.6 33.9 1.0 CB A:ASP103 4.6 38.4 1.0 C A:CYS33 4.6 35.0 1.0 CE A:LYS86 4.6 36.2 1.0 CA A:CYS101 4.7 32.0 1.0 CA A:ASP103 4.8 38.1 1.0 N A:ASP103 4.8 37.6 1.0 CG2 A:VAL40 4.8 30.9 1.0 CA A:LYS34 4.8 38.3 1.0 C A:CYS104 4.9 32.1 1.0 N A:VAL40 5.0 35.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the 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 of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:33.0 occ:0.60 SG A:CYS54 2.3 28.2 1.0 SG A:CYS59 2.3 36.7 1.0 SG A:CYS56 2.3 33.1 1.0 CB A:CYS59 3.0 31.8 1.0 CB A:CYS54 3.3 22.4 1.0 CB A:CYS56 3.4 26.3 1.0 N A:CYS56 3.7 23.7 1.0 CA A:CYS56 3.9 25.5 1.0 O A:CYS56 3.9 25.6 1.0 N A:CYS59 4.0 31.5 1.0 O A:HOH535 4.1 31.6 1.0 CA A:CYS59 4.1 31.0 1.0 C A:CYS56 4.1 26.0 1.0 OG A:SER68 4.2 30.1 1.0 C A:CYS54 4.2 20.9 1.0 CA A:CYS54 4.3 21.8 1.0 O A:CYS54 4.4 18.1 1.0 C A:GLY55 4.7 23.1 1.0 N A:GLY55 4.7 20.5 1.0 NH1 A:ARG98 4.9 32.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the 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 of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:34.2 occ:1.00 SG B:CYS101 2.3 27.4 1.0 SG B:CYS35 2.3 32.8 1.0 SG B:CYS33 2.4 31.9 1.0 SG B:CYS104 2.4 30.6 1.0 CB B:CYS101 3.2 30.6 1.0 CB B:CYS104 3.2 30.6 1.0 CB B:CYS33 3.4 31.2 1.0 CB B:CYS35 3.5 38.1 1.0 N B:CYS104 3.7 31.6 1.0 N B:CYS35 3.8 36.8 1.0 CA B:CYS104 4.0 30.8 1.0 CE B:LYS86 4.0 39.6 1.0 N B:LYS34 4.1 32.1 1.0 CA B:CYS35 4.2 38.2 1.0 C B:CYS33 4.5 31.8 1.0 CA B:CYS33 4.6 31.8 1.0 NZ B:LYS86 4.6 42.0 1.0 C B:ASP103 4.6 34.6 1.0 C B:LYS34 4.6 34.9 1.0 CA B:CYS101 4.6 30.1 1.0 CB B:ASP103 4.7 36.0 1.0 C B:CYS104 4.8 30.4 1.0 N B:ASP103 4.9 35.1 1.0 CA B:LYS34 4.9 33.9 1.0 CA B:ASP103 4.9 35.3 1.0 CG2 B:VAL40 4.9 29.6 1.0 N B:GLY105 5.0 28.7 1.0 N B:VAL40 5.0 33.7 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the 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 of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:32.5 occ:0.60 SG B:CYS59 2.3 35.4 1.0 SG B:CYS54 2.4 28.0 1.0 SG B:CYS56 2.4 40.5 1.0 CB B:CYS59 3.1 31.3 1.0 CB B:CYS54 3.2 24.2 1.0 CB B:CYS56 3.5 31.3 1.0 N B:CYS56 3.6 28.6 1.0 N B:CYS59 3.8 32.8 1.0 CA B:CYS56 3.8 30.9 1.0 O B:CYS56 3.9 31.9 1.0 CA B:CYS59 4.0 31.4 1.0 C B:CYS54 4.0 23.0 1.0 O B:CYS54 4.1 21.9 1.0 C B:CYS56 4.1 30.9 1.0 CA B:CYS54 4.2 23.4 1.0 OG B:SER68 4.4 26.9 1.0 O B:HOH664 4.4 36.6 1.0 CB B:SER68 4.6 25.7 1.0 N B:GLY55 4.6 23.4 1.0 C B:GLY55 4.6 26.7 1.0 O B:HOH665 4.9 33.1 1.0 C B:LYS58 4.9 33.2 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the 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 5 of Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn200 b:52.3 occ:1.00 SG C:CYS101 2.3 53.1 1.0 SG C:CYS104 2.3 49.8 1.0 SG C:CYS33 2.3 49.2 1.0 SG C:CYS35 2.4 53.9 1.0 CB C:CYS101 3.1 53.8 1.0 CB C:CYS33 3.3 50.0 1.0 CB C:CYS104 3.3 51.9 1.0 CB C:CYS35 3.4 54.6 1.0 N C:CYS35 3.8 54.5 1.0 N C:CYS104 3.8 52.8 1.0 CA C:CYS35 4.1 55.0 1.0 CA C:CYS104 4.1 51.4 1.0 N C:LYS34 4.1 51.4 1.0 NZ C:LYS86 4.4 55.3 1.0 CE C:LYS86 4.4 56.9 1.0 CA C:CYS33 4.5 50.0 1.0 CA C:CYS101 4.6 53.8 1.0 C C:CYS33 4.6 50.4 1.0 CG2 C:VAL40 4.6 50.5 1.0 CB C:ASP103 4.7 54.8 1.0 C C:ASP103 4.7 54.1 1.0 C C:LYS34 4.8 53.2 1.0 N C:VAL40 4.9 52.7 1.0 C C:CYS101 4.9 54.6 1.0 C C:CYS104 5.0 50.5 1.0 N C:ASP103 5.0 55.3 1.0 CA C:LYS34 5.0 52.5 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the 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 6 of Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:38.3 occ:0.60 SG C:CYS56 2.3 48.1 1.0 SG C:CYS59 2.4 45.3 1.0 SG C:CYS54 2.4 34.9 1.0 CB C:CYS54 3.3 33.7 1.0 CB C:CYS56 3.4 42.7 1.0 O C:CYS56 3.6 43.9 1.0 CB C:CYS59 3.6 44.3 1.0 N C:CYS56 3.7 41.0 1.0 CA C:CYS56 3.8 42.8 1.0 C C:CYS56 3.9 43.0 1.0 N C:CYS59 3.9 43.7 1.0 C C:CYS54 4.2 35.3 1.0 O C:CYS54 4.2 35.8 1.0 CA C:CYS59 4.2 43.6 1.0 CB C:SER68 4.3 32.5 1.0 CA C:CYS54 4.3 34.4 1.0 OG C:SER68 4.6 34.5 1.0 N C:GLY55 4.7 36.0 1.0 C C:GLY55 4.8 39.7 1.0 NZ C:LYS61 4.8 44.7 1.0 N C:THR57 4.9 43.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the 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 7 of Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn200 b:50.8 occ:1.00 SG D:CYS104 2.3 46.9 1.0 SG D:CYS101 2.3 46.0 1.0 SG D:CYS33 2.4 51.5 1.0 SG D:CYS35 2.4 51.9 1.0 CB D:CYS101 3.3 46.0 1.0 CB D:CYS33 3.3 49.0 1.0 CB D:CYS35 3.5 50.9 1.0 CB D:CYS104 3.6 47.1 1.0 N D:CYS35 3.8 51.8 1.0 N D:CYS104 3.9 48.1 1.0 NZ D:LYS86 4.0 48.7 1.0 N D:LYS34 4.2 50.8 1.0 CA D:CYS35 4.2 51.4 1.0 CA D:CYS104 4.3 46.7 1.0 CE D:LYS86 4.4 49.6 1.0 CA D:CYS33 4.6 48.6 1.0 CB D:ASP103 4.6 49.6 1.0 C D:ASP103 4.6 48.9 1.0 C D:CYS33 4.6 49.5 1.0 CA D:CYS101 4.7 45.8 1.0 N D:ASP103 4.8 50.0 1.0 CG2 D:VAL40 4.8 44.7 1.0 C D:LYS34 4.8 51.9 1.0 CA D:ASP103 4.9 49.2 1.0 N D:VAL40 4.9 47.1 1.0 C D:CYS101 5.0 46.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the 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 8 of Crystal Structure of the Glutathione-Dependent Formaldehyde-Activating Enzyme (Gfa) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:43.8 occ:0.60 SG D:CYS56 2.3 46.9 1.0 SG D:CYS59 2.3 50.6 1.0 SG D:CYS54 2.4 40.2 1.0 CB D:CYS54 3.3 38.2 1.0 CB D:CYS56 3.4 45.8 1.0 CB D:CYS59 3.6 49.4 1.0 O D:CYS56 3.6 46.3 1.0 N D:CYS56 3.6 43.8 1.0 CA D:CYS56 3.8 45.2 1.0 C D:CYS56 4.0 46.2 1.0 N D:CYS59 4.0 48.3 1.0 C D:CYS54 4.1 38.7 1.0 O D:CYS54 4.2 38.8 1.0 CA D:CYS59 4.3 48.5 1.0 CA D:CYS54 4.3 38.0 1.0 O D:HOH645 4.3 39.5 1.0 OG D:SER68 4.4 38.8 1.0 N D:GLY55 4.5 39.9 1.0 C D:GLY55 4.7 42.7 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