Zinc in PDB 1odh: Structure of the Gcm Domain Bound to Dna

The structure of Structure of the Gcm Domain Bound to Dna, PDB code: 1odh was solved by S.X.Cohen, C.W.Muller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.35 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.810, 52.910, 62.970, 90.00, 103.24, 90.00
R / Rfree (%)	21.9 / 28.1

The binding sites of Zinc atom in the Structure of the Gcm Domain Bound to Dna (pdb code 1odh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Gcm Domain Bound to Dna, PDB code: 1odh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Gcm Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Gcm Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1171 b:42.3 occ:1.00 ND1 A:HIS152 2.2 48.1 1.0 SG A:CYS125 2.3 39.9 1.0 SG A:CYS76 2.3 39.7 1.0 NE2 A:HIS154 2.3 42.1 1.0 CG A:HIS152 3.1 48.9 1.0 CB A:CYS125 3.1 41.8 1.0 CE1 A:HIS152 3.2 48.3 1.0 CE1 A:HIS154 3.2 42.6 1.0 CD2 A:HIS154 3.2 43.1 1.0 CB A:CYS76 3.3 37.5 1.0 CB A:HIS152 3.3 50.2 1.0 CA A:HIS152 3.9 51.2 1.0 CG2 A:VAL133 4.1 51.3 1.0 CD2 A:HIS152 4.2 47.6 1.0 NE2 A:HIS152 4.2 47.6 1.0 CB A:VAL133 4.3 50.6 1.0 ND1 A:HIS154 4.3 42.7 1.0 CE3 A:TRP59 4.3 52.4 1.0 CG A:HIS154 4.3 42.9 1.0 CA A:CYS125 4.3 42.9 1.0 CZ3 A:TRP59 4.5 52.2 1.0 CA A:CYS76 4.7 37.1 1.0 N A:HIS152 4.8 53.0 1.0 N A:VAL133 4.8 52.7 1.0 CD2 A:TRP59 4.9 51.6 1.0 C A:HIS152 4.9 51.4 1.0

Zinc binding site 2 out of 2 in the Structure of the Gcm Domain Bound to Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Gcm Domain Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1172 b:58.8 occ:1.00 SG A:CYS82 2.5 47.6 1.0 SG A:CYS86 2.5 61.8 1.0 SG A:CYS116 2.5 69.3 1.0 SG A:CYS113 2.7 50.3 1.0 CB A:CYS86 2.8 60.0 1.0 CB A:CYS82 3.1 49.3 1.0 CB A:CYS116 3.3 62.5 1.0 N A:CYS116 3.4 59.5 1.0 CB A:CYS113 3.5 51.4 1.0 CA A:CYS116 3.9 60.8 1.0 CB A:ASN115 4.1 60.5 1.0 CA A:CYS86 4.2 60.5 1.0 CA A:CYS82 4.5 50.5 1.0 C A:CYS116 4.5 60.2 1.0 N A:CYS86 4.5 60.5 1.0 C A:ASN115 4.5 59.0 1.0 N A:ASN117 4.7 60.4 1.0 ND2 A:ASN115 4.7 61.3 1.0 N A:GLY118 4.8 56.4 1.0 CA A:ASN115 4.8 58.8 1.0 C A:CYS86 4.8 61.1 1.0 N A:ASN115 4.9 57.0 1.0 CA A:CYS113 5.0 52.3 1.0

S.X.Cohen, M.Moulin, S.Hashemolhosseini, K.Kilian, M.Wegner, C.W.Muller. Crystal Structure of the Gcm Domain-Dna Complex: A Dna-Binding Domain with A Novel Fold and Mode of Target Site Recognition Embo J. V. 22 1835 2003.
ISSN: ISSN 0261-4189
PubMed: 12682016
DOI: 10.1093/EMBOJ/CDG182