Zinc in PDB 3dtk: Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae

The structure of Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae, PDB code: 3dtk was solved by A.Vujicic-Zagar, R.Dulermo, M.Le Gorrec, F.Vannier, P.Servant, S.Sommer, A.De Groot, L.Serre, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 3.24
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.260, 52.672, 63.221, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27.7

The structure of Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae (pdb code 3dtk). 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 the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae, PDB code: 3dtk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae


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 Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn283 b:79.8 occ:1.00 OE2 A:GLU113 2.0 80.3 1.0 OE1 A:GLU113 2.0 80.0 1.0 NE2 A:HIS82 2.1 73.9 1.0 CD A:GLU113 2.1 79.9 1.0 CL A:CL282 2.6 79.7 1.0 CD2 A:HIS82 2.9 72.8 1.0 CE1 A:HIS82 3.2 72.9 1.0 ZN A:ZN284 3.3 78.4 1.0 CG A:GLU113 3.5 79.6 1.0 CG A:HIS82 4.1 72.4 1.0 OE2 A:GLU83 4.1 73.8 1.0 ND1 A:HIS82 4.2 72.7 1.0 SG A:CYS116 4.3 74.4 1.0 CB A:GLU113 4.4 79.1 1.0 CB A:CYS116 4.5 74.0 1.0 OE1 A:GLU83 4.5 73.6 1.0 CA A:GLU113 4.6 78.8 1.0 CD A:GLU83 4.6 73.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae


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 Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn284 b:78.4 occ:1.00 ND1 A:HIS86 2.4 72.6 1.0 OE1 A:GLU83 2.5 73.6 1.0 CE1 A:HIS86 3.1 72.8 1.0 OE2 A:GLU83 3.1 73.8 1.0 CD A:GLU83 3.2 73.4 1.0 ZN A:ZN283 3.3 79.8 1.0 CG A:HIS86 3.4 72.4 1.0 CB A:HIS86 3.9 72.2 1.0 CL A:CL282 4.0 79.7 1.0 NE2 A:HIS86 4.2 72.7 1.0 CB A:TYR58 4.3 83.5 1.0 N A:TYR58 4.3 83.8 1.0 CD2 A:HIS86 4.4 72.6 1.0 OE1 A:GLU113 4.4 80.0 1.0 CD2 A:HIS82 4.6 72.8 1.0 NE2 A:HIS82 4.6 73.9 1.0 CG A:GLU83 4.7 72.9 1.0 C A:ALA57 4.9 83.9 1.0 CA A:TYR58 4.9 84.0 1.0 CA A:ALA57 4.9 84.3 1.0 CD A:GLU113 5.0 79.9 1.0

A.Vujicic-Zagar, R.Dulermo, M.Le Gorrec, F.Vannier, P.Servant, S.Sommer, A.De Groot, L.Serre. Crystal Structure of the Irre Protein, A Central Regulator of Dna Damage Repair in Deinococcaceae J.Mol.Biol. V. 386 704 2009.
ISSN: ISSN 0022-2836
PubMed: 19150362
DOI: 10.1016/J.JMB.2008.12.062