Zinc in PDB 2y3d: Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs

The structure of Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs, PDB code: 2y3d was solved by J.Trepreau, E.Girard, A.P.Maillard, E.De Rosny, I.Petit-Haertlein, R.Kahn, J.Coves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.953 / 2.30
Space group	I 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	155.721, 155.721, 155.721, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.93

The structure of Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Zinc atom in the Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs (pdb code 2y3d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs, PDB code: 2y3d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn149 b:28.2 occ:1.00 NE2 A:HIS119 2.1 19.9 1.0 NE2 A:HIS38 2.1 25.4 1.0 OE1 A:GLU63 2.1 33.4 1.0 CL A:CL1146 2.3 29.9 1.0 CD A:GLU63 2.9 31.2 1.0 CD2 A:HIS38 3.0 23.1 1.0 CD2 A:HIS119 3.0 22.1 1.0 OE2 A:GLU63 3.0 36.9 1.0 CE1 A:HIS119 3.1 18.4 1.0 CE1 A:HIS38 3.2 33.8 1.0 ND1 A:HIS42 3.9 46.5 1.0 CD2 A:PHE66 4.1 25.5 1.0 CG A:HIS38 4.2 37.6 1.0 CG A:HIS119 4.2 23.0 1.0 ND1 A:HIS119 4.2 23.0 1.0 ND1 A:HIS38 4.2 39.5 1.0 CG A:GLU63 4.4 31.6 1.0 CG A:MET123 4.5 29.2 1.0 CE1 A:HIS42 4.6 42.8 1.0 CE2 A:PHE66 4.6 30.0 1.0 CG A:HIS42 4.6 54.3 1.0 CB A:HIS42 4.8 47.2 1.0 CB A:GLU63 4.8 31.0 1.0 CG A:PHE66 4.8 28.2 1.0 CA A:GLU63 4.9 29.9 1.0

Zinc binding site 2 out of 3 in the Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn150 b:44.2 occ:1.00 OE2 A:GLU60 2.1 42.9 1.0 NE2 A:HIS42 2.2 47.1 1.0 NE2 A:HIS46 2.2 63.0 1.0 CL A:CL1147 2.3 63.1 1.0 CD A:GLU60 2.8 36.6 1.0 OE1 A:GLU60 2.9 31.1 1.0 CD2 A:HIS42 3.0 52.3 1.0 CD2 A:HIS46 3.0 67.5 1.0 CE1 A:HIS46 3.2 63.3 1.0 CE1 A:HIS42 3.2 42.8 1.0 CG A:HIS46 4.2 68.6 1.0 CG A:HIS42 4.2 54.3 1.0 ND1 A:HIS46 4.2 68.4 1.0 ND1 A:HIS42 4.3 46.5 1.0 CG A:GLU60 4.3 25.9 1.0 CD2 A:LEU59 4.3 39.9 1.0 O A:HOH2008 5.0 27.3 1.0

Zinc binding site 3 out of 3 in the Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn-Bound Form of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn149 b:34.3 occ:1.00 NE2 B:HIS119 2.0 25.5 1.0 NE2 B:HIS46 2.0 30.8 1.0 NE2 B:HIS42 2.1 37.1 1.0 OE1 B:GLU63 2.5 46.7 1.0 OE2 B:GLU63 2.6 50.5 1.0 CD B:GLU63 2.8 50.8 1.0 CE1 B:HIS119 2.9 32.8 1.0 CE1 B:HIS46 2.9 36.2 1.0 CD2 B:HIS119 3.0 30.9 1.0 CE1 B:HIS42 3.1 37.1 1.0 CD2 B:HIS42 3.1 30.6 1.0 CD2 B:HIS46 3.1 37.6 1.0 SD B:MET123 3.9 46.3 1.0 CE B:MET123 3.9 44.1 1.0 CD2 B:PHE66 4.0 31.4 1.0 ND1 B:HIS119 4.0 32.5 1.0 ND1 B:HIS46 4.1 38.7 1.0 CG B:HIS119 4.1 32.2 1.0 ND1 B:HIS42 4.2 39.3 1.0 CG B:HIS46 4.2 37.3 1.0 CG B:HIS42 4.2 38.1 1.0 CG B:GLU63 4.2 55.1 1.0 CE2 B:PHE66 4.3 34.4 1.0 O B:HOH2017 4.3 56.8 1.0 CG B:PHE66 4.8 30.8 1.0

J.Trepreau, E.Girard, A.P.Maillard, E.De Rosny, I.Petit-Haertlein, R.Kahn, J.Coves. Structural Basis For Metal Sensing By Cnrx. J.Mol.Biol. V. 408 766 2011.
ISSN: ISSN 0022-2836
PubMed: 21414325
DOI: 10.1016/J.JMB.2011.03.014