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

Protein crystallography data

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

Other elements in 2y3d:

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

Chlorine (Cl) 5 atoms

Zinc Binding Sites:

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 2y3d

Go back to Zinc Binding Sites List in 2y3d
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 2y3d

Go back to Zinc Binding Sites List in 2y3d
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 2y3d

Go back to Zinc Binding Sites List in 2y3d
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

Reference:

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
Page generated: Thu Oct 17 05:42:48 2024

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