Zinc in PDB 4clv: Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A

The structure of Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A, PDB code: 4clv was solved by P.Legrand, E.Girard, I.Petit-Hartlein, A.P.Maillard, J.Coves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.12
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.800, 53.800, 300.040, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 26.42

The binding sites of Zinc atom in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A (pdb code 4clv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A, PDB code: 4clv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1146 b:0.7 occ:1.00 OE1 A:GLU63 2.2 0.4 1.0 NE2 A:HIS119 2.2 0.5 1.0 NE2 A:HIS38 2.4 0.8 1.0 CD A:GLU63 3.1 0.5 1.0 CD2 A:HIS119 3.1 0.4 1.0 CD2 A:HIS38 3.2 0.9 1.0 CE1 A:HIS119 3.2 0.6 1.0 CE1 A:HIS38 3.3 0.1 1.0 OE2 A:GLU63 3.3 0.6 1.0 ND1 A:HIS42 3.4 0.1 1.0 CE A:MET123 3.7 0.4 1.0 CG A:MET123 3.9 0.8 1.0 CE1 A:HIS42 4.2 0.6 1.0 SD A:MET123 4.3 0.2 1.0 CG A:HIS119 4.3 1.0 1.0 CG A:HIS38 4.3 0.5 1.0 ND1 A:HIS38 4.3 0.9 1.0 ND1 A:HIS119 4.4 0.7 1.0 CG A:HIS42 4.4 0.4 1.0 CG A:GLU63 4.5 0.0 1.0 CB A:HIS42 4.5 0.9 1.0 O A:HIS38 5.0 0.7 1.0

Zinc binding site 2 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1147 b:0.0 occ:1.00 NE2 A:HIS42 2.1 0.5 1.0 NE2 A:HIS46 2.3 0.1 1.0 OE2 A:GLU60 2.5 0.9 1.0 CE1 A:HIS42 2.9 0.6 1.0 CE1 A:HIS46 3.1 0.3 1.0 CD A:GLU60 3.2 0.7 1.0 OE1 A:GLU60 3.2 0.1 1.0 CD2 A:HIS42 3.3 0.8 1.0 CD2 A:HIS46 3.4 0.7 1.0 ND1 A:HIS42 4.2 0.1 1.0 CG A:HIS42 4.3 0.4 1.0 ND1 A:HIS46 4.3 0.4 1.0 CG A:HIS46 4.4 1.0 1.0 CG A:GLU60 4.7 0.1 1.0

Zinc binding site 3 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1148 b:0.8 occ:1.00 OD1 A:ASP52 2.8 0.1 1.0 NE2 A:HIS131 2.8 1.0 1.0 CD2 A:HIS131 3.4 0.8 1.0 CG A:ASP52 3.8 0.0 1.0 OE1 A:GLU130 4.0 0.6 1.0 CE1 A:HIS131 4.0 0.2 1.0 CG A:PRO50 4.1 0.9 1.0 OD2 A:ASP52 4.4 0.4 1.0 CB A:PRO50 4.6 0.1 1.0 CG A:HIS131 4.7 0.6 1.0 CB A:ASP52 4.7 0.7 1.0 CB A:GLU130 4.9 0.4 1.0 ND1 A:HIS131 5.0 0.6 1.0 CD A:PRO50 5.0 0.7 1.0

Zinc binding site 4 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1149 b:0.5 occ:1.00 NE2 A:HIS32 2.4 0.3 1.0 OE1 B:GLU106 3.2 0.8 1.0 CD2 A:HIS32 3.2 0.9 1.0 CD B:GLU106 3.3 0.0 1.0 CE1 A:HIS32 3.3 0.1 1.0 CG B:GLU106 3.5 0.2 1.0 OE2 A:GLU36 3.7 0.5 1.0 OE2 B:GLU106 3.8 0.2 1.0 CG A:HIS32 4.2 0.3 1.0 ND1 A:HIS32 4.3 0.7 1.0 CD A:GLU36 4.4 0.7 1.0 CG A:GLU36 4.5 0.8 1.0 CB B:GLU106 4.6 0.4 1.0 CB A:GLU36 4.9 1.0 1.0

Zinc binding site 5 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1150 b:0.2 occ:1.00 OE2 B:GLU36 3.2 0.2 1.0 NE2 B:HIS32 3.3 0.4 1.0 CD A:GLU106 3.3 0.2 1.0 OE1 A:GLU106 3.4 0.2 1.0 CD2 B:HIS32 3.6 0.8 1.0 CG A:GLU106 3.6 0.9 1.0 OE2 A:GLU106 3.7 0.3 1.0 CD B:GLU36 4.1 0.4 1.0 CE1 B:HIS32 4.4 0.1 1.0 CG B:GLU36 4.5 0.8 1.0 CG B:HIS32 4.7 0.7 1.0 CB A:GLU106 4.8 0.6 1.0

Zinc binding site 6 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1151 b:0.3 occ:1.00 OD2 A:ASP47 2.0 0.0 1.0 CG A:ASP47 2.7 0.2 1.0 OD1 A:ASP47 2.8 0.9 1.0 OE2 A:GLU43 3.0 0.5 1.0 CD A:GLU43 3.1 0.1 1.0 CG A:GLU43 3.2 0.2 1.0 OE1 A:GLU43 3.7 0.1 1.0 CB A:ASP47 4.1 0.6 1.0 O A:GLU43 4.5 0.4 1.0 CB A:GLU43 4.6 0.2 1.0 C A:GLU43 4.9 0.8 1.0

Zinc binding site 7 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1146 b:0.5 occ:1.00 OE1 B:GLU63 2.2 0.6 1.0 NE2 B:HIS119 2.3 0.3 1.0 NE2 B:HIS38 2.3 0.1 1.0 CD B:GLU63 3.1 0.9 1.0 CD2 B:HIS119 3.2 0.8 1.0 CD2 B:HIS38 3.2 0.9 1.0 CE1 B:HIS38 3.2 0.0 1.0 CE1 B:HIS119 3.3 0.7 1.0 ND1 B:HIS42 3.3 0.4 1.0 OE2 B:GLU63 3.3 0.6 1.0 CE B:MET123 3.7 0.3 1.0 CG B:MET123 4.0 0.7 1.0 CE1 B:HIS42 4.2 0.2 1.0 CG B:HIS38 4.3 0.6 1.0 ND1 B:HIS38 4.3 0.4 1.0 SD B:MET123 4.3 0.5 1.0 CG B:HIS42 4.3 0.0 1.0 CG B:HIS119 4.3 0.4 1.0 ND1 B:HIS119 4.4 0.6 1.0 CB B:HIS42 4.5 0.6 1.0 CG B:GLU63 4.5 0.1 1.0 O B:HIS38 4.9 0.6 1.0

Zinc binding site 8 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


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 Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1147 b:0.4 occ:1.00 NE2 B:HIS42 2.1 0.0 1.0 NE2 B:HIS46 2.2 0.8 1.0 OE2 B:GLU60 2.4 0.3 1.0 CE1 B:HIS42 2.9 0.2 1.0 CE1 B:HIS46 3.1 0.4 1.0 CD B:GLU60 3.2 0.7 1.0 OE1 B:GLU60 3.3 0.8 1.0 CD2 B:HIS42 3.3 0.6 1.0 CD2 B:HIS46 3.3 0.7 1.0 ND1 B:HIS42 4.2 0.4 1.0 ND1 B:HIS46 4.3 0.5 1.0 CG B:HIS42 4.3 0.0 1.0 CG B:HIS46 4.4 0.8 1.0 CG B:GLU60 4.6 0.3 1.0

Zinc binding site 9 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1148 b:0.1 occ:1.00 OD1 B:ASP52 2.8 0.1 1.0 NE2 B:HIS131 2.8 0.3 1.0 CD2 B:HIS131 3.4 0.5 1.0 CG B:ASP52 3.8 0.1 1.0 CE1 B:HIS131 4.0 0.5 1.0 OE1 B:GLU130 4.0 0.1 1.0 CG B:PRO50 4.1 0.7 1.0 OD2 B:ASP52 4.4 0.3 1.0 CB B:PRO50 4.6 0.2 1.0 CG B:HIS131 4.6 0.5 1.0 CB B:ASP52 4.7 0.8 1.0 CB B:GLU130 4.9 0.1 1.0 ND1 B:HIS131 5.0 0.1 1.0 CD B:PRO50 5.0 0.0 1.0

Zinc binding site 10 out of 10 in the Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Dodecylphosphocholine-Solubilized Nccx From Cupriavidus Metallidurans 31A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1149 b:0.3 occ:1.00 OE1 B:GLU57 2.0 0.2 1.0 CD B:GLU57 2.8 1.0 1.0 OE2 B:GLU57 3.2 0.3 1.0 CG B:GLU57 4.0 0.8 1.0 CB B:GLU57 5.0 0.4 1.0

W.Ziani, A.P.Maillard, I.Petit-Hartlein, N.Garnier, S.Crouzy, E.Girard, J.Coves. The X-Ray Structure of Nccx From Cupriavidus Metallidurans 31A Illustrates Potential Dangers of Detergent Solubilization When Generating and Interpreting Crystal Structures of Membrane Proteins. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25258316
DOI: 10.1074/JBC.M114.586537