Sodium in PDB 4wwf: High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs

The structure of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs, PDB code: 4wwf was solved by A.Volbeda, J.Coves, A.P.Maillard, S.Kinnemann, C.Grosse, G.Schleuder, I.Petit-Hurtlein, E.De Rosny, D.H.Nies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.79 / 1.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.910, 47.520, 193.740, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 14.5

The structure of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs also contains other interesting chemical elements:

Nickel

(Ni)

3 atoms

The binding sites of Sodium atom in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs (pdb code 4wwf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs, PDB code: 4wwf:

Sodium binding site 1 out of 1 in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:33.0 occ:0.50 O B:GLU43 1.8 17.9 0.5 HG3 B:GLU47 2.0 28.3 0.5 O B:GLU43 2.1 28.2 0.5 OE1 B:GLU47 2.1 23.2 0.5 H B:GLU47 2.2 23.6 0.5 HG2 B:GLU47 2.4 27.5 0.5 H B:GLU47 2.5 21.9 0.5 HA B:ILE44 2.6 22.1 0.5 HA B:ILE44 2.7 33.6 0.5 O B:ILE44 2.7 36.8 0.5 HB2 B:HIS46 2.7 22.9 0.5 HB2 B:HIS46 2.8 19.4 0.5 C B:GLU43 2.8 23.5 0.5 CG B:GLU47 2.9 24.6 0.5 CD B:GLU47 2.9 37.1 0.5 C B:ILE44 2.9 27.2 0.5 H B:HIS46 2.9 21.0 1.0 CG B:GLU47 3.0 27.7 0.5 N B:GLU47 3.0 23.3 0.5 CA B:ILE44 3.0 19.9 0.5 HG2 B:GLU47 3.1 25.0 0.5 C B:ILE44 3.1 29.3 0.5 N B:GLU47 3.1 20.4 0.5 O B:ILE44 3.2 23.2 0.5 C B:GLU43 3.2 28.4 0.5 HB3 B:GLU47 3.2 22.2 0.5 CA B:ILE44 3.3 33.4 0.5 N B:HIS46 3.3 17.8 1.0 N B:ILE44 3.3 31.3 0.5 HB2 B:GLU47 3.4 20.9 0.5 CB B:GLU47 3.5 26.1 0.5 CB B:GLU47 3.5 21.7 0.5 CB B:HIS46 3.6 23.0 0.5 CB B:HIS46 3.6 18.7 0.5 CA B:HIS46 3.6 21.0 0.5 C B:HIS46 3.7 22.4 0.5 CA B:HIS46 3.7 19.5 0.5 N B:ILE44 3.7 33.4 0.5 N B:LEU45 3.8 24.8 1.0 C B:HIS46 3.8 19.8 0.5 HG3 B:GLU47 3.8 25.5 0.5 CA B:GLU47 3.9 22.5 0.5 CD B:GLU47 4.0 33.4 0.5 CA B:GLU47 4.0 22.5 0.5 C B:LEU45 4.0 20.6 1.0 HD11 B:ILE44 4.0 27.9 0.5 OE2 B:GLU47 4.1 65.7 0.5 HB3 B:HIS46 4.1 19.5 0.5 HB3 B:HIS46 4.1 23.5 0.5 CA B:GLU43 4.2 21.2 0.5 HA B:GLU43 4.2 23.2 0.5 HA B:GLU43 4.3 26.0 0.5 H B:LEU45 4.3 25.1 1.0 H B:ILE44 4.3 30.5 0.5 HA B:GLU47 4.3 23.1 0.5 CA B:GLU43 4.4 27.4 0.5 HB2 B:GLU47 4.4 27.9 0.5 CA B:LEU45 4.4 17.3 1.0 HB3 B:GLU47 4.5 23.7 0.5 CB B:ILE44 4.5 25.7 0.5 HB2 B:GLU43 4.5 29.9 0.5 CG B:HIS46 4.5 19.1 0.5 HA B:GLU47 4.6 22.5 0.5 OE1 B:GLU47 4.6 57.6 0.5 O B:HIS42 4.6 21.4 0.5 O B:HOH357 4.6 31.1 1.0 CB B:ILE44 4.6 37.9 0.5 HA B:HIS46 4.6 23.0 0.5 OE2 B:GLU47 4.6 46.5 0.5 HA B:HIS46 4.7 21.6 0.5 H B:ILE44 4.7 35.5 0.5 HB B:ILE44 4.7 42.9 0.5 HG13 B:ILE44 4.7 24.4 0.5 HG21 B:ILE44 4.7 44.9 0.5 HD1 B:HIS46 4.8 22.2 0.5 CG B:HIS46 4.8 14.7 0.5 O B:HIS46 4.8 21.9 0.5 CB B:GLU43 4.8 30.3 0.5 CD1 B:ILE44 4.9 32.7 0.5 O B:HIS46 4.9 26.4 0.5 HB B:ILE44 4.9 25.5 0.5 O B:LEU45 4.9 19.1 1.0 HA B:LEU45 4.9 18.9 1.0 CG1 B:ILE44 4.9 24.4 0.5 ND1 B:HIS46 5.0 20.8 0.5 HB2 B:GLU43 5.0 23.9 0.5 H B:ALA48 5.0 15.0 1.0 HB3 B:GLU43 5.0 28.7 0.5

A.P.Maillard, S.Kunnemann, C.Groe, A.Volbeda, G.Schleuder, I.Petit-Hartlein, E.De Rosny, D.H.Nies, J.Coves. Response of Cnrx From Cupriavidus Metallidurans CH34 to Nickel Binding. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25628016
DOI: 10.1039/C4MT00293H