Cobalt in PDB 4hei: 2A X-Ray Structure of Hpf From Vibrio Cholerae

The structure of 2A X-Ray Structure of Hpf From Vibrio Cholerae, PDB code: 4hei was solved by H.De Bari, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.62 / 1.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.354, 46.354, 174.492, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 28.1

The binding sites of Cobalt atom in the 2A X-Ray Structure of Hpf From Vibrio Cholerae (pdb code 4hei). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the 2A X-Ray Structure of Hpf From Vibrio Cholerae, PDB code: 4hei:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the 2A X-Ray Structure of Hpf From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of 2A X-Ray Structure of Hpf From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:14.8 occ:1.00 N A:SCN103 1.8 12.2 1.0 NE2 A:HIS64 1.9 19.0 1.0 OE1 B:GLU60 2.1 13.5 1.0 NE2 A:HIS62 2.1 14.7 1.0 OE2 B:GLU60 2.5 14.7 1.0 CD B:GLU60 2.6 13.0 1.0 CE1 A:HIS64 2.8 17.8 1.0 C A:SCN103 3.0 12.6 1.0 CD2 A:HIS64 3.0 17.6 1.0 CD2 A:HIS62 3.1 15.5 1.0 CE1 A:HIS62 3.1 16.2 1.0 OE2 A:GLU51 3.8 15.8 1.0 ND1 A:HIS64 4.0 17.8 1.0 CG B:GLU60 4.1 15.0 1.0 CG A:HIS64 4.1 18.2 1.0 CD A:GLU51 4.1 16.2 1.0 ND1 A:HIS62 4.2 18.1 1.0 CG A:HIS62 4.2 14.9 1.0 CB A:GLU51 4.3 12.8 1.0 CO B:3CO106 4.4 16.3 1.0 O B:HOH202 4.5 22.6 1.0 CG A:GLU51 4.5 13.8 1.0 CE1 B:HIS55 4.5 18.0 1.0 S A:SCN103 4.7 14.6 1.0 OE1 A:GLU51 4.7 17.0 1.0 CB B:GLU60 4.8 14.8 1.0 ND1 B:HIS55 4.9 16.3 1.0 OG1 A:THR53 5.0 14.4 1.0

Cobalt binding site 2 out of 4 in the 2A X-Ray Structure of Hpf From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of 2A X-Ray Structure of Hpf From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:18.7 occ:1.00 N B:SCN105 1.8 23.6 1.0 N B:SCN104 1.9 21.2 1.0 ND1 A:HIS55 2.0 16.1 1.0 OE2 B:GLU51 2.1 17.5 1.0 OE1 B:GLU51 2.3 19.1 1.0 CD B:GLU51 2.5 17.6 1.0 CE1 A:HIS55 2.8 18.6 1.0 C B:SCN105 2.9 27.0 1.0 C B:SCN104 2.9 22.1 1.0 CG A:HIS55 3.1 19.3 1.0 CB A:HIS55 3.7 15.9 1.0 OE2 A:GLU60 3.8 25.9 1.0 NE B:ARG42 3.9 23.0 1.0 NE2 A:HIS55 3.9 21.1 1.0 CG B:GLU51 4.0 15.6 1.0 CG A:GLU60 4.0 24.4 1.0 O A:HOH221 4.1 33.1 1.0 CD2 A:HIS55 4.1 17.5 1.0 CD A:GLU60 4.1 22.9 1.0 NH2 B:ARG42 4.2 24.8 1.0 CE1 B:HIS64 4.3 19.8 1.0 CZ B:ARG42 4.4 24.4 1.0 CD1 B:ILE40 4.5 21.2 1.0 CO B:3CO102 4.6 17.4 1.0 NE2 B:HIS64 4.6 19.6 1.0 CA A:HIS55 4.6 20.1 1.0 S B:SCN105 4.7 28.7 1.0 N B:SCN103 4.7 16.4 1.0 S B:SCN104 4.7 24.8 1.0 CB B:GLU51 4.8 14.9 1.0 CD B:ARG42 4.8 25.3 1.0

Cobalt binding site 3 out of 4 in the 2A X-Ray Structure of Hpf From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of 2A X-Ray Structure of Hpf From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Co106 b:16.3 occ:1.00 N B:SCN107 1.9 19.6 1.0 N B:SCN108 2.0 21.1 1.0 OE2 A:GLU51 2.1 15.8 1.0 ND1 B:HIS55 2.1 16.3 1.0 OE2 B:GLU60 2.2 14.7 1.0 OE1 A:GLU51 2.3 17.0 1.0 CD A:GLU51 2.5 16.2 1.0 C B:SCN108 2.8 27.0 1.0 CE1 B:HIS55 3.0 18.0 1.0 C B:SCN107 3.0 17.3 1.0 CG B:HIS55 3.2 18.8 1.0 CD B:GLU60 3.2 13.0 1.0 CG B:GLU60 3.6 15.0 1.0 CB B:HIS55 3.7 16.6 1.0 NE A:ARG42 4.0 21.7 1.0 CG A:GLU51 4.0 13.8 1.0 NE2 B:HIS55 4.1 18.9 1.0 CD2 B:HIS55 4.3 19.3 1.0 O B:HOH203 4.3 23.1 1.0 CE1 A:HIS64 4.3 17.8 1.0 OE1 B:GLU60 4.4 13.5 1.0 NH2 A:ARG42 4.4 23.7 1.0 S B:SCN108 4.4 31.9 1.0 CD1 A:ILE40 4.4 21.2 1.0 CO A:3CO102 4.4 14.8 1.0 N A:SCN103 4.5 12.2 1.0 CZ A:ARG42 4.6 23.9 1.0 CA B:HIS55 4.6 16.1 1.0 NE2 A:HIS64 4.6 19.0 1.0 CB A:GLU51 4.7 12.8 1.0 S B:SCN107 4.8 21.8 1.0 CD A:ARG42 4.9 25.0 1.0 C A:SCN103 4.9 12.6 1.0 CG2 A:ILE40 5.0 16.3 1.0

Cobalt binding site 4 out of 4 in the 2A X-Ray Structure of Hpf From Vibrio Cholerae


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of 2A X-Ray Structure of Hpf From Vibrio Cholerae within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:17.4 occ:1.00 N B:SCN103 1.8 16.4 1.0 OE2 A:GLU60 1.9 25.9 1.0 NE2 B:HIS64 2.0 19.6 1.0 NE2 B:HIS62 2.0 14.8 1.0 CD A:GLU60 2.5 22.9 1.0 OE1 A:GLU60 2.5 25.4 1.0 C B:SCN103 2.9 14.3 1.0 CE1 B:HIS62 2.9 17.6 1.0 CE1 B:HIS64 3.0 19.8 1.0 CD2 B:HIS64 3.1 18.0 1.0 CD2 B:HIS62 3.1 16.2 1.0 OE2 B:GLU51 3.9 17.5 1.0 CG A:GLU60 3.9 24.4 1.0 ND1 B:HIS64 4.1 18.6 1.0 ND1 B:HIS62 4.1 16.0 1.0 CG B:HIS64 4.2 18.5 1.0 CE1 A:HIS55 4.2 18.6 1.0 CG B:HIS62 4.2 15.1 1.0 CD B:GLU51 4.3 17.6 1.0 CB B:GLU51 4.5 14.9 1.0 O A:HOH254 4.5 36.9 1.0 CO A:3CO101 4.6 18.7 1.0 CG B:GLU51 4.6 15.6 1.0 S B:SCN103 4.7 17.4 1.0 O B:HOH201 4.8 17.2 1.0 ND1 A:HIS55 4.8 16.1 1.0 OG1 B:THR53 4.8 15.6 1.0 OE1 B:GLU51 4.9 19.1 1.0 CB A:GLU60 4.9 21.5 1.0 N B:SCN105 5.0 23.6 1.0

H.De Bari, E.A.Berry. Structure of Vibrio Cholerae Ribosome Hibernation Promoting Factor. Acta Crystallogr.,Sect.F V. 69 228 2013.
ISSN: ESSN 1744-3091
PubMed: 23519794
DOI: 10.1107/S1744309113000961