Cobalt in PDB 1vlx: Structure of Electron Transfer (Cobalt-Protein)

The structure of Structure of Electron Transfer (Cobalt-Protein), PDB code: 1vlx was solved by N.Bonander, T.Vanngard, L.-C.Tsai, V.Langer, H.Nar, L.Sjolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.400, 80.400, 110.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / n/a

The binding sites of Cobalt atom in the Structure of Electron Transfer (Cobalt-Protein) (pdb code 1vlx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of Electron Transfer (Cobalt-Protein), PDB code: 1vlx:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of Electron Transfer (Cobalt-Protein)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co129 b:2.1 occ:1.00 O A:GLY45 2.1 2.0 1.0 ND1 A:HIS46 2.3 2.0 1.0 SG A:CYS112 2.4 2.4 1.0 ND1 A:HIS117 2.4 4.3 1.0 CE1 A:HIS46 3.0 2.0 1.0 CG A:HIS117 3.3 3.8 1.0 C A:GLY45 3.3 3.7 1.0 CE1 A:HIS117 3.4 2.0 1.0 CG A:HIS46 3.4 5.7 1.0 CB A:HIS117 3.5 5.1 1.0 CA A:HIS46 3.5 2.0 1.0 SD A:MET121 3.6 2.2 1.0 CB A:CYS112 3.6 2.3 1.0 CB A:PHE114 3.8 2.0 1.0 N A:HIS46 3.8 2.0 1.0 CB A:HIS46 3.9 2.8 1.0 NE2 A:HIS46 4.2 4.0 1.0 CE A:MET121 4.4 2.0 1.0 CD2 A:HIS46 4.4 2.0 1.0 CD2 A:HIS117 4.4 2.0 1.0 NE2 A:HIS117 4.5 2.0 1.0 CG A:PHE114 4.6 2.6 1.0 CA A:GLY45 4.6 5.7 1.0 C A:HIS46 4.7 2.0 1.0 N A:ASN47 4.8 3.1 1.0 N A:GLY45 4.8 5.8 1.0 O A:MET44 4.9 5.3 1.0 C A:MET44 4.9 6.6 1.0 N A:PHE114 5.0 2.0 1.0 CA A:CYS112 5.0 2.0 1.0 CD1 A:PHE114 5.0 5.0 1.0 CA A:HIS117 5.0 6.9 1.0

Cobalt binding site 2 out of 4 in the Structure of Electron Transfer (Cobalt-Protein)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co129 b:2.0 occ:1.00 ND1 B:HIS117 2.3 6.4 1.0 SG B:CYS112 2.3 2.2 1.0 ND1 B:HIS46 2.3 10.1 1.0 O B:GLY45 2.3 2.0 1.0 CE1 B:HIS117 3.0 8.9 1.0 CE1 B:HIS46 3.2 11.4 1.0 CG B:HIS117 3.3 9.7 1.0 CA B:HIS46 3.3 4.3 1.0 CG B:HIS46 3.3 9.9 1.0 C B:GLY45 3.4 3.4 1.0 SD B:MET121 3.4 2.0 1.0 CB B:CYS112 3.5 2.0 1.0 CB B:PHE114 3.7 2.8 1.0 CB B:HIS46 3.7 6.3 1.0 CB B:HIS117 3.7 8.8 1.0 N B:HIS46 3.8 2.0 1.0 NE2 B:HIS117 4.1 8.8 1.0 CD2 B:HIS117 4.2 10.6 1.0 NE2 B:HIS46 4.3 12.8 1.0 CE B:MET121 4.3 2.0 1.0 CD2 B:HIS46 4.4 11.6 1.0 CG B:PHE114 4.4 2.0 1.0 C B:HIS46 4.6 2.2 1.0 N B:ASN47 4.7 4.5 1.0 CA B:GLY45 4.7 4.5 1.0 CA B:PHE114 4.8 4.2 1.0 N B:PHE114 4.8 3.7 1.0 N B:GLY45 4.9 2.0 1.0 CA B:CYS112 4.9 2.0 1.0 O B:MET44 4.9 5.1 1.0 CG B:MET121 5.0 2.0 1.0 CD1 B:PHE114 5.0 2.0 1.0

Cobalt binding site 3 out of 4 in the Structure of Electron Transfer (Cobalt-Protein)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co129 b:2.0 occ:1.00 ND1 C:HIS117 2.2 2.0 1.0 O C:GLY45 2.2 2.0 1.0 SG C:CYS112 2.4 2.1 1.0 ND1 C:HIS46 2.5 2.0 1.0 CE1 C:HIS117 3.0 2.0 1.0 CA C:HIS46 3.2 3.0 1.0 CG C:HIS117 3.3 2.0 1.0 CG C:HIS46 3.3 3.6 1.0 C C:GLY45 3.3 3.1 1.0 CB C:HIS46 3.4 2.0 1.0 CB C:CYS112 3.5 2.0 1.0 CE1 C:HIS46 3.5 2.0 1.0 CB C:HIS117 3.7 2.0 1.0 N C:HIS46 3.7 2.0 1.0 SD C:MET121 3.7 2.0 1.0 CB C:PHE114 3.7 2.0 1.0 CE C:MET121 3.9 2.0 1.0 NE2 C:HIS117 4.1 2.0 1.0 CD2 C:HIS117 4.3 3.8 1.0 C C:HIS46 4.4 3.6 1.0 CD2 C:HIS46 4.5 2.0 1.0 CG C:PHE114 4.5 3.3 1.0 NE2 C:HIS46 4.6 2.0 1.0 N C:ASN47 4.6 5.5 1.0 CA C:GLY45 4.6 4.4 1.0 O C:MET44 4.7 3.3 1.0 N C:PHE114 4.8 2.6 1.0 CA C:CYS112 4.9 3.4 1.0 N C:GLY45 4.9 3.8 1.0 CA C:PHE114 4.9 2.0 1.0 C C:MET44 5.0 2.6 1.0

Cobalt binding site 4 out of 4 in the Structure of Electron Transfer (Cobalt-Protein)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Electron Transfer (Cobalt-Protein) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co129 b:2.4 occ:1.00 O D:GLY45 2.2 2.0 1.0 ND1 D:HIS117 2.3 3.2 1.0 SG D:CYS112 2.3 5.0 1.0 ND1 D:HIS46 2.5 4.7 1.0 CE1 D:HIS117 3.1 2.0 1.0 CG D:HIS117 3.3 2.4 1.0 CE1 D:HIS46 3.4 2.0 1.0 C D:GLY45 3.4 2.9 1.0 CA D:HIS46 3.5 2.0 1.0 SD D:MET121 3.6 2.0 1.0 CB D:CYS112 3.6 2.0 1.0 CB D:PHE114 3.6 2.0 1.0 CG D:HIS46 3.6 2.5 1.0 CB D:HIS117 3.7 3.9 1.0 N D:HIS46 3.9 2.0 1.0 CB D:HIS46 4.0 2.4 1.0 CE D:MET121 4.1 3.5 1.0 NE2 D:HIS117 4.3 2.0 1.0 CG D:PHE114 4.3 2.0 1.0 CD2 D:HIS117 4.4 2.0 1.0 NE2 D:HIS46 4.5 2.0 1.0 CA D:GLY45 4.7 2.0 1.0 CD2 D:HIS46 4.7 5.2 1.0 C D:HIS46 4.8 4.5 1.0 N D:PHE114 4.8 5.7 1.0 CA D:PHE114 4.8 4.8 1.0 N D:ASN47 4.8 5.1 1.0 O D:MET44 4.9 6.1 1.0 CD1 D:PHE114 4.9 2.0 1.0 CA D:CYS112 4.9 4.4 1.0 N D:GLY45 5.0 2.8 1.0 CD2 D:PHE114 5.0 2.0 1.0 C D:MET44 5.0 5.2 1.0

N.Bonander, T.Vanngard, L.C.Tsai, V.Langer, H.Nar, L.Sjolin. The Metal Site of Pseudomonas Aeruginosa Azurin, Revealed By A Crystal Structure Determination of the Co(II) Derivative and Co-Epr Spectroscopy. Proteins V. 27 385 1997.
ISSN: ISSN 0887-3585
PubMed: 9094740
DOI: 10.1002/(SICI)1097-0134(199703)27:3<385::AID-PROT6>3.0.CO;2-C