Cobalt in PDB 3g5k: Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target

All present enzymatic activity of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target:
3.5.1.88;

The structure of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target, PDB code: 3g5k was solved by S.Escobar-Alvarez, Y.Goldgur, G.Yang, O.Ouerfelli, Y.Li, D.A.Scheinberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.144, 77.830, 110.532, 90.00, 107.46, 90.00
R / Rfree (%)	16.4 / 19.3

The binding sites of Cobalt atom in the Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target (pdb code 3g5k). 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 and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target, PDB code: 3g5k:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:9.2 occ:1.00 NE2 A:HIS156 2.0 7.0 1.0 NE2 A:HIS160 2.1 6.7 1.0 O4 A:BB21001 2.1 18.5 1.0 SG A:CYS114 2.3 8.9 1.0 O2 A:BB21001 2.3 22.3 1.0 CD2 A:HIS156 3.0 7.7 1.0 CE1 A:HIS160 3.0 4.8 1.0 CE1 A:HIS156 3.0 6.3 1.0 C3 A:BB21001 3.1 7.0 1.0 CD2 A:HIS160 3.1 8.1 1.0 N1 A:BB21001 3.1 21.7 1.0 CB A:CYS114 3.3 5.9 1.0 NE2 A:GLN57 3.3 7.3 1.0 O A:HOH1009 3.6 7.0 1.0 CA A:CYS114 3.7 5.6 1.0 CD A:GLN57 4.1 8.7 1.0 N A:GLU115 4.1 6.0 1.0 CG A:HIS156 4.2 5.4 1.0 ND1 A:HIS156 4.2 8.2 1.0 ND1 A:HIS160 4.2 7.6 1.0 CG A:HIS160 4.2 6.1 1.0 OE1 A:GLN57 4.3 9.1 1.0 C A:CYS114 4.4 5.9 1.0 C5 A:BB21001 4.4 19.9 1.0 OE1 A:GLU157 4.6 16.7 1.0 O A:HOH1006 4.6 8.0 1.0 C6 A:BB21001 4.8 22.6 1.0 N A:SER116 4.8 6.6 1.0 O A:GLY113 4.8 13.3 1.0 OE2 A:GLU157 4.9 14.3 1.0 N A:CYS114 5.0 7.1 1.0

Cobalt binding site 2 out of 4 in the Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1003 b:9.6 occ:1.00 NE2 B:HIS156 2.0 7.9 1.0 NE2 B:HIS160 2.0 6.4 1.0 O4 B:BB21002 2.1 20.1 1.0 SG B:CYS114 2.3 8.3 1.0 O2 B:BB21002 2.4 24.9 1.0 CD2 B:HIS156 3.0 8.2 1.0 CE1 B:HIS160 3.0 5.6 1.0 CE1 B:HIS156 3.0 7.3 1.0 CD2 B:HIS160 3.1 6.9 1.0 C3 B:BB21002 3.1 6.9 1.0 N1 B:BB21002 3.1 22.4 1.0 CB B:CYS114 3.4 5.3 1.0 NE2 B:GLN57 3.4 6.0 1.0 O B:HOH1009 3.5 6.8 1.0 CA B:CYS114 3.7 5.5 1.0 CD B:GLN57 4.1 8.8 1.0 N B:GLU115 4.1 4.9 1.0 CG B:HIS156 4.1 6.2 1.0 ND1 B:HIS156 4.2 8.2 1.0 ND1 B:HIS160 4.2 6.2 1.0 CG B:HIS160 4.2 6.0 1.0 OE1 B:GLN57 4.3 9.7 1.0 C B:CYS114 4.4 5.9 1.0 C5 B:BB21002 4.5 17.6 1.0 O B:HOH1006 4.5 8.8 1.0 OE1 B:GLU157 4.7 15.7 1.0 N B:SER116 4.8 7.5 1.0 C6 B:BB21002 4.9 21.2 1.0 OE2 B:GLU157 4.9 13.3 1.0 O B:GLY113 4.9 15.8 1.0

Cobalt binding site 3 out of 4 in the Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1 b:9.0 occ:1.00 NE2 C:HIS156 2.0 6.5 1.0 NE2 C:HIS160 2.0 7.5 1.0 O2 C:BB21003 2.1 21.6 1.0 O4 C:BB21003 2.2 18.2 1.0 SG C:CYS114 2.4 8.2 1.0 CD2 C:HIS156 3.0 9.4 1.0 C3 C:BB21003 3.0 10.2 1.0 N1 C:BB21003 3.0 17.7 1.0 CE1 C:HIS160 3.0 7.9 1.0 CE1 C:HIS156 3.1 6.4 1.0 CD2 C:HIS160 3.1 8.7 1.0 NE2 C:GLN57 3.3 7.4 1.0 CB C:CYS114 3.4 4.9 1.0 O C:HOH1010 3.6 8.2 1.0 CA C:CYS114 3.7 5.0 1.0 CD C:GLN57 4.0 9.1 1.0 CG C:HIS156 4.2 7.2 1.0 ND1 C:HIS156 4.2 8.6 1.0 N C:GLU115 4.2 6.9 1.0 ND1 C:HIS160 4.2 8.8 1.0 OE1 C:GLN57 4.2 10.5 1.0 CG C:HIS160 4.2 7.7 1.0 C5 C:BB21003 4.4 13.8 1.0 C C:CYS114 4.4 5.3 1.0 O C:HOH1011 4.6 8.7 1.0 OE2 C:GLU157 4.6 15.3 1.0 C6 C:BB21003 4.7 17.4 1.0 OE1 C:GLU157 4.8 11.6 1.0 N C:SER116 4.9 7.8 1.0 O C:GLY113 4.9 13.4 1.0 CD C:GLU157 5.0 11.5 1.0

Cobalt binding site 4 out of 4 in the Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target within 5.0Å range: probe atom residue distance (Å) B Occ D:Co2 b:10.2 occ:1.00 NE2 D:HIS160 2.0 6.2 1.0 NE2 D:HIS156 2.1 8.9 1.0 O2 D:BB21004 2.1 18.2 1.0 O4 D:BB21004 2.2 16.8 1.0 SG D:CYS114 2.3 8.9 1.0 C3 D:BB21004 3.0 10.0 1.0 CE1 D:HIS160 3.0 8.0 1.0 CD2 D:HIS156 3.0 7.7 1.0 N1 D:BB21004 3.1 16.2 1.0 CD2 D:HIS160 3.1 7.3 1.0 CE1 D:HIS156 3.1 7.8 1.0 NE2 D:GLN57 3.3 9.5 1.0 CB D:CYS114 3.4 6.1 1.0 O D:HOH1014 3.6 8.0 1.0 CA D:CYS114 3.8 5.5 1.0 CD D:GLN57 4.1 8.9 1.0 N D:GLU115 4.2 7.5 1.0 ND1 D:HIS160 4.2 9.2 1.0 CG D:HIS156 4.2 6.7 1.0 CG D:HIS160 4.2 9.0 1.0 ND1 D:HIS156 4.2 8.5 1.0 OE1 D:GLN57 4.3 10.4 1.0 C5 D:BB21004 4.4 14.5 1.0 C D:CYS114 4.4 6.6 1.0 O D:HOH1008 4.6 10.1 1.0 OE1 D:GLU157 4.7 17.9 1.0 C6 D:BB21004 4.7 18.8 1.0 OE2 D:GLU157 4.8 15.9 1.0 O D:GLY113 4.9 14.5 1.0 N D:SER116 4.9 7.6 1.0

S.Escobar-Alvarez, Y.Goldgur, G.Yang, O.Ouerfelli, Y.Li, D.A.Scheinberg. Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target J.Mol.Biol. V. 387 1211 2009.
ISSN: ISSN 0022-2836
PubMed: 19236878
DOI: 10.1016/J.JMB.2009.02.032