Cobalt in PDB 3g5p: 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: 3g5p 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)	37.53 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.332, 77.825, 111.041, 90.00, 107.93, 90.00
R / Rfree (%)	16.1 / 18.7

The binding sites of Cobalt atom in the Structure and Activity of Human Mitochondrial Peptide Deformylase, A Novel Cancer Target (pdb code 3g5p). 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: 3g5p:
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:Co186 b:9.7 occ:1.00 O2 A:PO42 1.9 14.2 1.0 NE2 A:HIS160 2.0 10.5 1.0 NE2 A:HIS156 2.1 8.3 1.0 CE1 A:HIS160 3.0 10.4 1.0 CD2 A:HIS156 3.0 10.3 1.0 CD2 A:HIS160 3.1 13.6 1.0 CE1 A:HIS156 3.1 8.6 1.0 P A:PO42 3.2 13.9 1.0 CB A:CYS114 3.3 10.8 1.0 NE2 A:GLN57 3.5 9.1 1.0 O A:HOH193 3.5 10.9 1.0 CA A:CYS114 3.6 8.4 1.0 O1 A:PO42 3.7 14.4 1.0 O3 A:PO42 3.8 16.3 1.0 N A:GLU115 4.1 8.2 1.0 CD A:GLN57 4.1 11.8 1.0 ND1 A:HIS160 4.1 9.5 1.0 CG A:HIS156 4.2 7.8 1.0 CG A:HIS160 4.2 10.3 1.0 ND1 A:HIS156 4.2 11.4 1.0 C A:CYS114 4.2 9.7 1.0 OE1 A:GLN57 4.3 10.7 1.0 O4 A:PO42 4.4 16.2 1.0 O A:HOH190 4.5 11.3 1.0 SG A:CYS114 4.6 43.7 1.0 OE1 A:GLU157 4.7 13.0 1.0 O A:GLY113 4.7 10.2 1.0 O A:HOH342 4.7 20.1 1.0 N A:SER116 4.8 9.8 1.0 N A:CYS114 4.9 9.2 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:Co186 b:10.1 occ:1.00 O2 B:PO4188 1.9 12.4 1.0 NE2 B:HIS156 2.0 7.7 1.0 NE2 B:HIS160 2.0 8.0 1.0 SG B:CYS114 2.3 9.1 1.0 CE1 B:HIS160 3.0 10.1 1.0 CD2 B:HIS156 3.0 11.7 1.0 CE1 B:HIS156 3.0 11.0 1.0 CD2 B:HIS160 3.1 8.9 1.0 P B:PO4188 3.2 13.4 1.0 CB B:CYS114 3.3 8.3 1.0 O B:HOH194 3.5 9.2 1.0 NE2 B:GLN57 3.6 7.9 1.0 CA B:CYS114 3.6 8.2 1.0 O1 B:PO4188 3.7 12.6 1.0 O3 B:PO4188 3.7 15.0 1.0 N B:GLU115 4.1 6.3 1.0 ND1 B:HIS156 4.1 11.3 1.0 CG B:HIS156 4.1 8.2 1.0 ND1 B:HIS160 4.1 9.8 1.0 CD B:GLN57 4.2 10.8 1.0 CG B:HIS160 4.2 8.7 1.0 C B:CYS114 4.3 8.0 1.0 O4 B:PO4188 4.3 12.5 1.0 OE1 B:GLN57 4.4 10.9 1.0 O B:HOH191 4.5 9.4 1.0 OE1 B:GLU157 4.6 13.4 1.0 O B:HOH317 4.7 21.0 1.0 O B:GLY113 4.7 10.1 1.0 N B:SER116 4.8 8.2 1.0 N B:CYS114 4.9 9.3 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:10.5 occ:1.00 O2 C:PO4187 1.7 14.2 1.0 NE2 C:HIS160 2.1 10.5 1.0 NE2 C:HIS156 2.1 7.4 1.0 CE1 C:HIS160 3.0 12.9 1.0 CD2 C:HIS156 3.1 12.1 1.0 CE1 C:HIS156 3.1 9.9 1.0 CD2 C:HIS160 3.1 11.2 1.0 P C:PO4187 3.1 15.7 1.0 SG C:CYS114 3.3 43.4 1.0 O C:HOH194 3.5 12.5 1.0 NE2 C:GLN57 3.5 9.1 1.0 CB C:CYS114 3.6 9.8 1.0 CA C:CYS114 3.6 8.8 1.0 O1 C:PO4187 3.7 16.9 1.0 O3 C:PO4187 3.7 17.9 1.0 CD C:GLN57 4.1 12.2 1.0 N C:GLU115 4.2 9.8 1.0 ND1 C:HIS160 4.2 9.1 1.0 CG C:HIS156 4.2 7.6 1.0 ND1 C:HIS156 4.2 10.2 1.0 CG C:HIS160 4.2 8.0 1.0 C C:CYS114 4.3 10.2 1.0 OE1 C:GLN57 4.3 10.7 1.0 O4 C:PO4187 4.3 14.2 1.0 O C:HOH195 4.5 10.7 1.0 O C:HOH328 4.6 20.0 1.0 OE2 C:GLU157 4.7 15.0 1.0 O C:GLY113 4.7 10.8 1.0 N C:SER116 4.8 9.9 1.0 N C:CYS114 5.0 10.5 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:11.7 occ:1.00 O2 D:PO4187 1.9 15.5 1.0 NE2 D:HIS160 2.0 8.4 1.0 NE2 D:HIS156 2.0 8.3 1.0 SG D:CYS114 2.3 10.6 1.0 CE1 D:HIS160 2.9 8.7 1.0 CD2 D:HIS156 3.0 12.2 1.0 CE1 D:HIS156 3.1 11.3 1.0 CD2 D:HIS160 3.1 10.1 1.0 P D:PO4187 3.1 16.0 1.0 CB D:CYS114 3.3 10.0 1.0 NE2 D:GLN57 3.5 8.9 1.0 O D:HOH197 3.5 11.4 1.0 CA D:CYS114 3.7 9.1 1.0 O1 D:PO4187 3.7 16.2 1.0 O3 D:PO4187 3.8 18.7 1.0 ND1 D:HIS160 4.1 10.6 1.0 CD D:GLN57 4.1 11.8 1.0 N D:GLU115 4.1 9.3 1.0 CG D:HIS156 4.2 10.3 1.0 CG D:HIS160 4.2 8.2 1.0 ND1 D:HIS156 4.2 11.8 1.0 OE1 D:GLN57 4.3 11.8 1.0 O4 D:PO4187 4.3 15.0 1.0 C D:CYS114 4.3 9.0 1.0 O D:HOH191 4.4 12.2 1.0 O D:HOH321 4.6 22.4 1.0 O D:GLY113 4.7 11.6 1.0 OE1 D:GLU157 4.7 16.0 1.0 N D:SER116 4.8 8.6 1.0 N D:CYS114 5.0 10.0 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