Cobalt in PDB 5v7y: Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu

The structure of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu, PDB code: 5v7y was solved by N.J.Schnicker, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.40 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.238, 106.826, 81.056, 90.00, 103.65, 90.00
R / Rfree (%)	16.1 / 20.9

The structure of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu also contains other interesting chemical elements:

Fluorine

(F)

9 atoms

The binding sites of Cobalt atom in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu (pdb code 5v7y). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu, PDB code: 5v7y:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:15.0 occ:1.00 N3 A:IMD302 2.0 16.2 1.0 NE2 A:HIS193 2.0 14.5 1.0 OD1 A:ASP129 2.0 13.7 1.0 NE2 A:HIS127 2.1 16.1 1.0 C4 A:IMD302 2.7 20.0 1.0 CG A:ASP129 2.9 16.0 1.0 CE1 A:HIS193 2.9 13.8 1.0 CD2 A:HIS127 2.9 17.0 1.0 OD2 A:ASP129 3.0 12.6 1.0 CD2 A:HIS193 3.1 15.9 1.0 CE1 A:HIS127 3.1 18.0 1.0 C2 A:IMD302 3.2 18.9 1.0 C5 A:IMD302 4.0 18.7 1.0 ND1 A:HIS193 4.1 12.5 1.0 CG A:HIS127 4.1 20.4 1.0 ND1 A:HIS127 4.1 14.8 1.0 CG A:HIS193 4.2 15.1 1.0 N1 A:IMD302 4.2 12.6 1.0 O A:HOH534 4.3 30.3 1.0 CB A:ASP129 4.3 13.2 1.0 F3 A:TFA303 4.5 26.9 1.0 NE1 A:TRP209 4.6 14.0 1.0 CA A:ASP129 4.7 16.6 1.0 N A:ASP129 4.8 13.7 1.0 CZ A:PHE178 4.8 8.8 1.0 F2 A:TFA303 4.8 37.9 1.0 O A:HIS193 4.9 16.4 1.0 O A:HIS127 5.0 17.1 1.0

Cobalt binding site 2 out of 4 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:13.6 occ:1.00 O1 B:AKG302 2.0 16.2 1.0 OD1 B:ASP129 2.0 8.8 1.0 NE2 B:HIS193 2.1 11.8 1.0 NE2 B:HIS127 2.1 17.9 1.0 O5 B:AKG302 2.4 18.8 1.0 CG B:ASP129 2.8 15.9 1.0 C1 B:AKG302 2.8 14.7 1.0 CE1 B:HIS193 2.9 11.7 1.0 CE1 B:HIS127 3.0 16.0 1.0 OD2 B:ASP129 3.0 11.3 1.0 C2 B:AKG302 3.0 16.3 1.0 CD2 B:HIS127 3.1 10.9 1.0 CD2 B:HIS193 3.1 7.3 1.0 O B:HOH491 3.6 18.4 1.0 ND1 B:HIS193 4.0 11.2 1.0 O2 B:AKG302 4.0 12.3 1.0 ND1 B:HIS127 4.1 14.0 1.0 CG B:HIS193 4.2 8.9 1.0 CG B:HIS127 4.2 15.2 1.0 CB B:ASP129 4.3 11.3 1.0 CE2 B:TYR124 4.4 19.1 1.0 NE1 B:TRP209 4.4 10.3 1.0 C3 B:AKG302 4.5 17.1 1.0 OH B:TYR124 4.7 20.0 1.0 CA B:ASP129 4.7 11.1 1.0 CZ B:TYR124 4.7 22.1 1.0 CZ B:PHE178 4.8 10.4 1.0 N B:ASP129 4.8 14.6 1.0

Cobalt binding site 3 out of 4 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:12.1 occ:1.00 N1 D:IMD302 1.9 17.8 1.0 OD1 D:ASP129 2.0 12.3 1.0 NE2 D:HIS193 2.0 13.6 1.0 NE2 D:HIS127 2.1 13.3 1.0 OD2 D:ASP129 2.5 12.5 1.0 CG D:ASP129 2.6 14.1 1.0 C5 D:IMD302 2.9 23.4 1.0 C2 D:IMD302 3.0 12.8 1.0 CD2 D:HIS193 3.0 10.8 1.0 CE1 D:HIS127 3.0 13.8 1.0 CE1 D:HIS193 3.0 12.0 1.0 CD2 D:HIS127 3.0 12.9 1.0 CB D:ASP129 4.1 14.4 1.0 ND1 D:HIS127 4.1 15.5 1.0 N3 D:IMD302 4.1 12.6 1.0 C4 D:IMD302 4.1 17.3 1.0 ND1 D:HIS193 4.1 11.7 1.0 CG D:HIS193 4.1 12.0 1.0 CG D:HIS127 4.1 17.1 1.0 NE1 D:TRP209 4.4 12.5 1.0 O D:HOH527 4.5 28.7 1.0 F1 D:TFA305 4.6 22.3 0.7 CA D:ASP129 4.6 13.0 1.0 N D:ASP129 4.7 11.5 1.0 CZ D:PHE178 4.8 8.9 1.0 F3 D:TFA305 4.8 26.2 0.7 O D:HIS127 5.0 12.2 1.0 CZ2 D:TRP209 5.0 14.1 1.0

Cobalt binding site 4 out of 4 in the Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:16.2 occ:1.00 N1 C:IMD302 1.9 10.7 1.0 NE2 C:HIS193 2.0 19.0 1.0 OD1 C:ASP129 2.1 20.0 1.0 NE2 C:HIS127 2.1 20.1 1.0 OD2 C:ASP129 2.4 16.9 1.0 C5 C:IMD302 2.5 21.0 1.0 CG C:ASP129 2.6 16.0 1.0 CE1 C:HIS193 2.9 17.6 1.0 CE1 C:HIS127 3.0 18.2 1.0 CD2 C:HIS127 3.0 16.6 1.0 CD2 C:HIS193 3.0 15.1 1.0 C2 C:IMD302 3.2 19.7 1.0 C4 C:IMD302 3.8 18.2 1.0 ND1 C:HIS193 4.0 14.7 1.0 CB C:ASP129 4.1 16.2 1.0 ND1 C:HIS127 4.1 16.2 1.0 N3 C:IMD302 4.1 14.1 1.0 CG C:HIS193 4.1 20.1 1.0 CG C:HIS127 4.1 18.6 1.0 F2 C:TFA303 4.6 32.2 1.0 F3 C:TFA303 4.6 29.4 1.0 CA C:ASP129 4.7 17.1 1.0 CZ C:PHE178 4.7 14.9 1.0 NE1 C:TRP209 4.7 16.8 1.0 N C:ASP129 4.8 14.6 1.0 F1 C:TFA303 4.9 28.6 1.0 C2 C:TFA303 5.0 23.9 1.0

N.J.Schnicker, M.Razzaghi, S.Guha Thakurta, S.Chakravarthy, M.Dey. Bacillus Anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry V. 56 5771 2017.
ISSN: ISSN 1520-4995
PubMed: 28981257
DOI: 10.1021/ACS.BIOCHEM.7B00601