Cobalt in PDB 7xnt: Crystal Structure of Pfhppd-Y13161 Complex

The structure of Crystal Structure of Pfhppd-Y13161 Complex, PDB code: 7xnt was solved by H.-Y.Lin, G.-F.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.90 / 1.82
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.943, 73.041, 87.963, 66.13, 79.56, 69.1
R / Rfree (%)	23.8 / 27.1

The binding sites of Cobalt atom in the Crystal Structure of Pfhppd-Y13161 Complex (pdb code 7xnt). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Pfhppd-Y13161 Complex, PDB code: 7xnt:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Pfhppd-Y13161 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Pfhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Co401 b:28.0 occ:1.00 OE1 G:GLU322 2.1 29.9 1.0 O7 G:94L402 2.1 35.9 1.0 NE2 G:HIS161 2.1 20.9 1.0 O11 G:94L402 2.1 36.7 1.0 NE2 G:HIS240 2.2 36.9 1.0 O G:HOH511 2.3 35.9 1.0 CE1 G:HIS161 3.0 24.3 1.0 CE1 G:HIS240 3.1 35.8 1.0 CD G:GLU322 3.1 27.5 1.0 C9 G:94L402 3.1 40.9 1.0 CD2 G:HIS161 3.2 19.7 1.0 C6 G:94L402 3.2 40.2 1.0 CD2 G:HIS240 3.3 27.5 1.0 OE2 G:GLU322 3.4 26.5 1.0 C5 G:94L402 3.6 38.7 1.0 ND1 G:HIS161 4.2 22.7 1.0 ND1 G:HIS240 4.3 30.5 1.0 CG G:HIS161 4.3 27.3 1.0 C10 G:94L402 4.3 37.5 1.0 CE1 G:PHE311 4.4 31.2 1.0 CG G:HIS240 4.4 30.5 1.0 CG G:GLU322 4.5 26.6 1.0 CB G:ALA242 4.5 26.3 1.0 CD1 G:PHE332 4.5 31.0 1.0 O G:PHE332 4.5 33.8 1.0 C1 G:94L402 4.5 45.9 1.0 CZ G:PHE311 4.6 29.3 1.0 CB G:PHE332 4.6 36.0 1.0 CG2 G:THR163 4.7 32.2 1.0 CB G:GLU322 4.7 25.5 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Pfhppd-Y13161 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Pfhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:30.1 occ:1.00 OE1 A:GLU322 2.1 31.4 1.0 O11 A:94L402 2.2 36.4 1.0 O8 A:94L402 2.2 34.6 1.0 NE2 A:HIS161 2.2 30.6 1.0 NE2 A:HIS240 2.3 26.2 1.0 O A:HOH526 2.4 36.7 1.0 CE1 A:HIS161 3.1 26.6 1.0 CE1 A:HIS240 3.2 31.0 1.0 CD A:GLU322 3.2 35.8 1.0 CD2 A:HIS161 3.2 25.8 1.0 C4 A:94L402 3.2 36.9 1.0 C9 A:94L402 3.2 37.1 1.0 CD2 A:HIS240 3.4 28.3 1.0 OE2 A:GLU322 3.6 34.8 1.0 C5 A:94L402 3.7 36.1 1.0 CG2 A:THR163 4.0 24.7 1.0 ND1 A:HIS161 4.3 26.2 1.0 ND1 A:HIS240 4.3 30.2 1.0 CG A:HIS161 4.3 27.6 1.0 O A:PHE332 4.4 31.4 1.0 C10 A:94L402 4.4 40.1 1.0 CE2 A:PHE311 4.4 35.2 1.0 CG A:HIS240 4.4 29.9 1.0 CD2 A:PHE332 4.5 32.1 1.0 CG A:GLU322 4.5 28.4 1.0 CB A:ALA242 4.5 27.3 1.0 C3 A:94L402 4.5 38.7 1.0 CB A:PHE332 4.6 26.6 1.0 CB A:GLU322 4.7 26.7 1.0 CZ A:PHE311 4.8 34.6 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Pfhppd-Y13161 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Pfhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:58.1 occ:1.00 O11 B:94L402 1.9 53.6 1.0 OE1 B:GLU322 2.2 46.7 1.0 O8 B:94L402 2.2 55.7 1.0 NE2 B:HIS161 2.2 37.4 1.0 O B:HOH527 2.3 43.2 1.0 NE2 B:HIS240 2.3 41.8 1.0 CE1 B:HIS161 2.9 40.3 1.0 C9 B:94L402 3.0 52.4 1.0 CD B:GLU322 3.1 47.3 1.0 CE1 B:HIS240 3.1 41.9 1.0 C4 B:94L402 3.2 53.2 1.0 CD2 B:HIS161 3.4 43.8 1.0 CD2 B:HIS240 3.4 43.0 1.0 OE2 B:GLU322 3.4 45.3 1.0 C5 B:94L402 3.6 57.3 1.0 ND1 B:HIS161 4.2 38.5 1.0 C10 B:94L402 4.2 56.2 1.0 ND1 B:HIS240 4.3 44.5 1.0 CG B:HIS161 4.4 45.4 1.0 CG B:HIS240 4.5 44.1 1.0 CG B:GLU322 4.5 40.7 1.0 CE1 B:PHE311 4.5 45.4 1.0 CB B:ALA242 4.5 46.9 1.0 C3 B:94L402 4.5 53.2 1.0 CD1 B:PHE332 4.5 49.6 1.0 O B:PHE332 4.5 48.1 1.0 CG2 B:THR163 4.6 42.6 1.0 CZ B:PHE311 4.6 47.4 1.0 CB B:PHE332 4.6 49.2 1.0 CB B:GLU322 4.7 41.8 1.0 C16 B:94L402 4.8 53.6 1.0 C6 B:94L402 4.9 58.4 1.0 C12 B:94L402 5.0 53.6 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Pfhppd-Y13161 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Pfhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:64.6 occ:1.00 OE1 C:GLU322 2.0 57.7 1.0 O8 C:94L402 2.1 57.5 1.0 O11 C:94L402 2.1 56.8 1.0 NE2 C:HIS161 2.2 49.4 1.0 O C:HOH512 2.3 49.9 1.0 NE2 C:HIS240 2.4 46.4 1.0 CE1 C:HIS161 2.9 53.3 1.0 CE1 C:HIS240 3.0 48.1 1.0 CD C:GLU322 3.0 57.7 1.0 C4 C:94L402 3.1 55.5 1.0 C9 C:94L402 3.2 57.1 1.0 OE2 C:GLU322 3.4 62.7 1.0 CD2 C:HIS161 3.5 52.4 1.0 CD2 C:HIS240 3.6 48.5 1.0 C5 C:94L402 3.6 57.7 1.0 ND1 C:HIS161 4.1 49.8 1.0 ND1 C:HIS240 4.2 45.6 1.0 CG C:GLU322 4.4 56.7 1.0 CE1 C:PHE311 4.4 58.0 1.0 C10 C:94L402 4.4 60.5 1.0 C3 C:94L402 4.4 58.2 1.0 CG C:HIS161 4.4 51.6 1.0 CB C:ALA242 4.4 48.3 1.0 CG2 C:THR163 4.4 52.9 1.0 CD1 C:PHE332 4.5 54.7 1.0 O C:PHE332 4.5 59.7 1.0 CB C:PHE332 4.5 55.1 1.0 CG C:HIS240 4.5 50.1 1.0 CB C:GLU322 4.6 52.2 1.0 CZ C:PHE311 4.7 59.1 1.0 C6 C:94L402 5.0 61.6 1.0 CG C:PHE332 5.0 53.8 1.0 C16 C:94L402 5.0 60.8 1.0

J.Dong, J.Dong, X.H.Yu, Y.C.Yan, J.X.Nan, B.He, B.Q.Ye, W.C.Yang, H.Y.Lin, G.F.Yang. Structural Insights of 4-Hydrophenylpyruvate Dioxygenase Inhibition By Structurally Diverse Small Molecules Adv Agrochem 2022.
ISSN: ESSN 2773-2371
DOI: 10.1016/J.AAC.2022.10.002