Cobalt in PDB 7x7l: Crystal Structure of Zmhppd-Y13161 Complex

The structure of Crystal Structure of Zmhppd-Y13161 Complex, PDB code: 7x7l was solved by H.-Y.Lin, J.Dong, G.-F.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.952, 83.428, 85.61, 89.78, 97.46, 107.64
R / Rfree (%)	17.3 / 20.8

The binding sites of Cobalt atom in the Crystal Structure of Zmhppd-Y13161 Complex (pdb code 7x7l). 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 Zmhppd-Y13161 Complex, PDB code: 7x7l:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Zmhppd-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 Zmhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:15.1 occ:1.00 O11 A:94L502 2.0 16.9 1.0 OE1 A:GLU387 2.1 13.3 1.0 O8 A:94L502 2.1 16.8 1.0 NE2 A:HIS219 2.2 14.4 1.0 NE2 A:HIS301 2.3 18.9 1.0 O A:HOH654 2.5 19.2 1.0 CD2 A:HIS219 3.1 13.7 1.0 CE1 A:HIS301 3.1 17.4 1.0 CD A:GLU387 3.1 13.8 1.0 C4 A:94L502 3.1 17.7 1.0 CE1 A:HIS219 3.2 14.4 1.0 C9 A:94L502 3.2 20.0 1.0 CD2 A:HIS301 3.4 14.8 1.0 OE2 A:GLU387 3.5 15.3 1.0 C5 A:94L502 3.7 18.2 1.0 ND1 A:HIS219 4.3 12.9 1.0 CG A:HIS219 4.3 14.2 1.0 C10 A:94L502 4.3 19.6 1.0 ND1 A:HIS301 4.3 17.3 1.0 C3 A:94L502 4.4 18.9 1.0 CG A:GLU387 4.4 12.8 1.0 CG A:HIS301 4.4 19.0 1.0 O A:PHE412 4.5 17.7 1.0 CB A:ALA303 4.5 13.9 1.0 CG2 A:VAL221 4.5 16.3 1.0 CE1 A:PHE374 4.5 15.9 1.0 CB A:GLU387 4.6 13.9 1.0 CD1 A:PHE412 4.8 20.2 1.0 CZ A:PHE374 4.8 18.5 1.0 C16 A:94L502 4.9 20.2 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Zmhppd-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 Zmhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co501 b:14.2 occ:1.00 O11 B:94L502 2.0 17.8 1.0 O8 B:94L502 2.0 20.0 1.0 OE1 B:GLU387 2.0 17.0 1.0 NE2 B:HIS301 2.3 14.8 1.0 NE2 B:HIS219 2.3 18.6 1.0 O B:HOH672 2.3 14.6 1.0 CD B:GLU387 3.0 16.3 1.0 C4 B:94L502 3.1 20.4 1.0 C9 B:94L502 3.2 20.7 1.0 CE1 B:HIS301 3.2 19.5 1.0 CD2 B:HIS219 3.2 18.4 1.0 CD2 B:HIS301 3.3 14.4 1.0 CE1 B:HIS219 3.3 13.6 1.0 OE2 B:GLU387 3.4 18.2 1.0 C5 B:94L502 3.7 20.3 1.0 C10 B:94L502 4.3 21.7 1.0 ND1 B:HIS301 4.3 15.0 1.0 CG B:GLU387 4.4 15.7 1.0 C3 B:94L502 4.4 20.6 1.0 CG B:HIS301 4.4 12.6 1.0 ND1 B:HIS219 4.4 15.7 1.0 CG B:HIS219 4.4 16.4 1.0 CE1 B:PHE374 4.4 14.4 1.0 O B:PHE412 4.4 19.8 1.0 CG2 B:VAL221 4.5 16.0 1.0 CB B:ALA303 4.5 12.0 1.0 CB B:GLU387 4.6 14.6 1.0 CZ B:PHE374 4.7 16.0 1.0 CD1 B:PHE412 4.9 19.9 1.0 C16 B:94L502 4.9 18.0 1.0 CB B:PHE412 4.9 19.2 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Zmhppd-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 Zmhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co501 b:18.4 occ:1.00 O11 C:94L502 2.0 19.6 1.0 O8 C:94L502 2.1 17.4 1.0 OE1 C:GLU387 2.1 15.6 1.0 NE2 C:HIS219 2.2 16.0 1.0 NE2 C:HIS301 2.3 17.8 1.0 O C:HOH650 2.4 18.7 1.0 C4 C:94L502 3.1 20.2 1.0 CD C:GLU387 3.1 18.9 1.0 CE1 C:HIS219 3.1 16.2 1.0 CE1 C:HIS301 3.1 16.3 1.0 C9 C:94L502 3.2 23.7 1.0 CD2 C:HIS219 3.3 15.9 1.0 CD2 C:HIS301 3.4 15.5 1.0 OE2 C:GLU387 3.4 17.2 1.0 C5 C:94L502 3.6 20.8 1.0 ND1 C:HIS219 4.3 19.2 1.0 C10 C:94L502 4.3 18.9 1.0 ND1 C:HIS301 4.3 18.7 1.0 CG C:HIS219 4.4 17.9 1.0 C3 C:94L502 4.4 18.3 1.0 O C:PHE412 4.4 20.4 1.0 CG C:GLU387 4.4 14.8 1.0 CG C:HIS301 4.5 18.1 1.0 CE1 C:PHE374 4.5 18.2 1.0 CG2 C:VAL221 4.5 15.7 1.0 CB C:ALA303 4.6 18.3 1.0 CB C:GLU387 4.7 15.8 1.0 CZ C:PHE374 4.7 18.1 1.0 CD1 C:PHE412 4.8 19.4 1.0 CB C:PHE412 4.8 23.0 1.0 C6 C:94L502 4.9 25.5 1.0 C16 C:94L502 5.0 21.3 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Zmhppd-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 Zmhppd-Y13161 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Co501 b:19.4 occ:1.00 O11 D:94L502 2.0 19.7 1.0 O8 D:94L502 2.0 21.7 1.0 OE1 D:GLU387 2.0 20.8 1.0 NE2 D:HIS219 2.1 19.4 1.0 NE2 D:HIS301 2.3 18.6 1.0 O D:HOH632 2.4 17.5 1.0 CE1 D:HIS219 3.0 18.4 1.0 CD D:GLU387 3.1 17.7 1.0 C9 D:94L502 3.1 20.2 1.0 CD2 D:HIS219 3.2 17.7 1.0 CE1 D:HIS301 3.2 20.9 1.0 C4 D:94L502 3.2 22.1 1.0 CD2 D:HIS301 3.3 18.4 1.0 OE2 D:GLU387 3.5 19.3 1.0 C5 D:94L502 3.7 21.1 1.0 ND1 D:HIS219 4.2 17.1 1.0 C10 D:94L502 4.3 23.0 1.0 CG D:HIS219 4.3 16.6 1.0 ND1 D:HIS301 4.3 18.9 1.0 C3 D:94L502 4.4 19.0 1.0 CE1 D:PHE374 4.4 20.6 1.0 CG D:GLU387 4.4 19.5 1.0 O D:PHE412 4.4 21.4 1.0 CG D:HIS301 4.4 17.2 1.0 CG2 D:VAL221 4.5 17.0 1.0 CB D:ALA303 4.5 17.7 1.0 CB D:GLU387 4.7 15.4 1.0 CZ D:PHE374 4.7 22.7 1.0 CD1 D:PHE412 4.9 21.5 1.0 C16 D:94L502 4.9 23.6 1.0 CB D:PHE412 4.9 23.5 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