Cobalt in PDB 7x8e: Crystal Structure of Pfhppd-Y13287 Complex

The structure of Crystal Structure of Pfhppd-Y13287 Complex, PDB code: 7x8e was solved by J.Dong, 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)	38.15 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.699, 161.203, 121.984, 90, 90.02, 90
R / Rfree (%)	19.6 / 27.7

The binding sites of Cobalt atom in the Crystal Structure of Pfhppd-Y13287 Complex (pdb code 7x8e). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of Pfhppd-Y13287 Complex, PDB code: 7x8e:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Crystal Structure of Pfhppd-Y13287 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-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:36.8 occ:1.00 O11 A:92X402 2.0 44.5 1.0 OE1 A:GLU322 2.2 38.6 1.0 O7 A:92X402 2.3 36.0 1.0 NE2 A:HIS240 2.3 36.8 1.0 NE2 A:HIS161 2.3 38.3 1.0 O A:HOH509 2.4 30.0 1.0 CE1 A:HIS240 3.0 33.5 1.0 CE1 A:HIS161 3.1 42.1 1.0 C8 A:92X402 3.1 45.3 1.0 CD A:GLU322 3.2 39.5 1.0 CD2 A:HIS161 3.4 38.7 1.0 C6 A:92X402 3.4 43.9 1.0 CD2 A:HIS240 3.4 35.3 1.0 OE2 A:GLU322 3.5 46.7 1.0 C5 A:92X402 3.8 51.6 1.0 CG2 A:THR163 4.1 36.5 1.0 ND1 A:HIS240 4.2 37.7 1.0 ND1 A:HIS161 4.3 42.6 1.0 C10 A:92X402 4.3 52.4 1.0 CE1 A:PHE311 4.4 39.7 1.0 CG A:HIS240 4.4 34.3 1.0 O A:PHE332 4.4 53.9 1.0 CG A:HIS161 4.5 40.6 1.0 CG A:GLU322 4.5 35.5 1.0 CZ A:PHE311 4.5 43.2 1.0 CD1 A:PHE332 4.5 40.0 1.0 CB A:ALA242 4.6 32.8 1.0 CB A:PHE332 4.6 48.8 1.0 CB A:GLU322 4.7 39.3 1.0 C1 A:92X402 4.7 38.3 1.0 C17 A:92X402 4.8 56.9 1.0 C12 A:92X402 5.0 56.0 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of Pfhppd-Y13287 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-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:42.0 occ:1.00 O11 B:92X402 1.8 56.6 1.0 OE1 B:GLU322 2.0 41.5 1.0 NE2 B:HIS161 2.3 38.3 1.0 O7 B:92X402 2.3 41.1 1.0 O B:HOH502 2.4 30.0 1.0 NE2 B:HIS240 2.4 43.2 1.0 CE1 B:HIS161 2.8 40.8 1.0 CD B:GLU322 2.9 39.9 1.0 CD2 B:HIS240 3.0 38.9 1.0 C8 B:92X402 3.0 47.8 1.0 OE2 B:GLU322 3.2 42.6 1.0 C6 B:92X402 3.5 43.6 1.0 CD2 B:HIS161 3.5 38.3 1.0 CE1 B:HIS240 3.5 43.5 1.0 C5 B:92X402 3.7 49.8 1.0 C10 B:92X402 4.1 46.0 1.0 ND1 B:HIS161 4.1 46.0 1.0 CG B:HIS240 4.1 38.6 1.0 CG B:GLU322 4.3 38.9 1.0 CG2 B:THR163 4.3 37.7 1.0 ND1 B:HIS240 4.4 40.8 1.0 CG B:HIS161 4.4 38.7 1.0 CE1 B:PHE311 4.5 42.1 1.0 CB B:ALA242 4.5 34.9 1.0 CZ B:PHE311 4.5 45.8 1.0 CD1 B:PHE332 4.6 44.1 1.0 C12 B:92X402 4.6 57.4 1.0 O B:PHE332 4.6 50.6 1.0 CB B:GLU322 4.6 40.5 1.0 CB B:PHE332 4.7 51.9 1.0 NE2 B:GLN309 4.8 43.0 1.0 C1 B:92X402 4.8 42.6 1.0 C16 B:92X402 5.0 54.0 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of Pfhppd-Y13287 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-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:37.6 occ:1.00 OE1 C:GLU322 2.1 37.0 1.0 O11 C:92X402 2.1 48.7 1.0 NE2 C:HIS240 2.2 35.0 1.0 NE2 C:HIS161 2.3 40.5 1.0 O7 C:92X402 2.3 35.7 1.0 O C:HOH503 2.6 30.0 1.0 CD C:GLU322 3.0 37.5 1.0 CE1 C:HIS161 3.1 41.0 1.0 CE1 C:HIS240 3.1 35.5 1.0 OE2 C:GLU322 3.2 40.3 1.0 C8 C:92X402 3.2 47.6 1.0 CD2 C:HIS240 3.3 36.6 1.0 CD2 C:HIS161 3.3 37.3 1.0 C6 C:92X402 3.5 46.7 1.0 C5 C:92X402 3.8 50.5 1.0 CG2 C:THR163 4.1 34.4 1.0 ND1 C:HIS161 4.2 39.9 1.0 ND1 C:HIS240 4.2 39.0 1.0 CG C:GLU322 4.3 33.5 1.0 CG C:HIS240 4.4 35.5 1.0 CG C:HIS161 4.4 41.1 1.0 CE1 C:PHE311 4.4 42.0 1.0 C10 C:92X402 4.4 54.4 1.0 CB C:ALA242 4.5 37.2 1.0 CD1 C:PHE332 4.5 40.6 1.0 O C:PHE332 4.6 47.1 1.0 CB C:GLU322 4.6 36.8 1.0 CZ C:PHE311 4.7 44.8 1.0 C17 C:92X402 4.7 58.3 1.0 CB C:PHE332 4.7 48.0 1.0 C1 C:92X402 4.8 42.8 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of Pfhppd-Y13287 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-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Co401 b:39.0 occ:1.00 OE1 D:GLU322 2.0 36.0 1.0 NE2 D:HIS240 2.2 37.5 1.0 NE2 D:HIS161 2.2 40.2 1.0 O11 D:92X402 2.3 43.3 1.0 O7 D:92X402 2.4 38.1 1.0 O D:HOH505 2.4 30.0 1.0 CD D:GLU322 3.0 36.7 1.0 CE1 D:HIS240 3.0 36.4 1.0 CE1 D:HIS161 3.1 41.5 1.0 CD2 D:HIS240 3.2 38.2 1.0 OE2 D:GLU322 3.2 41.0 1.0 CD2 D:HIS161 3.3 39.3 1.0 C8 D:92X402 3.4 46.6 1.0 C6 D:92X402 3.6 45.8 1.0 C5 D:92X402 4.0 50.7 1.0 ND1 D:HIS240 4.1 39.7 1.0 ND1 D:HIS161 4.2 45.5 1.0 OG1 D:THR163 4.2 37.9 1.0 CG D:HIS240 4.3 36.8 1.0 CG D:GLU322 4.3 36.4 1.0 CG D:HIS161 4.4 40.4 1.0 CE1 D:PHE311 4.5 37.4 1.0 CD1 D:PHE332 4.5 42.2 1.0 CB D:ALA242 4.5 36.1 1.0 C10 D:92X402 4.6 52.5 1.0 CB D:GLU322 4.6 38.9 1.0 O D:PHE332 4.6 49.0 1.0 CB D:PHE332 4.6 47.8 1.0 CZ D:PHE311 4.6 41.6 1.0 C1 D:92X402 4.9 42.1 1.0 C17 D:92X402 4.9 54.7 1.0 NE2 D:GLN309 5.0 44.8 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of Pfhppd-Y13287 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Pfhppd-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Co401 b:77.0 occ:1.00 O7 E:92X402 1.8 54.8 1.0 OE2 E:GLU322 1.8 60.0 1.0 O11 E:92X402 1.8 68.4 1.0 NE2 E:HIS161 2.4 58.8 1.0 NE2 E:HIS240 2.5 52.1 1.0 O E:HOH501 2.6 30.0 1.0 CD E:GLU322 2.8 61.8 1.0 C8 E:92X402 2.9 64.7 1.0 C6 E:92X402 3.0 55.7 1.0 OE1 E:GLU322 3.1 66.2 1.0 CE1 E:HIS161 3.2 55.9 1.0 CE1 E:HIS240 3.3 51.0 1.0 CD2 E:HIS161 3.4 53.1 1.0 C5 E:92X402 3.5 58.8 1.0 CD2 E:HIS240 3.5 48.5 1.0 C10 E:92X402 4.1 62.8 1.0 CG E:GLU322 4.1 49.2 1.0 O E:PHE332 4.3 61.5 1.0 C1 E:92X402 4.3 54.7 1.0 ND1 E:HIS161 4.4 57.4 1.0 CD1 E:PHE332 4.4 58.6 1.0 CB E:PHE332 4.4 58.6 1.0 CE1 E:PHE311 4.5 55.0 1.0 CB E:GLU322 4.5 47.9 1.0 CB E:ALA242 4.5 50.0 1.0 ND1 E:HIS240 4.5 44.6 1.0 CG2 E:THR163 4.5 46.2 1.0 CG E:HIS161 4.5 57.6 1.0 C17 E:92X402 4.6 69.6 1.0 CG E:HIS240 4.6 46.5 1.0 C16 E:92X402 4.9 67.3 1.0 C12 E:92X402 4.9 62.5 1.0 CG E:PHE332 4.9 56.3 1.0 CZ E:PHE311 4.9 60.3 1.0 C4 E:92X402 5.0 65.9 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of Pfhppd-Y13287 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Pfhppd-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Co401 b:47.6 occ:1.00 OE2 F:GLU322 2.0 48.8 1.0 O11 F:92X402 2.1 54.7 1.0 O7 F:92X402 2.2 48.1 1.0 NE2 F:HIS161 2.4 53.2 1.0 O F:HOH507 2.4 30.0 1.0 NE2 F:HIS240 2.5 46.2 1.0 CD F:GLU322 3.0 51.9 1.0 CE1 F:HIS161 3.2 56.9 1.0 C8 F:92X402 3.2 51.5 1.0 OE1 F:GLU322 3.2 51.1 1.0 CE1 F:HIS240 3.3 45.4 1.0 CD2 F:HIS161 3.4 51.4 1.0 C6 F:92X402 3.4 49.4 1.0 CD2 F:HIS240 3.7 45.4 1.0 C5 F:92X402 3.9 52.4 1.0 C10 F:92X402 4.3 54.0 1.0 CG F:GLU322 4.3 47.4 1.0 O F:PHE332 4.4 56.5 1.0 ND1 F:HIS161 4.4 56.0 1.0 CE1 F:PHE311 4.4 45.4 1.0 CD1 F:PHE332 4.4 56.0 1.0 ND1 F:HIS240 4.5 44.7 1.0 CG F:HIS161 4.5 54.5 1.0 CG2 F:THR163 4.5 40.9 1.0 CZ F:PHE311 4.5 51.6 1.0 CB F:PHE332 4.5 54.2 1.0 CB F:GLU322 4.6 51.9 1.0 C1 F:92X402 4.7 48.6 1.0 CG F:HIS240 4.7 46.1 1.0 CB F:ALA242 4.7 48.9 1.0 C17 F:92X402 4.8 64.2 1.0 NE2 F:GLN309 4.9 51.4 1.0 CG F:PHE332 5.0 57.2 1.0 C16 F:92X402 5.0 59.4 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of Pfhppd-Y13287 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Pfhppd-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Co401 b:45.5 occ:1.00 O7 G:92X402 1.9 49.5 1.0 OE1 G:GLU322 2.0 48.8 1.0 O11 G:92X402 2.2 56.8 1.0 NE2 G:HIS161 2.4 52.4 1.0 NE2 G:HIS240 2.4 45.3 1.0 O G:HOH503 2.5 30.0 1.0 CD G:GLU322 3.0 53.6 1.0 CE1 G:HIS240 3.1 46.6 1.0 CE1 G:HIS161 3.2 55.1 1.0 C6 G:92X402 3.2 49.0 1.0 OE2 G:GLU322 3.3 56.5 1.0 C8 G:92X402 3.3 53.2 1.0 CD2 G:HIS161 3.4 49.6 1.0 CD2 G:HIS240 3.5 41.5 1.0 C5 G:92X402 3.8 50.6 1.0 CG2 G:THR163 4.3 44.7 1.0 CD1 G:PHE332 4.3 53.1 1.0 CG G:GLU322 4.3 46.8 1.0 ND1 G:HIS240 4.4 43.1 1.0 ND1 G:HIS161 4.4 52.3 1.0 C1 G:92X402 4.4 48.2 1.0 CE1 G:PHE311 4.4 48.2 1.0 O G:PHE332 4.5 61.1 1.0 C10 G:92X402 4.5 58.1 1.0 CG G:HIS161 4.5 51.8 1.0 CG G:HIS240 4.6 42.4 1.0 CB G:GLU322 4.6 49.1 1.0 CB G:PHE332 4.6 54.8 1.0 CB G:ALA242 4.7 45.9 1.0 CZ G:PHE311 4.7 56.8 1.0 CG G:PHE332 4.9 55.1 1.0 C17 G:92X402 4.9 65.3 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of Pfhppd-Y13287 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Pfhppd-Y13287 Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Co401 b:51.4 occ:1.00 OE1 H:GLU322 1.9 46.7 1.0 O7 H:92X402 2.0 46.4 1.0 O11 H:92X402 2.1 55.8 1.0 NE2 H:HIS161 2.3 52.5 1.0 NE2 H:HIS240 2.4 44.4 1.0 O H:HOH507 2.6 30.0 1.0 CD H:GLU322 2.9 50.8 1.0 OE2 H:GLU322 3.1 50.1 1.0 CE1 H:HIS161 3.2 54.2 1.0 C8 H:92X402 3.2 51.2 1.0 CE1 H:HIS240 3.3 48.1 1.0 C6 H:92X402 3.3 50.0 1.0 CD2 H:HIS161 3.4 54.8 1.0 CD2 H:HIS240 3.5 43.4 1.0 C5 H:92X402 3.8 52.8 1.0 CG H:GLU322 4.3 44.5 1.0 ND1 H:HIS161 4.3 57.1 1.0 C10 H:92X402 4.4 52.9 1.0 CB H:PHE332 4.4 52.2 1.0 O H:PHE332 4.4 58.1 1.0 CE1 H:PHE311 4.5 48.0 1.0 ND1 H:HIS240 4.5 45.8 1.0 CG H:HIS161 4.5 57.6 1.0 C1 H:92X402 4.5 50.0 1.0 CG2 H:THR163 4.5 41.7 1.0 CG H:HIS240 4.6 44.2 1.0 CB H:GLU322 4.6 46.7 1.0 CD1 H:PHE332 4.6 59.3 1.0 CZ H:PHE311 4.6 54.7 1.0 CB H:ALA242 4.6 46.5 1.0 C17 H:92X402 4.9 64.3 1.0 CG H:PHE332 5.0 56.5 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