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Cobalt in PDB 8im2: Crystal Structure of Human Hppd Complexed with Ntbc

Enzymatic activity of Crystal Structure of Human Hppd Complexed with Ntbc

All present enzymatic activity of Crystal Structure of Human Hppd Complexed with Ntbc:
1.13.11.27;

Protein crystallography data

The structure of Crystal Structure of Human Hppd Complexed with Ntbc, PDB code: 8im2 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) 29.67 / 2.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.55, 147.442, 133.93, 90, 97.12, 90
R / Rfree (%) 21.3 / 25.4

Other elements in 8im2:

The structure of Crystal Structure of Human Hppd Complexed with Ntbc also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Human Hppd Complexed with Ntbc (pdb code 8im2). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Human Hppd Complexed with Ntbc, PDB code: 8im2:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 8im2

Go back to Cobalt Binding Sites List in 8im2
Cobalt binding site 1 out of 6 in the Crystal Structure of Human Hppd Complexed with Ntbc


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 Human Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:39.1
occ:1.00
NE2 A:HIS183 2.0 30.1 1.0
O5 A:NTD402 2.1 45.7 1.0
OE1 A:GLU349 2.1 45.9 1.0
O7 A:NTD402 2.2 41.5 1.0
O A:HOH504 2.4 40.9 1.0
NE2 A:HIS266 2.6 36.7 1.0
CE1 A:HIS183 2.8 36.3 1.0
CD A:GLU349 3.1 43.1 1.0
CD2 A:HIS183 3.1 37.1 1.0
C1 A:NTD402 3.2 40.7 1.0
C7 A:NTD402 3.4 44.1 1.0
OE2 A:GLU349 3.4 43.3 1.0
CE1 A:HIS266 3.4 40.6 1.0
CD2 A:HIS266 3.6 40.2 1.0
C6 A:NTD402 3.9 44.0 1.0
ND1 A:HIS183 4.0 42.2 1.0
CG A:HIS183 4.1 37.9 1.0
CD2 A:PHE359 4.4 41.3 1.0
CE1 A:PHE336 4.4 43.6 1.0
CG A:GLU349 4.4 41.4 1.0
C4 A:NTD402 4.4 43.3 1.0
CB A:ALA268 4.5 38.6 1.0
ND1 A:HIS266 4.5 42.8 1.0
CG2 A:VAL185 4.5 39.9 1.0
C8 A:NTD402 4.6 44.0 1.0
O A:PHE359 4.6 43.2 1.0
CG A:HIS266 4.7 39.3 1.0
CB A:PHE359 4.7 37.6 1.0
CB A:GLU349 4.8 38.1 1.0
CZ A:PHE336 4.8 45.2 1.0

Cobalt binding site 2 out of 6 in 8im2

Go back to Cobalt Binding Sites List in 8im2
Cobalt binding site 2 out of 6 in the Crystal Structure of Human Hppd Complexed with Ntbc


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 Human Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co501

b:50.4
occ:1.00
O7 B:NTD502 2.0 51.4 1.0
O5 B:NTD502 2.0 59.3 1.0
NE2 B:HIS183 2.2 42.7 1.0
OE2 B:GLU349 2.2 64.0 1.0
CE1 B:HIS266 2.8 46.6 1.0
CE1 B:HIS183 3.0 47.2 1.0
C1 B:NTD502 3.1 56.3 1.0
C7 B:NTD502 3.1 53.5 1.0
CD2 B:HIS183 3.2 43.9 1.0
CD B:GLU349 3.2 55.5 1.0
NE2 B:HIS266 3.5 52.3 1.0
OE1 B:GLU349 3.6 57.3 1.0
C6 B:NTD502 3.6 59.0 1.0
ND1 B:HIS266 3.8 54.0 1.0
ND1 B:HIS183 4.2 46.5 1.0
CG B:HIS183 4.3 43.8 1.0
C8 B:NTD502 4.3 58.2 1.0
C4 B:NTD502 4.4 59.0 1.0
CG2 B:VAL185 4.4 51.1 1.0
CD2 B:PHE359 4.4 53.9 1.0
CE1 B:PHE336 4.5 52.9 1.0
O B:PHE359 4.5 61.7 1.0
CG B:GLU349 4.5 54.5 1.0
CB B:PHE359 4.6 58.5 1.0
CZ B:PHE336 4.7 58.2 1.0
CD2 B:HIS266 4.7 49.8 1.0
CB B:ALA268 4.8 48.2 1.0
C13 B:NTD502 4.8 59.5 1.0
CB B:GLU349 4.8 51.8 1.0
CG B:HIS266 4.9 52.0 1.0

Cobalt binding site 3 out of 6 in 8im2

Go back to Cobalt Binding Sites List in 8im2
Cobalt binding site 3 out of 6 in the Crystal Structure of Human Hppd Complexed with Ntbc


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 Human Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co401

b:45.4
occ:1.00
O5 C:NTD402 1.9 47.1 1.0
O7 C:NTD402 1.9 46.9 1.0
OE1 C:GLU349 2.1 54.4 1.0
NE2 C:HIS183 2.1 39.3 1.0
CE1 C:HIS266 2.6 43.7 1.0
CE1 C:HIS183 2.9 43.8 1.0
NE2 C:HIS266 2.9 38.6 1.0
C1 C:NTD402 3.0 45.2 1.0
C7 C:NTD402 3.1 45.6 1.0
CD C:GLU349 3.1 54.0 1.0
CD2 C:HIS183 3.3 40.3 1.0
OE2 C:GLU349 3.5 55.4 1.0
C6 C:NTD402 3.5 45.5 1.0
ND1 C:HIS266 3.8 43.5 1.0
ND1 C:HIS183 4.1 44.7 1.0
C4 C:NTD402 4.2 48.6 1.0
CD2 C:HIS266 4.2 42.2 1.0
C8 C:NTD402 4.3 50.7 1.0
CG C:HIS183 4.3 41.6 1.0
CE1 C:PHE336 4.4 48.4 1.0
CG C:GLU349 4.5 48.6 1.0
O C:PHE359 4.6 57.3 1.0
CB C:ALA268 4.6 45.5 1.0
CG C:HIS266 4.7 46.4 1.0
ON1 C:NTD402 4.7 56.2 1.0
CB C:PHE359 4.7 43.8 1.0
CB C:GLU349 4.7 46.5 1.0
CD2 C:PHE359 4.8 46.8 1.0
C13 C:NTD402 4.9 49.0 1.0
CZ C:PHE336 4.9 43.8 1.0
C5 C:NTD402 5.0 48.0 1.0

Cobalt binding site 4 out of 6 in 8im2

Go back to Cobalt Binding Sites List in 8im2
Cobalt binding site 4 out of 6 in the Crystal Structure of Human Hppd Complexed with Ntbc


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 Human Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co402

b:44.8
occ:1.00
O5 D:NTD403 1.8 49.6 1.0
OE1 D:GLU349 2.0 50.8 1.0
NE2 D:HIS183 2.1 40.3 1.0
O7 D:NTD403 2.1 46.6 1.0
NE2 D:HIS266 2.7 41.4 1.0
CE1 D:HIS183 2.8 41.7 1.0
C1 D:NTD403 3.0 44.8 1.0
CD D:GLU349 3.0 47.8 1.0
C7 D:NTD403 3.2 48.8 1.0
CD2 D:HIS183 3.2 40.7 1.0
CE1 D:HIS266 3.4 43.0 1.0
OE2 D:GLU349 3.6 43.4 1.0
C6 D:NTD403 3.6 47.9 1.0
CD2 D:HIS266 3.8 44.8 1.0
ND1 D:HIS183 4.0 43.3 1.0
CG D:GLU349 4.1 45.1 1.0
C4 D:NTD403 4.2 48.5 1.0
CG D:HIS183 4.2 40.0 1.0
O D:PHE359 4.4 50.5 1.0
C8 D:NTD403 4.5 51.2 1.0
CG2 D:VAL185 4.5 43.1 1.0
CB D:ALA268 4.5 44.9 1.0
ND1 D:HIS266 4.6 41.5 1.0
CE1 D:PHE336 4.6 44.4 1.0
CB D:PHE359 4.7 47.3 1.0
CG D:HIS266 4.8 42.4 1.0
NE2 D:GLN334 4.8 47.7 1.0
CD1 D:PHE359 4.8 45.6 1.0
C13 D:NTD403 4.9 49.9 1.0

Cobalt binding site 5 out of 6 in 8im2

Go back to Cobalt Binding Sites List in 8im2
Cobalt binding site 5 out of 6 in the Crystal Structure of Human Hppd Complexed with Ntbc


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 Human Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co401

b:34.7
occ:1.00
O5 E:NTD402 1.9 37.2 1.0
O7 E:NTD402 2.0 35.3 1.0
OE2 E:GLU349 2.1 35.1 1.0
NE2 E:HIS183 2.1 37.9 1.0
O E:HOH509 2.4 30.1 1.0
NE2 E:HIS266 2.5 32.7 1.0
CE1 E:HIS183 2.9 35.7 1.0
C1 E:NTD402 3.0 35.1 1.0
C7 E:NTD402 3.1 37.6 1.0
CD E:GLU349 3.2 34.5 1.0
CD2 E:HIS183 3.2 34.5 1.0
CE1 E:HIS266 3.3 34.8 1.0
CD2 E:HIS266 3.6 32.2 1.0
C6 E:NTD402 3.6 37.5 1.0
OE1 E:GLU349 3.7 36.2 1.0
ND1 E:HIS183 4.1 35.4 1.0
C4 E:NTD402 4.2 34.7 1.0
CG E:HIS183 4.3 33.0 1.0
CG2 E:VAL185 4.4 38.8 1.0
C8 E:NTD402 4.4 35.6 1.0
CE1 E:PHE336 4.4 29.6 1.0
ND1 E:HIS266 4.4 35.4 1.0
CB E:ALA268 4.5 31.7 1.0
CG E:GLU349 4.5 29.9 1.0
O E:PHE359 4.6 35.3 1.0
CG E:HIS266 4.6 29.2 1.0
CB E:GLU349 4.7 33.0 1.0
CZ E:PHE336 4.7 29.7 1.0
CD1 E:PHE359 4.8 36.5 1.0
CB E:PHE359 4.9 33.2 1.0
C5 E:NTD402 5.0 35.8 1.0
C13 E:NTD402 5.0 37.2 1.0

Cobalt binding site 6 out of 6 in 8im2

Go back to Cobalt Binding Sites List in 8im2
Cobalt binding site 6 out of 6 in the Crystal Structure of Human Hppd Complexed with Ntbc


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 Human Hppd Complexed with Ntbc within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co401

b:49.0
occ:1.00
OE2 F:GLU349 1.7 59.7 1.0
O7 F:NTD402 2.0 49.5 1.0
O5 F:NTD402 2.0 59.2 1.0
NE2 F:HIS183 2.3 43.0 1.0
NE2 F:HIS266 2.4 51.3 1.0
C1 F:NTD402 2.9 47.0 1.0
CE1 F:HIS183 3.0 46.7 1.0
CD F:GLU349 3.0 53.0 1.0
CE1 F:HIS266 3.0 47.9 1.0
C7 F:NTD402 3.1 50.1 1.0
CD2 F:HIS183 3.4 42.8 1.0
CD2 F:HIS266 3.5 49.3 1.0
C6 F:NTD402 3.6 46.0 1.0
OE1 F:GLU349 3.8 51.5 1.0
CG F:GLU349 4.0 45.6 1.0
C4 F:NTD402 4.2 42.0 1.0
ND1 F:HIS266 4.2 47.6 1.0
ND1 F:HIS183 4.2 43.8 1.0
C8 F:NTD402 4.3 48.6 1.0
CE2 F:PHE336 4.3 46.0 1.0
CG F:HIS183 4.5 45.7 1.0
CG F:HIS266 4.5 50.0 1.0
CB F:ALA268 4.5 46.9 1.0
CZ F:PHE336 4.6 42.6 1.0
CD2 F:PHE359 4.7 40.6 1.0
O F:PHE359 4.7 47.7 1.0
CB F:GLU349 4.8 47.9 1.0
C5 F:NTD402 4.9 50.2 1.0
CB F:PHE359 5.0 42.4 1.0
C13 F:NTD402 5.0 47.2 1.0

Reference:

J.Dong, H.Xiao, J.N.Chen, B.F.Zheng, Y.L.Xu, M.X.Chen, W.C.Yang, H.Y.Lin, G.F.Yang. Structure-Based Discovery of Pyrazole-Benzothiadiazole Hybrid As Human Hppd Inhibitors. Structure 2023.
ISSN: ISSN 0969-2126
PubMed: 37794595
DOI: 10.1016/J.STR.2023.09.005
Page generated: Sun Jul 13 21:59:36 2025

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