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Chlorine in PDB 5oog: Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex

Enzymatic activity of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex

All present enzymatic activity of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex:
1.3.1.24; 1.5.1.30;

Protein crystallography data

The structure of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex, PDB code: 5oog was solved by J.A.Manso, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.95 / 1.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.261, 49.474, 107.612, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 14.5

Other elements in 5oog:

The structure of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex (pdb code 5oog). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex, PDB code: 5oog:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5oog

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Chlorine binding site 1 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:23.5
occ:0.00
 CL A:A0B601 0.0 23.5 0.0
C18 A:A0B601 1.7 24.4 0.0
O A:HOH889 2.0 36.5 1.0
HE1 A:HIS153 2.5 25.2 1.0
H71N A:NAP604 2.6 12.4 1.0
C13 A:A0B601 2.7 27.8 1.0
C17 A:A0B601 2.7 22.3 0.0
H1 A:A0B601 2.7 40.6 1.0
C2 A:A0B601 3.0 29.6 1.0
O7N A:NAP604 3.0 8.4 1.0
CE1 A:HIS153 3.0 21.0 1.0
CL1 A:A0B601 3.1 21.6 0.0
ND1 A:HIS153 3.1 18.5 1.0
C4 A:A0B601 3.2 33.8 1.0
N7N A:NAP604 3.2 10.3 1.0
C3 A:A0B601 3.3 31.2 1.0
C7N A:NAP604 3.4 8.2 1.0
O A:HOH808 3.5 11.1 1.0
C1 A:A0B601 3.9 37.1 1.0
C16 A:A0B601 4.0 21.6 0.0
C14 A:A0B601 4.0 23.9 0.0
H72N A:NAP604 4.0 12.4 1.0
C5 A:A0B601 4.2 43.1 1.0
H A:A0B601 4.2 56.1 1.0
NE2 A:HIS153 4.3 24.6 1.0
H A:ILE154 4.4 4.0 1.0
C8 A:A0B601 4.5 31.5 1.0
C A:A0B601 4.5 46.7 1.0
CG A:HIS153 4.5 15.1 1.0
C15 A:A0B601 4.5 22.1 0.0
O A:HOH989 4.6 29.0 1.0
HA A:HIS153 4.7 5.2 1.0
HE2 A:HIS153 4.8 29.6 1.0
C3N A:NAP604 4.8 6.5 1.0
O A:HOH905 4.9 29.9 1.0
C9 A:A0B601 4.9 36.7 1.0
BR3 A:A0B601 5.0 59.2 1.0

Chlorine binding site 2 out of 4 in 5oog

Go back to Chlorine Binding Sites List in 5oog
Chlorine binding site 2 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:21.6
occ:0.00
 CL1 A:A0B601 0.0 21.6 0.0
C17 A:A0B601 1.7 22.3 0.0
C16 A:A0B601 2.7 21.6 0.0
C18 A:A0B601 2.7 24.4 0.0
O A:HOH989 2.8 29.0 1.0
CL2 A:A0B601 3.1 20.9 0.0
CL A:A0B601 3.1 23.5 0.0
HE1 A:HIS153 3.2 25.2 1.0
O A:HOH889 3.2 36.5 1.0
C13 A:A0B601 4.0 27.8 1.0
C15 A:A0B601 4.0 22.1 0.0
CE1 A:HIS153 4.0 21.0 1.0
H1 A:A0B601 4.3 40.6 1.0
C14 A:A0B601 4.5 23.9 0.0
HH12 A:ARG124 4.6 51.2 0.0
O A:HOH905 4.7 29.9 1.0
ND1 A:HIS153 4.8 18.5 1.0
NE2 A:HIS153 4.9 24.6 1.0
HH11 A:ARG124 5.0 51.2 0.0
HE2 A:HIS153 5.0 29.6 1.0

Chlorine binding site 3 out of 4 in 5oog

Go back to Chlorine Binding Sites List in 5oog
Chlorine binding site 3 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:20.9
occ:0.00
 CL2 A:A0B601 0.0 20.9 0.0
C16 A:A0B601 1.7 21.6 0.0
C15 A:A0B601 2.7 22.1 0.0
C17 A:A0B601 2.7 22.3 0.0
CL3 A:A0B601 3.1 21.4 0.0
CL1 A:A0B601 3.1 21.6 0.0
HH11 A:ARG124 3.5 51.2 0.0
HH12 A:ARG124 3.8 51.2 0.0
NH1 A:ARG124 3.9 42.7 0.0
C14 A:A0B601 4.0 23.9 0.0
O A:HOH905 4.0 29.9 1.0
C18 A:A0B601 4.0 24.4 0.0
C13 A:A0B601 4.5 27.8 1.0

Chlorine binding site 4 out of 4 in 5oog

Go back to Chlorine Binding Sites List in 5oog
Chlorine binding site 4 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:21.4
occ:0.00
 CL3 A:A0B601 0.0 21.4 0.0
C15 A:A0B601 1.7 22.1 0.0
HH11 A:ARG124 2.5 51.2 0.0
O4 A:A0B601 2.7 21.3 0.0
C14 A:A0B601 2.7 23.9 0.0
C16 A:A0B601 2.7 21.6 0.0
C19 A:A0B601 3.0 22.0 0.0
CL2 A:A0B601 3.1 20.9 0.0
HE A:ARG124 3.3 44.4 0.0
NH1 A:ARG124 3.3 42.7 0.0
O A:HOH905 3.4 29.9 1.0
HH12 A:ARG124 3.9 51.2 0.0
NE A:ARG124 3.9 37.0 0.0
C17 A:A0B601 4.0 22.3 0.0
C13 A:A0B601 4.0 27.8 1.0
CZ A:ARG124 4.1 41.2 0.0
O3 A:A0B601 4.2 21.3 0.0
C18 A:A0B601 4.5 24.4 0.0
H A:A0B601 4.6 56.1 1.0

Reference:

N.M.Nesbitt, X.Zheng, Z.Li, J.A.Manso, W.Y.Yen, L.E.Malone, J.Ripoll-Rozada, P.J.B.Pereira, T.J.Mantle, J.Wang, W.F.Bahou. In Silicoand Crystallographic Studies Identify Key Structural Features of Biliverdin IX Beta Reductase Inhibitors Having Nanomolar Potency. J. Biol. Chem. V. 293 5431 2018.
ISSN: ESSN 1083-351X
PubMed: 29487133
DOI: 10.1074/JBC.RA118.001803
Page generated: Fri Jul 26 14:38:27 2024

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