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Bromine 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:

Chlorine (Cl) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 4 binding sites of Bromine where determined in the Human Biliverdin IX Beta Reductase: Nadp/Phloxine B Ternary Complex, PDB code: 5oog:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5oog

Go back to Bromine Binding Sites List in 5oog
Bromine 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 Bromine with other atoms in the Br 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:Br601

b:88.0
occ:1.00
 BR A:A0B601 0.0 88.0 1.0
C12 A:A0B601 1.9 62.6 1.0
C A:A0B601 2.8 46.7 1.0
C11 A:A0B601 2.8 52.1 1.0
H A:A0B601 2.9 56.1 1.0
HB2 A:HIS153 3.0 9.9 1.0
O2 A:A0B601 3.1 46.2 1.0
CB A:HIS153 3.9 8.3 1.0
O A:HOH905 4.0 29.9 1.0
C1 A:A0B601 4.1 37.1 1.0
C10 A:A0B601 4.1 48.2 1.0
HB3 A:HIS153 4.2 9.9 1.0
H A:HIS153 4.3 5.2 1.0
O4 A:A0B601 4.5 21.3 0.0
HB3 A:ARG174 4.6 12.2 1.0
CG A:HIS153 4.6 15.1 1.0
C9 A:A0B601 4.6 36.7 1.0
C19 A:A0B601 4.7 22.0 0.0
O A:ARG174 4.8 5.6 1.0
N A:HIS153 4.9 4.3 1.0
CA A:HIS153 4.9 4.3 1.0
ND1 A:HIS153 4.9 18.5 1.0
HA A:HIS153 5.0 5.2 1.0

Bromine binding site 2 out of 4 in 5oog

Go back to Bromine Binding Sites List in 5oog
Bromine 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 Bromine with other atoms in the Br 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:Br601

b:65.6
occ:1.00
 BR1 A:A0B601 0.0 65.6 1.0
C10 A:A0B601 1.9 48.2 1.0
C9 A:A0B601 2.8 36.7 1.0
C11 A:A0B601 2.9 52.1 1.0
O1 A:A0B601 3.0 36.6 1.0
HA A:PRO152 3.0 4.4 1.0
O2 A:A0B601 3.1 46.2 1.0
H5N A:NAP604 3.4 8.9 1.0
HB3 A:ALA112 3.5 6.3 1.0
HZ3 A:TRP116 3.5 17.8 1.0
CE2 A:PHE113 3.6 15.7 1.0
HE2 A:PHE113 3.6 18.8 1.0
HB2 A:SER111 3.7 8.8 1.0
O A:PRO151 3.7 3.0 1.0
H A:ALA112 3.8 3.7 1.0
H4N A:NAP604 3.8 8.4 1.0
CZ A:PHE113 3.8 14.0 1.0
CA A:PRO152 3.8 3.7 1.0
CD2 A:PHE113 3.9 12.9 1.0
C A:PRO152 3.9 5.0 1.0
H A:PHE113 3.9 5.6 1.0
CZ3 A:TRP116 4.0 14.9 1.0
C5N A:NAP604 4.0 7.4 1.0
HZ A:PHE113 4.0 16.8 1.0
HH2 A:TRP116 4.1 16.7 1.0
HD2 A:PHE113 4.1 15.5 1.0
C12 A:A0B601 4.1 62.6 1.0
C1 A:A0B601 4.1 37.1 1.0
HG A:SER111 4.1 10.3 1.0
N A:HIS153 4.1 4.3 1.0
C4N A:NAP604 4.2 7.0 1.0
H A:HIS153 4.2 5.2 1.0
CE1 A:PHE113 4.3 12.8 1.0
OG A:SER111 4.3 8.6 1.0
CH2 A:TRP116 4.3 13.9 1.0
C8 A:A0B601 4.3 31.5 1.0
O A:PRO152 4.3 6.7 1.0
N A:ALA112 4.4 3.1 1.0
CG A:PHE113 4.4 9.2 1.0
CB A:ALA112 4.4 5.3 1.0
CB A:SER111 4.5 7.3 1.0
HA A:HIS153 4.5 5.2 1.0
N A:PHE113 4.5 4.7 1.0
CD1 A:PHE113 4.5 11.0 1.0
C A:PRO151 4.7 2.7 1.0
C A:A0B601 4.7 46.7 1.0
HB2 A:ALA112 4.7 6.3 1.0
N A:PRO152 4.7 2.8 1.0
HE1 A:PHE113 4.8 15.4 1.0
CA A:ALA112 4.8 3.7 1.0
BR2 A:A0B601 4.8 29.2 1.0
CE3 A:TRP116 4.9 12.8 1.0
CB A:PRO152 4.9 4.4 1.0
CA A:HIS153 4.9 4.3 1.0
HB2 A:PRO152 5.0 5.3 1.0
HB3 A:PRO152 5.0 5.3 1.0

Bromine binding site 3 out of 4 in 5oog

Go back to Bromine Binding Sites List in 5oog
Bromine 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 Bromine with other atoms in the Br 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:Br601

b:29.2
occ:1.00
 BR2 A:A0B601 0.0 29.2 1.0
C7 A:A0B601 1.9 31.5 1.0
C6 A:A0B601 2.9 38.4 1.0
C8 A:A0B601 2.9 31.5 1.0
HE1 A:HIS132 3.0 5.7 1.0
O A:A0B601 3.1 39.5 1.0
O1 A:A0B601 3.2 36.6 1.0
HB2 A:SER111 3.4 8.8 1.0
O A:HOH736 3.4 14.6 1.0
HG A:SER111 3.4 10.3 1.0
HB3 A:SER111 3.4 8.8 1.0
HD2 A:PHE113 3.7 15.5 1.0
HE2 A:PHE113 3.7 18.8 1.0
CB A:SER111 3.8 7.3 1.0
C6N A:NAP604 3.8 6.7 1.0
N1N A:NAP604 3.8 5.6 1.0
CE1 A:HIS132 3.9 4.7 1.0
HD13 A:LEU125 3.9 16.0 1.0
O2D A:NAP604 3.9 6.8 1.0
OG A:SER111 4.0 8.6 1.0
C5N A:NAP604 4.0 7.4 1.0
C2N A:NAP604 4.1 5.7 1.0
H6N A:NAP604 4.1 8.1 1.0
HD22 A:LEU125 4.1 20.7 1.0
H1D A:NAP604 4.2 6.7 1.0
C5 A:A0B601 4.2 43.1 1.0
C3N A:NAP604 4.2 6.5 1.0
C3 A:A0B601 4.3 31.2 1.0
C4N A:NAP604 4.3 7.0 1.0
HG12 A:VAL128 4.3 14.0 1.0
HG11 A:VAL128 4.3 14.0 1.0
CD2 A:PHE113 4.3 12.9 1.0
CE2 A:PHE113 4.3 15.7 1.0
C1D A:NAP604 4.4 5.6 1.0
ND1 A:HIS132 4.4 4.7 1.0
H5N A:NAP604 4.5 8.9 1.0
HB3 A:LEU125 4.5 13.2 1.0
HO2N A:NAP604 4.5 8.2 1.0
C9 A:A0B601 4.5 36.7 1.0
H2N A:NAP604 4.6 6.9 1.0
C2D A:NAP604 4.6 5.3 1.0
C4 A:A0B601 4.7 33.8 1.0
CG1 A:VAL128 4.8 11.7 1.0
BR1 A:A0B601 4.8 65.6 1.0
HG1 A:THR129 4.8 7.2 1.0
CD1 A:LEU125 4.8 13.4 1.0
H4N A:NAP604 4.9 8.4 1.0
H2D A:NAP604 4.9 6.4 1.0

Bromine binding site 4 out of 4 in 5oog

Go back to Bromine Binding Sites List in 5oog
Bromine 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 Bromine with other atoms in the Br 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:Br601

b:59.2
occ:1.00
 BR3 A:A0B601 0.0 59.2 1.0
C5 A:A0B601 1.9 43.1 1.0
C4 A:A0B601 2.8 33.8 1.0
C6 A:A0B601 2.8 38.4 1.0
H1 A:A0B601 2.9 40.6 1.0
O A:A0B601 3.0 39.5 1.0
HD21 A:LEU81 3.3 21.8 1.0
O A:HOH748 3.8 9.6 1.0
H72N A:NAP604 3.8 12.4 1.0
O A:HOH750 4.0 15.9 1.0
O A:ARG78 4.1 16.4 1.0
HD21 A:LEU125 4.1 20.7 1.0
CD2 A:LEU81 4.1 18.2 1.0
C3 A:A0B601 4.2 31.2 1.0
C7 A:A0B601 4.2 31.5 1.0
HD23 A:LEU81 4.2 21.8 1.0
N7N A:NAP604 4.2 10.3 1.0
H71N A:NAP604 4.3 12.4 1.0
HD22 A:LEU125 4.3 20.7 1.0
O A:HOH889 4.4 36.5 1.0
HD22 A:LEU81 4.4 21.8 1.0
HA A:ASN79 4.6 21.1 1.0
CD2 A:LEU125 4.6 17.2 1.0
C8 A:A0B601 4.7 31.5 1.0
H2N A:NAP604 4.8 6.9 1.0
HD23 A:LEU125 4.9 20.7 1.0
CL A:A0B601 5.0 23.5 0.0
O A:HOH841 5.0 14.7 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: Sat Dec 12 02:28:54 2020

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