Iodine in PDB 5ooh: Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex

All present enzymatic activity of Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex:
1.3.1.24; 1.5.1.30;

The structure of Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex, PDB code: 5ooh 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)	32.19 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.263, 40.259, 107.231, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 14.7

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

Iodine binding site 1 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:31.5 occ:1.00 I A:9ZZ303 0.0 31.5 1.0 C A:9ZZ303 2.0 28.3 1.0 C11 A:9ZZ303 2.8 27.2 1.0 O2 A:9ZZ303 2.8 27.8 1.0 C1 A:9ZZ303 2.9 26.0 1.0 H A:9ZZ303 3.0 31.2 1.0 O A:HOH439 3.1 23.4 1.0 HD23 A:LEU81 3.2 21.5 1.0 O A:HOH558 3.2 24.2 1.0 OG1 A:THR77 3.4 11.7 1.0 HG1 A:THR77 3.4 14.1 1.0 HD21 A:LEU81 3.4 21.5 1.0 HG21 A:VAL128 3.6 14.0 1.0 HG11 A:VAL128 3.6 14.9 1.0 HO2N A:NAP301 3.7 8.5 1.0 CD2 A:LEU81 3.7 17.9 1.0 N A:ASN79 3.8 18.6 1.0 CA A:ASN79 3.8 23.2 1.0 HD22 A:LEU81 4.0 21.5 1.0 O A:HOH483 4.0 9.1 1.0 C10 A:9ZZ303 4.0 28.1 1.0 H A:THR77 4.2 9.0 1.0 OD1 A:ASN79 4.2 34.5 1.0 C2 A:9ZZ303 4.2 22.7 1.0 O2D A:NAP301 4.3 7.1 1.0 H2D A:NAP301 4.5 6.3 1.0 C A:ASN79 4.5 21.3 1.0 CG2 A:VAL128 4.5 11.7 1.0 O A:ASP80 4.5 12.8 1.0 CG1 A:VAL128 4.5 12.4 1.0 C3 A:9ZZ303 4.6 25.1 1.0 HD22 A:LEU125 4.7 18.4 1.0 H72N A:NAP301 4.7 10.8 1.0 CB A:THR77 4.8 10.8 1.0 N A:ASP80 4.8 17.6 1.0 HG22 A:VAL128 4.9 14.0 1.0 H A:ASP80 4.9 21.1 1.0 HG13 A:VAL128 4.9 14.9 1.0 HA A:LEU81 4.9 15.2 1.0 C2D A:NAP301 4.9 5.3 1.0 N A:THR77 4.9 7.5 1.0 H2N A:NAP301 5.0 6.3 1.0 HB A:VAL128 5.0 10.7 1.0 CB A:VAL128 5.0 8.9 1.0 CB A:ASN79 5.0 28.6 1.0

Iodine binding site 2 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:37.4 occ:1.00 I1 A:9ZZ303 0.0 37.4 1.0 C5 A:9ZZ303 2.1 32.4 1.0 C4 A:9ZZ303 3.0 28.2 1.0 O A:9ZZ303 3.0 24.9 1.0 C6 A:9ZZ303 3.0 36.8 1.0 O1 A:9ZZ303 3.1 37.3 1.0 HE2 A:PHE113 3.2 16.6 1.0 HA A:HIS153 3.4 6.5 1.0 H4N A:NAP301 3.4 7.6 1.0 HZ A:PHE113 3.7 16.9 1.0 HB2 A:HIS153 3.7 11.0 1.0 CE2 A:PHE113 3.7 13.8 1.0 HO1 A:9ZZ303 3.8 44.8 1.0 O A:HOH603 3.8 26.8 1.0 N A:HIS153 3.9 5.1 1.0 CZ A:PHE113 4.0 14.1 1.0 H A:HIS153 4.0 6.2 1.0 CA A:HIS153 4.0 5.4 1.0 C4N A:NAP301 4.1 6.3 1.0 HD2 A:HIS153 4.1 14.8 1.0 HD13 A:LEU125 4.2 17.3 1.0 C9 A:9ZZ303 4.3 27.5 1.0 C7 A:9ZZ303 4.3 42.3 1.0 CB A:HIS153 4.3 9.2 1.0 C3 A:9ZZ303 4.3 25.1 1.0 O7N A:NAP301 4.4 7.6 1.0 C A:PRO152 4.4 4.8 1.0 HD11 A:LEU125 4.4 17.3 1.0 I3 A:9ZZ303 4.4 33.0 1.0 HA A:PRO152 4.5 5.1 1.0 HZ3 A:TRP116 4.5 15.4 1.0 CD1 A:LEU125 4.6 14.4 1.0 H5N A:NAP301 4.7 8.0 1.0 HD12 A:LEU125 4.7 17.3 1.0 C5N A:NAP301 4.7 6.7 1.0 CD2 A:PHE113 4.8 11.3 1.0 CD2 A:HIS153 4.8 12.4 1.0 C8 A:9ZZ303 4.8 34.5 1.0 C10 A:9ZZ303 4.8 28.1 1.0 C7N A:NAP301 4.8 6.7 1.0 C3N A:NAP301 4.8 5.3 1.0 O A:PRO152 4.8 6.2 1.0 CG A:HIS153 4.9 12.9 1.0 HD2 A:PHE113 5.0 13.6 1.0 CA A:PRO152 5.0 4.2 1.0

Iodine binding site 3 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:54.7 occ:1.00 I2 A:9ZZ303 0.0 54.7 1.0 C7 A:9ZZ303 2.1 42.3 1.0 C8 A:9ZZ303 3.0 34.5 1.0 C6 A:9ZZ303 3.0 36.8 1.0 HO1 A:9ZZ303 3.0 44.8 1.0 H1 A:9ZZ303 3.0 41.4 1.0 O1 A:9ZZ303 3.2 37.3 1.0 O A:HOH488 3.8 34.7 1.0 NE2 A:HIS153 4.1 16.2 1.0 HH11 A:ARG124 4.2 52.3 1.0 HE2 A:HIS153 4.2 19.5 1.0 CD2 A:HIS153 4.2 12.4 1.0 C5 A:9ZZ303 4.3 32.4 1.0 C9 A:9ZZ303 4.3 27.5 1.0 HH12 A:ARG124 4.4 52.3 1.0 CE1 A:HIS153 4.4 19.1 1.0 HD2 A:HIS153 4.4 14.8 1.0 O A:HOH587 4.5 41.3 1.0 CG A:HIS153 4.6 12.9 1.0 O4 A:9ZZ303 4.6 21.4 1.0 NH1 A:ARG124 4.6 43.6 1.0 ND1 A:HIS153 4.7 20.0 1.0 HE1 A:HIS153 4.7 22.9 1.0 C4 A:9ZZ303 4.8 28.2 1.0 HB2 A:HIS153 5.0 11.0 1.0

Iodine binding site 4 out of 4 in the Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Human Biliverdin IX Beta Reductase: Nadp/Erythrosin Extra Bluish Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:33.0 occ:1.00 I3 A:9ZZ303 0.0 33.0 1.0 C10 A:9ZZ303 2.0 28.1 1.0 C11 A:9ZZ303 2.8 27.2 1.0 O2 A:9ZZ303 3.0 27.8 1.0 C3 A:9ZZ303 3.0 25.1 1.0 O A:9ZZ303 3.1 24.9 1.0 HB2 A:SER111 3.5 9.1 1.0 HE1 A:HIS132 3.5 6.5 1.0 HE2 A:PHE113 3.5 16.6 1.0 HD13 A:LEU125 3.6 17.3 1.0 HD2 A:PHE113 3.7 13.6 1.0 HB3 A:SER111 3.7 9.1 1.0 HG A:SER111 3.7 11.0 1.0 C6N A:NAP301 3.7 6.2 1.0 N1N A:NAP301 3.8 5.8 1.0 C2N A:NAP301 3.8 5.3 1.0 C5N A:NAP301 3.8 6.7 1.0 O A:HOH430 3.8 12.9 1.0 C3N A:NAP301 3.8 5.3 1.0 C4N A:NAP301 3.8 6.3 1.0 CB A:SER111 4.0 7.6 1.0 C A:9ZZ303 4.1 28.3 1.0 HD22 A:LEU125 4.1 18.4 1.0 O2D A:NAP301 4.2 7.1 1.0 CE2 A:PHE113 4.2 13.8 1.0 H6N A:NAP301 4.2 7.5 1.0 H5N A:NAP301 4.3 8.0 1.0 OG A:SER111 4.3 9.1 1.0 C2 A:9ZZ303 4.3 22.7 1.0 CD2 A:PHE113 4.3 11.3 1.0 H2N A:NAP301 4.3 6.3 1.0 CE1 A:HIS132 4.3 5.4 1.0 H4N A:NAP301 4.4 7.6 1.0 I1 A:9ZZ303 4.4 37.4 1.0 C4 A:9ZZ303 4.4 28.2 1.0 H1D A:NAP301 4.5 7.0 1.0 C1D A:NAP301 4.5 5.9 1.0 CD1 A:LEU125 4.5 14.4 1.0 HB3 A:LEU125 4.5 13.0 1.0 C7N A:NAP301 4.6 6.7 1.0 HG11 A:VAL128 4.7 14.9 1.0 C1 A:9ZZ303 4.8 26.0 1.0 HD11 A:LEU125 4.8 17.3 1.0 C2D A:NAP301 4.8 5.3 1.0 HG12 A:VAL128 4.8 14.9 1.0 H72N A:NAP301 4.8 10.8 1.0 HO2N A:NAP301 4.8 8.5 1.0 ND1 A:HIS132 4.9 5.7 1.0 H2D A:NAP301 4.9 6.3 1.0 CD2 A:LEU125 5.0 15.3 1.0

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