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Fluorine in PDB 7erd: Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)

Enzymatic activity of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)

All present enzymatic activity of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg):
1.3.1.24; 1.5.1.30;

Protein crystallography data

The structure of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg), PDB code: 7erd was solved by C.Griesinger, D.Lee, K.S.Ryu, M.Kim, J.H.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.59 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.821, 116.996, 41.615, 90, 90, 90
R / Rfree (%) 18 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) (pdb code 7erd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg), PDB code: 7erd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7erd

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Fluorine binding site 1 out of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:41.0
occ:1.00
 F01 A:JBO402 0.0 41.0 1.0
C02 A:JBO402 1.4 41.1 1.0
F21 A:JBO402 2.2 42.2 1.0
F03 A:JBO402 2.2 41.9 1.0
C04 A:JBO402 2.4 38.6 1.0
C20 A:JBO402 2.6 36.3 1.0
O A:HOH508 3.4 32.3 1.0
O A:HOH535 3.6 19.9 1.0
O A:ARG78 3.6 33.5 1.0
C05 A:JBO402 3.7 38.0 1.0
CD2 A:LEU81 3.9 28.0 1.0
O A:HOH511 3.9 23.8 1.0
C19 A:JBO402 4.0 36.0 1.0
O2D A:NAP401 4.1 20.6 1.0
C06 A:JBO402 4.3 38.6 1.0
OG1 A:THR77 4.7 25.0 1.0
C07 A:JBO402 4.8 36.8 1.0
CG1 A:VAL128 4.8 18.7 1.0
C A:ARG78 4.8 34.0 1.0
C2D A:NAP401 4.9 21.8 1.0
CD2 A:LEU125 4.9 23.9 1.0
C18 A:JBO402 4.9 36.3 1.0
CA A:ASN79 4.9 39.6 1.0

Fluorine binding site 2 out of 6 in 7erd

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:41.9
occ:1.00
 F03 A:JBO402 0.0 41.9 1.0
C02 A:JBO402 1.3 41.1 1.0
F21 A:JBO402 2.2 42.2 1.0
F01 A:JBO402 2.2 41.0 1.0
C04 A:JBO402 2.4 38.6 1.0
C06 A:JBO402 2.9 38.6 1.0
C05 A:JBO402 3.0 38.0 1.0
CD2 A:LEU81 3.4 28.0 1.0
C20 A:JBO402 3.4 36.3 1.0
CD2 A:LEU125 3.7 23.9 1.0
C07 A:JBO402 4.3 36.8 1.0
C19 A:JBO402 4.6 36.0 1.0
CG A:LEU81 4.7 28.8 1.0
C18 A:JBO402 4.9 36.3 1.0
O A:ARG78 5.0 33.5 1.0

Fluorine binding site 3 out of 6 in 7erd

Go back to Fluorine Binding Sites List in 7erd
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:42.2
occ:1.00
 F21 A:JBO402 0.0 42.2 1.0
C02 A:JBO402 1.4 41.1 1.0
F03 A:JBO402 2.2 41.9 1.0
F01 A:JBO402 2.2 41.0 1.0
C04 A:JBO402 2.4 38.6 1.0
O A:HOH511 3.0 23.8 1.0
C05 A:JBO402 3.0 38.0 1.0
C06 A:JBO402 3.0 38.6 1.0
O7N A:NAP401 3.3 25.3 1.0
C20 A:JBO402 3.5 36.3 1.0
C7N A:NAP401 3.8 24.3 1.0
O A:HOH508 3.9 32.3 1.0
C2N A:NAP401 4.3 21.3 1.0
C07 A:JBO402 4.3 36.8 1.0
O A:ARG78 4.4 33.5 1.0
C3N A:NAP401 4.4 23.1 1.0
O A:HOH596 4.6 34.4 1.0
N7N A:NAP401 4.6 24.9 1.0
C19 A:JBO402 4.6 36.0 1.0
C18 A:JBO402 5.0 36.3 1.0

Fluorine binding site 4 out of 6 in 7erd

Go back to Fluorine Binding Sites List in 7erd
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:45.8
occ:1.00
 F01 B:JBO402 0.0 45.8 1.0
C02 B:JBO402 1.4 45.8 1.0
F03 B:JBO402 2.2 46.4 1.0
F21 B:JBO402 2.2 46.6 1.0
C04 B:JBO402 2.5 43.6 1.0
O B:HOH519 2.8 31.1 1.0
C05 B:JBO402 3.1 42.2 1.0
C06 B:JBO402 3.2 41.1 1.0
C20 B:JBO402 3.5 43.0 1.0
N7N B:NAP401 3.5 25.0 1.0
CG B:ARG78 4.0 61.5 1.0
O B:HOH522 4.1 38.7 1.0
C07 B:JBO402 4.5 42.1 1.0
C7N B:NAP401 4.5 26.6 1.0
NH2 B:ARG78 4.5 67.7 1.0
CB B:ARG78 4.6 58.4 1.0
C2N B:NAP401 4.6 28.0 1.0
CA B:ARG78 4.7 55.7 1.0
C19 B:JBO402 4.7 42.3 1.0
O B:HOH533 4.8 29.6 1.0
C3N B:NAP401 4.8 27.0 1.0
O2D B:NAP401 4.9 30.4 1.0

Fluorine binding site 5 out of 6 in 7erd

Go back to Fluorine Binding Sites List in 7erd
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:46.4
occ:1.00
 F03 B:JBO402 0.0 46.4 1.0
C02 B:JBO402 1.3 45.8 1.0
F21 B:JBO402 2.2 46.6 1.0
F01 B:JBO402 2.2 45.8 1.0
C04 B:JBO402 2.4 43.6 1.0
C20 B:JBO402 2.8 43.0 1.0
O B:HOH533 3.6 29.6 1.0
C05 B:JBO402 3.7 42.2 1.0
CA B:ARG78 3.8 55.7 1.0
O B:ARG78 3.9 57.0 1.0
CD2 B:LEU125 4.0 25.2 1.0
O B:HOH522 4.1 38.7 1.0
C19 B:JBO402 4.1 42.3 1.0
CG B:ARG78 4.3 61.5 1.0
C B:ARG78 4.3 57.5 1.0
O B:HOH519 4.3 31.1 1.0
C06 B:JBO402 4.3 41.1 1.0
O2D B:NAP401 4.4 30.4 1.0
CB B:ARG78 4.4 58.4 1.0
CG2 B:VAL128 4.6 26.3 1.0
N B:ARG78 4.7 52.4 1.0
O B:THR77 4.8 50.2 1.0
C07 B:JBO402 4.8 42.1 1.0
CG1 B:VAL128 4.9 26.7 1.0

Fluorine binding site 6 out of 6 in 7erd

Go back to Fluorine Binding Sites List in 7erd
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:46.6
occ:1.00
 F21 B:JBO402 0.0 46.6 1.0
C02 B:JBO402 1.4 45.8 1.0
F03 B:JBO402 2.2 46.4 1.0
F01 B:JBO402 2.2 45.8 1.0
C04 B:JBO402 2.4 43.6 1.0
C06 B:JBO402 3.0 41.1 1.0
C05 B:JBO402 3.1 42.2 1.0
CD2 B:LEU125 3.2 25.2 1.0
O A:HOH615 3.4 51.7 1.0
C20 B:JBO402 3.5 43.0 1.0
CG B:LEU125 4.4 25.5 1.0
CD1 B:LEU125 4.4 26.3 1.0
C07 B:JBO402 4.4 42.1 1.0
O B:ARG78 4.6 57.0 1.0
O A:HOH558 4.6 36.7 1.0
C19 B:JBO402 4.7 42.3 1.0
CG B:ARG78 4.8 61.5 1.0
O B:HOH577 4.8 46.3 1.0

Reference:

M.Kim, J.H.Ha, J.Choi, B.R.Kim, V.Gapsys, K.O.Lee, J.G.Jee, K.S.Chakrabarti, B.L.De Groot, C.Griesinger, K.S.Ryu, D.Lee. Repositioning Food and Drug Administration-Approved Drugs For Inhibiting Biliverdin IX Beta Reductase B As A Novel Thrombocytopenia Therapeutic Target. J.Med.Chem. V. 65 2548 2022.
ISSN: ISSN 0022-2623
PubMed: 34957824
DOI: 10.1021/ACS.JMEDCHEM.1C01664
Page generated: Fri Aug 2 06:45:24 2024

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