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Fluorine in PDB 3vgn: Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol

Enzymatic activity of Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol

All present enzymatic activity of Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol:
5.3.3.1;

Protein crystallography data

The structure of Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol, PDB code: 3vgn was solved by J.M.M.Caaveiro, B.Pybus, D.Ringe, G.A.Petsko, P.A.Sigala, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.25 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.483, 72.315, 95.282, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol (pdb code 3vgn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol, PDB code: 3vgn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3vgn

Go back to Fluorine Binding Sites List in 3vgn
Fluorine binding site 1 out of 2 in the Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol


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 Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F140

b:24.1
occ:1.00
F A:FNN140 0.0 24.1 1.0
C3 A:FNN140 1.3 19.3 1.0
C2 A:FNN140 2.3 19.1 1.0
C4 A:FNN140 2.4 21.6 1.0
O2 A:FNN140 2.6 24.6 1.0
N A:FNN140 2.8 23.3 1.0
C1 A:FNN140 3.6 14.9 1.0
C5 A:FNN140 3.7 18.5 1.0
CG2 A:VAL88 3.7 18.4 1.0
CG1 A:VAL88 4.0 21.1 1.0
C6 A:FNN140 4.1 16.6 1.0
O1 A:FNN140 4.2 25.5 1.0
CG1 A:VAL20 4.3 14.6 1.0
CB A:VAL88 4.4 17.6 1.0
O A:FNN140 4.7 13.0 1.0
CE2 A:PHE86 5.0 13.1 1.0

Fluorine binding site 2 out of 2 in 3vgn

Go back to Fluorine Binding Sites List in 3vgn
Fluorine binding site 2 out of 2 in the Crystal Structure of Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol


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 Ketosteroid Isomerase D40N From Pseudomonas Putida (Pksi) with Bound 3-Fluoro-4-Nitrophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F140

b:35.0
occ:1.00
F B:FNN140 0.0 35.0 1.0
C3 B:FNN140 1.3 24.6 1.0
C2 B:FNN140 2.3 24.3 1.0
C4 B:FNN140 2.4 25.9 1.0
O2 B:FNN140 2.6 33.9 1.0
N B:FNN140 2.8 33.2 1.0
C1 B:FNN140 3.6 15.1 1.0
C5 B:FNN140 3.6 24.3 1.0
CG2 B:VAL88 3.8 21.0 1.0
C6 B:FNN140 4.1 17.9 1.0
CG1 B:VAL20 4.1 17.8 1.0
CG1 B:VAL88 4.1 23.4 1.0
O1 B:FNN140 4.2 31.0 1.0
CB B:VAL88 4.5 22.5 1.0
O B:FNN140 4.6 15.4 1.0
CD2 B:LEU61 4.8 28.1 1.0
CE2 B:PHE86 5.0 13.8 1.0

Reference:

P.A.Sigala, A.T.Fafarman, J.P.Schwans, S.D.Fried, T.D.Fenn, J.M.M.Caaveiro, B.Pybus, D.Ringe, G.A.Petsko, S.G.Boxer, D.Herschlag. Quantitative Dissection of Hydrogen Bond-Mediated Proton Transfer in the Ketosteroid Isomerase Active Site Proc.Natl.Acad.Sci.Usa V. 110 E2552 2013.
ISSN: ISSN 0027-8424
PubMed: 23798390
DOI: 10.1073/PNAS.1302191110
Page generated: Wed Jul 31 23:17:23 2024

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