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Fluorine in PDB 4lxi: Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda

Enzymatic activity of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda

All present enzymatic activity of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda:
3.7.1.8;

Protein crystallography data

The structure of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda, PDB code: 4lxi was solved by S.Bhowmik, J.T.Bolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.26 / 2.17
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 66.155, 66.155, 342.180, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 25.8

Other elements in 4lxi:

The structure of Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda (pdb code 4lxi). 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 the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda, PDB code: 4lxi:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4lxi

Go back to Fluorine Binding Sites List in 4lxi
Fluorine binding site 1 out of 2 in the Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda


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 the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:74.2
occ:1.00
 FA5 A:22J301 0.0 74.2 1.0
CA5 A:22J301 1.4 63.4 1.0
CA6 A:22J301 2.4 61.2 1.0
CA4 A:22J301 2.5 65.8 1.0
CB1 A:22J301 2.8 63.2 1.0
CA3 A:22J301 2.9 61.2 1.0
CB2 A:22J301 3.2 77.2 1.0
CE A:MET229 3.3 55.7 1.0
CG2 A:VAL149 3.4 50.2 1.0
CG1 A:VAL149 3.5 46.2 1.0
OA4 A:22J301 3.5 52.2 1.0
FB2 A:22J301 3.6 83.4 1.0
CB6 A:22J301 3.6 64.8 1.0
CB A:VAL149 3.9 48.4 1.0
N A:GLY35 4.1 44.1 1.0
CD2 A:LEU166 4.2 55.1 1.0
CB5 A:22J301 4.2 73.6 1.0
CA A:GLY35 4.3 43.1 1.0
CG A:MET229 4.4 54.5 1.0
CA2 A:22J301 4.4 66.5 1.0
SD A:MET229 4.4 63.2 1.0
CB3 A:22J301 4.6 66.8 1.0
C A:GLY34 4.8 45.9 1.0
CB4 A:22J301 4.8 68.9 1.0
CB A:MET229 4.9 48.2 1.0
CB A:ALA105 4.9 37.7 1.0
OA1 A:22J301 4.9 60.5 1.0

Fluorine binding site 2 out of 2 in 4lxi

Go back to Fluorine Binding Sites List in 4lxi
Fluorine binding site 2 out of 2 in the Crystal Structure of the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda


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 the S105A Mutant of A Carbon-Carbon Bond Hydrolase, DXNB2 From Sphingomonas Wittichii RW1, in Complex with 5, 8-Dif Hopda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:83.4
occ:1.00
 FB2 A:22J301 0.0 83.4 1.0
CB2 A:22J301 1.3 77.2 1.0
CB5 A:22J301 2.0 73.6 1.0
CB1 A:22J301 2.6 63.2 1.0
CA6 A:22J301 3.2 61.2 1.0
CB4 A:22J301 3.3 68.9 1.0
CA5 A:22J301 3.3 63.4 1.0
CB A:MET229 3.5 48.2 1.0
CE A:MET229 3.5 55.7 1.0
FA5 A:22J301 3.6 74.2 1.0
CB6 A:22J301 3.7 64.8 1.0
CB A:ALA105 3.7 37.7 1.0
OA4 A:22J301 3.7 52.2 1.0
CG2 A:VAL230 3.9 44.3 1.0
CB3 A:22J301 3.9 66.8 1.0
CG A:MET229 4.2 54.5 1.0
CA4 A:22J301 4.3 65.8 1.0
O A:MET229 4.4 45.7 1.0
C A:MET229 4.5 47.9 1.0
CA A:MET229 4.5 48.9 1.0
CA A:ALA105 4.7 38.5 1.0
CB A:ALA131 4.7 37.0 1.0
SD A:MET229 4.8 63.2 1.0
N A:VAL230 4.9 47.4 1.0
CD2 A:LEU146 5.0 62.5 1.0

Reference:

A.C.Ruzzini, S.Bhowmik, S.Ghosh, K.C.Yam, J.T.Bolin, L.D.Eltis. A Substrate-Assisted Mechanism of Nucleophile Activation in A Ser-His-Asp Containing C-C Bond Hydrolase. Biochemistry V. 52 7428 2013.
ISSN: ISSN 0006-2960
PubMed: 24067021
DOI: 10.1021/BI401156A
Page generated: Sun Dec 13 12:07:25 2020

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