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Fluorine in PDB 6bpu: Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor

Enzymatic activity of Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor

All present enzymatic activity of Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor:
1.13.11.20;

Protein crystallography data

The structure of Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor, PDB code: 6bpu was solved by A.Liu, J.Li, I.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.93 / 1.80
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 131.385, 131.385, 34.246, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 18.9

Other elements in 6bpu:

The structure of Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor also contains other interesting chemical elements:

Iron (Fe) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor (pdb code 6bpu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor, PDB code: 6bpu:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6bpu

Go back to Fluorine Binding Sites List in 6bpu
Fluorine binding site 1 out of 3 in the Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor


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 Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F157

b:29.0
occ:0.47
 F1 A:F2Y157 0.0 29.0 0.5
CE1 A:F2Y157 1.3 28.6 0.5
CE1 A:F2Y157 1.6 28.5 0.5
CZ A:F2Y157 1.7 29.6 0.5
OH A:F2Y157 2.0 31.8 0.5
SG A:CYS93 2.0 30.5 0.5
CD1 A:F2Y157 2.4 28.5 0.5
CZ A:F2Y157 2.4 29.8 0.5
CD1 A:F2Y157 2.7 29.0 0.5
OH A:F2Y157 2.8 32.5 0.5
CE2 A:F2Y157 2.8 30.7 0.5
O A:HOH411 3.2 28.3 1.0
ND1 A:HIS155 3.3 27.4 1.0
O A:PHE94 3.4 23.0 1.0
CB A:CYS93 3.5 27.2 0.5
CB A:HIS155 3.5 22.9 1.0
CB A:CYS93 3.5 27.2 0.5
CG A:F2Y157 3.6 28.4 0.5
CD2 A:F2Y157 3.6 30.0 0.5
CE2 A:F2Y157 3.6 29.6 0.5
CG A:F2Y157 3.6 28.4 0.5
F2 A:F2Y157 3.7 38.4 0.5
CG A:HIS155 3.8 28.1 1.0
N A:PHE94 3.8 24.7 1.0
CA A:CYS93 3.9 24.6 0.5
CA A:CYS93 3.9 24.6 0.5
C A:PHE94 4.0 24.1 1.0
C A:CYS93 4.0 23.8 1.0
O A:LEU156 4.1 24.7 1.0
CD2 A:F2Y157 4.1 29.9 0.5
CA A:HIS155 4.1 18.6 1.0
N A:LEU156 4.2 22.4 1.0
SG A:CYS93 4.2 29.3 0.5
CE1 A:HIS155 4.5 31.6 1.0
C A:LEU156 4.5 22.6 1.0
C A:HIS155 4.5 22.3 1.0
CA A:PHE94 4.6 20.7 1.0
O A:HOH408 4.6 31.8 1.0
F2 A:F2Y157 4.7 34.1 0.5
N A:LEU95 4.8 20.6 1.0
O A:CYS93 4.8 26.0 1.0
CB A:LEU95 4.9 28.0 1.0
CB A:F2Y157 4.9 27.2 0.5
CB A:F2Y157 4.9 27.2 0.5
N A:F2Y157 4.9 22.6 1.0
CA A:LEU95 5.0 22.0 1.0

Fluorine binding site 2 out of 3 in 6bpu

Go back to Fluorine Binding Sites List in 6bpu
Fluorine binding site 2 out of 3 in the Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor


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 Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F157

b:34.1
occ:0.47
 F2 A:F2Y157 0.0 34.1 0.5
CE2 A:F2Y157 1.3 29.6 0.5
F2 A:F2Y157 2.2 38.4 0.5
CE2 A:F2Y157 2.3 30.7 0.5
CZ A:F2Y157 2.3 29.8 0.5
CD2 A:F2Y157 2.4 29.9 0.5
OH A:F2Y157 2.7 32.5 0.5
CD2 A:F2Y157 2.8 30.0 0.5
NH1 A:ARG60 2.8 42.3 0.4
CZ A:F2Y157 3.0 29.6 0.5
CE A:MET179 3.1 50.7 1.0
O A:HOH405 3.1 48.0 1.0
O A:HOH408 3.4 31.8 1.0
OH A:F2Y157 3.5 31.8 0.5
NH1 A:ARG60 3.5 42.7 0.6
CE1 A:F2Y157 3.6 28.6 0.5
CG A:F2Y157 3.6 28.4 0.5
CZ A:PHE161 3.6 35.8 1.0
CG A:F2Y157 3.7 28.4 0.5
O A:HOH474 3.9 35.0 1.0
CE1 A:F2Y157 3.9 28.5 0.5
CZ A:ARG60 4.0 41.1 0.4
CE1 A:PHE161 4.1 36.9 1.0
CD1 A:F2Y157 4.1 28.5 0.5
CD1 A:F2Y157 4.2 29.0 0.5
O A:HOH406 4.2 46.5 1.0
O A:HOH439 4.4 41.2 1.0
O A:HOH539 4.4 57.1 1.0
CE2 A:PHE161 4.4 30.4 1.0
CZ A:ARG60 4.6 43.3 0.6
NH2 A:ARG60 4.6 40.8 0.4
SD A:MET73 4.6 40.2 1.0
CE A:MET73 4.7 38.9 1.0
F1 A:F2Y157 4.7 29.0 0.5
SD A:MET179 4.8 75.3 1.0
CB A:F2Y157 4.9 27.2 0.5
CB A:F2Y157 4.9 27.2 0.5
NE A:ARG60 5.0 42.5 0.4

Fluorine binding site 3 out of 3 in 6bpu

Go back to Fluorine Binding Sites List in 6bpu
Fluorine binding site 3 out of 3 in the Crystal Structure of Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor


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 Ferrous Form of the F2-TYR157 Human Cysteine Dioxygenase with Both Uncrosslinked and Crosslinked Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F157

b:38.4
occ:0.53
 F2 A:F2Y157 0.0 38.4 0.5
CE2 A:F2Y157 1.3 30.7 0.5
CZ A:F2Y157 1.9 29.8 0.5
CE2 A:F2Y157 1.9 29.6 0.5
OH A:F2Y157 2.2 32.5 0.5
F2 A:F2Y157 2.2 34.1 0.5
CZ A:F2Y157 2.3 29.6 0.5
CD2 A:F2Y157 2.4 30.0 0.5
OH A:F2Y157 2.7 31.8 0.5
CE1 A:F2Y157 2.8 28.6 0.5
CD2 A:F2Y157 2.9 29.9 0.5
O A:HOH405 2.9 48.0 1.0
NH1 A:ARG60 2.9 42.3 0.4
CB A:HIS155 3.4 22.9 1.0
SD A:MET73 3.4 40.2 1.0
CD1 A:F2Y157 3.6 28.5 0.5
ND1 A:HIS155 3.6 27.4 1.0
CG A:F2Y157 3.6 28.4 0.5
NH1 A:ARG60 3.6 42.7 0.6
CE1 A:F2Y157 3.6 28.5 0.5
CG A:F2Y157 3.6 28.4 0.5
F1 A:F2Y157 3.7 29.0 0.5
CG A:HIS155 3.8 28.1 1.0
CE A:MET73 3.9 38.9 1.0
CG A:MET73 4.1 29.6 1.0
CD1 A:F2Y157 4.1 29.0 0.5
CZ A:ARG60 4.1 41.1 0.4
O A:HOH408 4.2 31.8 1.0
CE1 A:HIS155 4.6 31.6 1.0
NH2 A:ARG60 4.7 40.8 0.4
CD1 A:LEU75 4.7 28.5 1.0
CA A:HIS155 4.8 18.6 1.0
CE A:MET179 4.9 50.7 1.0
CZ A:ARG60 4.9 43.3 0.6
CB A:F2Y157 4.9 27.2 0.5
CB A:F2Y157 4.9 27.2 0.5
CD2 A:HIS155 4.9 28.1 1.0
O A:HOH406 5.0 46.5 1.0

Reference:

J.Li, W.P.Griffith, I.Davis, I.Shin, J.Wang, F.Li, Y.Wang, D.J.Wherritt, A.Liu. Cleavage of A Carbon-Fluorine Bond By An Engineered Cysteine Dioxygenase. Nat. Chem. Biol. V. 14 853 2018.
ISSN: ESSN 1552-4469
PubMed: 29942080
DOI: 10.1038/S41589-018-0085-5
Page generated: Thu Aug 1 18:14:54 2024

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