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Fluorine in PDB 4kgj: Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride

Enzymatic activity of Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride

All present enzymatic activity of Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride:
3.2.1.76;

Protein crystallography data

The structure of Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride, PDB code: 4kgj was solved by H.Bie, J.Yin, X.He, A.R.Kermode, E.D.Goddard-Borger, S.G.Withers, M.N.G.James, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.05 / 2.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 259.343, 259.343, 71.379, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 22.7

Other elements in 4kgj:

The structure of Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride (pdb code 4kgj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride, PDB code: 4kgj:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4kgj

Go back to Fluorine Binding Sites List in 4kgj
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride


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 Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F911

b:59.5
occ:1.00
 F5 A:IDF911 0.0 59.5 1.0
C5 A:IDF911 1.4 58.7 1.0
O5 A:IDF911 2.3 60.8 1.0
C6 A:IDF911 2.4 58.2 1.0
C4 A:IDF911 2.4 58.1 1.0
O6B A:IDF911 2.5 57.7 1.0
C1 A:IDF911 2.8 60.3 1.0
F1 A:IDF911 2.9 59.7 1.0
C2 A:IDF911 3.0 60.2 1.0
C3 A:IDF911 3.2 58.2 1.0
O6A A:IDF911 3.4 57.4 1.0
O4 A:IDF911 3.7 55.6 1.0
O3 A:IDF911 3.9 57.1 1.0
O2 A:IDF911 4.4 61.8 1.0
CD1 A:TRP306 4.9 34.3 1.0

Fluorine binding site 2 out of 4 in 4kgj

Go back to Fluorine Binding Sites List in 4kgj
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride


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 Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F911

b:59.7
occ:1.00
 F1 A:IDF911 0.0 59.7 1.0
C1 A:IDF911 1.4 60.3 1.0
O5 A:IDF911 2.3 60.8 1.0
C2 A:IDF911 2.4 60.2 1.0
F5 A:IDF911 2.9 59.5 1.0
OE1 A:GLU182 3.1 39.0 1.0
O2 A:IDF911 3.1 61.8 1.0
C5 A:IDF911 3.1 58.7 1.0
C3 A:IDF911 3.7 58.2 1.0
CD A:GLU182 3.9 37.9 1.0
C4 A:IDF911 4.0 58.1 1.0
OE2 A:GLU182 4.1 38.9 1.0
C6 A:IDF911 4.3 58.2 1.0
OE1 A:GLU299 4.6 44.9 1.0
O3 A:IDF911 4.7 57.1 1.0
O6A A:IDF911 4.8 57.4 1.0
CG2 A:VAL304 4.9 31.8 1.0

Fluorine binding site 3 out of 4 in 4kgj

Go back to Fluorine Binding Sites List in 4kgj
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride


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 Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F920

b:54.8
occ:1.00
 F5 B:IDF920 0.0 54.8 1.0
C5 B:IDF920 1.4 52.5 1.0
O5 B:IDF920 2.3 54.0 1.0
C6 B:IDF920 2.3 51.2 1.0
C4 B:IDF920 2.5 52.1 1.0
O6B B:IDF920 2.6 50.5 1.0
O3 B:MAN910 2.6 0.9 1.0
F1 B:IDF920 2.8 53.1 1.0
C1 B:IDF920 2.8 53.2 1.0
C2 B:IDF920 3.1 52.4 1.0
C4 B:MAN910 3.2 0.3 1.0
C3 B:IDF920 3.2 51.7 1.0
O6A B:IDF920 3.3 49.0 1.0
O4 B:MAN910 3.4 0.5 1.0
C3 B:MAN910 3.4 1.0 1.0
O4 B:IDF920 3.7 51.1 1.0
O2 B:MAN910 3.9 0.3 1.0
O3 B:IDF920 4.1 49.8 1.0
C2 B:MAN910 4.3 1.0 1.0
O2 B:IDF920 4.5 51.6 1.0
C5 B:MAN910 4.6 0.5 1.0
NZ B:LYS264 4.8 29.9 1.0
CD1 B:TRP306 4.9 26.6 1.0
N B:GLY305 5.0 28.0 1.0

Fluorine binding site 4 out of 4 in 4kgj

Go back to Fluorine Binding Sites List in 4kgj
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride


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 Alpha-L-Iduronidase Complex with 5-Fluoro- Alpha-L-Idopyranosyluronic Acid Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F920

b:53.1
occ:1.00
 F1 B:IDF920 0.0 53.1 1.0
C1 B:IDF920 1.4 53.2 1.0
O5 B:IDF920 2.3 54.0 1.0
C2 B:IDF920 2.4 52.4 1.0
F5 B:IDF920 2.8 54.8 1.0
OE1 B:GLU182 2.9 44.7 1.0
C5 B:IDF920 3.1 52.5 1.0
O2 B:IDF920 3.1 51.6 1.0
O3 B:MAN910 3.4 0.9 1.0
OE2 B:GLU182 3.5 45.0 1.0
CD B:GLU182 3.5 43.8 1.0
C3 B:IDF920 3.7 51.7 1.0
C4 B:IDF920 3.9 52.1 1.0
C6 B:IDF920 4.3 51.2 1.0
OE1 B:GLU299 4.5 44.0 1.0
O3 B:IDF920 4.7 49.8 1.0
C3 B:MAN910 4.7 1.0 1.0
O6A B:IDF920 4.8 49.0 1.0
ND2 B:ASN181 4.8 35.5 1.0
CG B:GLU182 4.9 41.6 1.0
NZ B:LYS264 4.9 29.9 1.0

Reference:

H.Bie, J.Yin, X.He, A.R.Kermode, E.D.Goddard-Borger, S.G.Withers, M.N.James. Insights Into Mucopolysaccharidosis I From the Structure and Action of Alpha-L-Iduronidase. Nat.Chem.Biol. V. 9 739 2013.
ISSN: ISSN 1552-4450
PubMed: 24036510
DOI: 10.1038/NCHEMBIO.1357
Page generated: Mon Jul 14 22:51:42 2025

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