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Fluorine in PDB 1kjr: Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine

Protein crystallography data

The structure of Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine, PDB code: 1kjr was solved by P.Sorme, P.Arnoux, B.Kahl-Knutsson, H.Leffler, J.M.Rini, U.J.Nilsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.600, 58.400, 64.000, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.2

Other elements in 1kjr:

The structure of Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine (pdb code 1kjr). 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 the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine, PDB code: 1kjr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 1kjr

Go back to Fluorine Binding Sites List in 1kjr
Fluorine binding site 1 out of 4 in the Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine


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 Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:27.0
occ:1.00
F3 A:BEK500 0.0 27.0 1.0
C3 A:BEK500 1.2 24.3 1.0
C4 A:BEK500 2.3 24.9 1.0
C2 A:BEK500 2.3 21.6 1.0
F4 A:BEK500 2.5 29.1 1.0
C1 A:BEK500 2.7 20.5 1.0
O A:BEK500 2.9 22.2 1.0
C5 A:BEK500 3.6 25.4 1.0
C7 A:BEK500 3.6 21.6 1.0
N A:BEK500 3.7 19.0 1.0
O A:HOH770 3.8 31.1 1.0
O A:HOH790 4.1 36.1 1.0
C6 A:BEK500 4.1 22.4 1.0
NH1 A:ARG144 4.3 25.5 1.0
NH2 A:ARG144 4.4 28.0 1.0
O5 A:BEK500 4.5 27.7 1.0
O A:HOH769 4.6 32.4 1.0
CZ A:ARG144 4.6 25.8 1.0
F7 A:BEK500 4.6 20.8 1.0
O A:HOH674 4.7 23.4 1.0
O A:HOH613 4.8 17.6 1.0
C3 A:GAL501 4.9 15.5 1.0

Fluorine binding site 2 out of 4 in 1kjr

Go back to Fluorine Binding Sites List in 1kjr
Fluorine binding site 2 out of 4 in the Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine


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 Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:20.8
occ:1.00
F7 A:BEK500 0.0 20.8 1.0
C7 A:BEK500 1.2 21.6 1.0
C6 A:BEK500 2.3 22.4 1.0
C2 A:BEK500 2.4 21.6 1.0
F6 A:BEK500 2.5 21.9 1.0
C1 A:BEK500 2.9 20.5 1.0
N A:BEK500 3.0 19.0 1.0
O A:HOH691 3.0 22.6 1.0
CE1 A:HIS158 3.2 13.3 1.0
OD1 A:ASN160 3.3 15.3 1.0
ND2 A:ASN160 3.3 13.3 1.0
CG A:ASN160 3.4 14.1 1.0
NE2 A:HIS158 3.5 13.0 1.0
O4 A:GAL501 3.5 13.7 1.0
C5 A:BEK500 3.6 25.4 1.0
C3 A:BEK500 3.7 24.3 1.0
O A:HOH613 3.7 17.6 1.0
O A:BEK500 4.1 22.2 1.0
CB A:ALA146 4.1 12.6 1.0
C4 A:BEK500 4.1 24.9 1.0
NH1 A:ARG144 4.1 25.5 1.0
C3 A:GAL501 4.1 15.5 1.0
C4 A:GAL501 4.2 14.5 1.0
CB A:ASN160 4.2 13.4 1.0
ND1 A:HIS158 4.5 11.4 1.0
CD A:ARG144 4.5 25.3 1.0
O5 A:BEK500 4.6 27.7 1.0
F3 A:BEK500 4.6 27.0 1.0
CZ A:ARG144 4.8 25.8 1.0
CD2 A:HIS158 4.8 12.3 1.0
O A:HOH674 4.9 23.4 1.0
NE A:ARG144 4.9 27.5 1.0

Fluorine binding site 3 out of 4 in 1kjr

Go back to Fluorine Binding Sites List in 1kjr
Fluorine binding site 3 out of 4 in the Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine


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 the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:29.1
occ:1.00
F4 A:BEK500 0.0 29.1 1.0
C4 A:BEK500 1.1 24.9 1.0
C3 A:BEK500 2.2 24.3 1.0
C5 A:BEK500 2.2 25.4 1.0
F3 A:BEK500 2.5 27.0 1.0
O5 A:BEK500 2.5 27.7 1.0
C2 A:BEK500 3.5 21.6 1.0
NH2 A:ARG144 3.5 28.0 1.0
C6 A:BEK500 3.6 22.4 1.0
O A:HOH791 3.6 36.9 1.0
O A:HOH674 3.8 23.4 1.0
O A:HOH790 3.8 36.1 1.0
C8 A:BEK500 3.9 29.5 1.0
O A:HOH768 4.0 36.4 1.0
O A:HOH767 4.0 37.0 1.0
CZ A:ARG144 4.0 25.8 1.0
C7 A:BEK500 4.0 21.6 1.0
NH1 A:ARG144 4.4 25.5 1.0
F6 A:BEK500 4.5 21.9 1.0
C1 A:BEK500 4.6 20.5 1.0
NE A:ARG144 4.6 27.5 1.0

Fluorine binding site 4 out of 4 in 1kjr

Go back to Fluorine Binding Sites List in 1kjr
Fluorine binding site 4 out of 4 in the Crystal Structure of the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine


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 the Human Galectin-3 Crd in Complex with A 3'- Derivative of N-Acetyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:21.9
occ:1.00
F6 A:BEK500 0.0 21.9 1.0
C6 A:BEK500 1.1 22.4 1.0
C7 A:BEK500 2.2 21.6 1.0
C5 A:BEK500 2.3 25.4 1.0
F7 A:BEK500 2.5 20.8 1.0
O5 A:BEK500 2.7 27.7 1.0
C8 A:BEK500 2.8 29.5 1.0
CB A:ALA146 3.5 12.6 1.0
CD A:ARG144 3.5 25.3 1.0
C2 A:BEK500 3.5 21.6 1.0
C4 A:BEK500 3.6 24.9 1.0
ND2 A:ASN160 3.6 13.3 1.0
CG A:ARG144 3.6 24.1 1.0
NE A:ARG144 3.8 27.5 1.0
O A:HOH674 4.0 23.4 1.0
C3 A:BEK500 4.1 24.3 1.0
CB A:ARG144 4.1 20.6 1.0
O A:ILE145 4.2 12.4 1.0
CZ A:ARG144 4.2 25.8 1.0
C A:ILE145 4.3 13.4 1.0
O A:HOH613 4.3 17.6 1.0
N A:ALA146 4.3 12.6 1.0
NH1 A:ARG144 4.3 25.5 1.0
O A:HOH691 4.3 22.6 1.0
CG A:ASN160 4.4 14.1 1.0
CA A:ALA146 4.4 12.4 1.0
F4 A:BEK500 4.5 29.1 1.0
N A:ILE145 4.7 13.6 1.0
C1 A:BEK500 4.8 20.5 1.0
OG A:SER237 4.8 14.6 1.0
OD1 A:ASN160 4.8 15.3 1.0
C A:ARG144 4.9 15.4 1.0
CA A:ILE145 5.0 14.1 1.0

Reference:

P.Sorme, P.Arnoux, B.Kahl-Knutsson, H.Leffler, J.M.Rini, U.J.Nilsson. Structural and Thermodynamic Studies on Cation-Pi Interactions in Lectin-Ligand Complexes: High-Affinity Galectin-3 Inhibitors Through Fine-Tuning of An Arginine-Arene Interaction. J.Am.Chem.Soc. V. 127 1737 2005.
ISSN: ISSN 0002-7863
PubMed: 15701008
DOI: 10.1021/JA043475P
Page generated: Sun Dec 13 11:30:40 2020

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