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Fluorine in PDB 7cxd: Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group

Protein crystallography data

The structure of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group, PDB code: 7cxd was solved by A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.17 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.241, 58.712, 70.773, 90, 113.85, 90
R / Rfree (%) 22.6 / 24.8

Other elements in 7cxd:

The structure of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group also contains other interesting chemical elements:

Bromine (Br) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group (pdb code 7cxd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group, PDB code: 7cxd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7cxd

Go back to Fluorine Binding Sites List in 7cxd
Fluorine binding site 1 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:44.7
occ:1.00
F18 A:TD2302 0.0 44.7 1.0
C14 A:TD2302 1.3 34.7 1.0
C15 A:TD2302 2.4 29.6 1.0
C13 A:TD2302 2.4 29.5 1.0
H24 A:TD2302 2.6 29.4 1.0
H8 A:TD2302 2.6 29.4 1.0
O A:HOH404 2.7 40.8 1.0
ND2 A:ASN178 2.9 56.5 1.0
OE1 A:GLU177 3.2 29.9 1.0
C12 A:TD2302 3.6 28.4 1.0
C16 A:TD2302 3.6 29.5 1.0
CD A:GLU177 3.7 36.0 1.0
CG A:ASN178 3.9 69.2 1.0
C17 A:TD2302 4.1 29.5 1.0
CB A:ASN178 4.2 40.3 1.0
CG A:GLU177 4.2 26.5 1.0
OE2 A:GLU177 4.3 30.2 1.0
NH1 A:ARG198 4.5 24.1 1.0
H25 A:TD2302 4.5 29.4 1.0
O A:GLU177 4.6 39.9 1.0
C9 A:TD2302 4.8 26.2 1.0
C A:GLU177 4.9 39.7 1.0
OD1 A:ASN178 5.0 70.7 1.0
H22 A:TD2302 5.0 29.4 1.0

Fluorine binding site 2 out of 8 in 7cxd

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Fluorine binding site 2 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:41.0
occ:1.00
F28 A:TD2302 0.0 41.0 1.0
C26 A:TD2302 1.3 34.3 1.0
C27 A:TD2302 2.3 29.6 1.0
C25 A:TD2302 2.3 29.6 1.0
H30 A:TD2302 2.5 29.4 1.0
H29 A:TD2302 2.6 29.4 1.0
C22 A:TD2302 3.6 33.1 1.0
C24 A:TD2302 3.6 29.6 1.0
C23 A:TD2302 4.1 29.6 1.0
O D:HOH477 4.2 42.6 1.0
H28 A:TD2302 4.5 29.4 1.0
C10 A:TD2302 4.8 33.3 1.0
CG2 A:ILE249 4.8 31.7 1.0

Fluorine binding site 3 out of 8 in 7cxd

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Fluorine binding site 3 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:39.7
occ:1.00
F18 B:TD2302 0.0 39.7 1.0
C14 B:TD2302 1.3 33.2 1.0
C13 B:TD2302 2.3 29.4 1.0
C15 B:TD2302 2.4 29.5 1.0
H8 B:TD2302 2.5 29.4 1.0
H24 B:TD2302 2.6 29.4 1.0
O B:HOH406 2.7 43.5 1.0
ND2 B:ASN178 3.0 51.5 1.0
OE1 B:GLU177 3.2 36.9 1.0
C12 B:TD2302 3.6 29.4 1.0
C16 B:TD2302 3.6 29.5 1.0
CD B:GLU177 3.7 41.0 1.0
NH2 B:ARG180 3.8 44.7 1.0
C17 B:TD2302 4.1 29.5 1.0
CG B:ASN178 4.1 57.8 1.0
OE2 B:GLU177 4.2 37.4 1.0
CG B:GLU177 4.2 30.9 1.0
NH1 B:ARG198 4.5 31.6 1.0
H25 B:TD2302 4.5 29.4 1.0
CB B:ASN178 4.5 35.3 1.0
C9 B:TD2302 4.8 28.6 1.0
H22 B:TD2302 4.8 29.4 1.0
CZ B:ARG180 4.9 58.5 1.0
O B:GLU177 4.9 32.9 1.0

Fluorine binding site 4 out of 8 in 7cxd

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Fluorine binding site 4 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:46.5
occ:1.00
F28 B:TD2302 0.0 46.5 1.0
C26 B:TD2302 1.3 36.8 1.0
C27 B:TD2302 2.4 29.6 1.0
C25 B:TD2302 2.4 29.6 1.0
H30 B:TD2302 2.6 29.4 1.0
H29 B:TD2302 2.6 29.4 1.0
C22 B:TD2302 3.6 32.6 1.0
C24 B:TD2302 3.7 29.5 1.0
O B:HOH462 3.8 37.2 1.0
CD1 B:ILE249 3.8 44.4 1.0
C23 B:TD2302 4.2 29.6 1.0
H28 B:TD2302 4.5 29.4 1.0
C10 B:TD2302 4.8 32.3 1.0

Fluorine binding site 5 out of 8 in 7cxd

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Fluorine binding site 5 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F303

b:33.4
occ:1.00
F18 D:TD2303 0.0 33.4 1.0
C14 D:TD2303 1.3 30.5 1.0
C13 D:TD2303 2.4 29.4 1.0
C15 D:TD2303 2.4 29.4 1.0
H8 D:TD2303 2.6 29.4 1.0
H24 D:TD2303 2.6 29.4 1.0
ND2 D:ASN178 2.8 29.8 1.0
O D:HOH411 2.9 28.0 1.0
OE1 D:GLU177 3.0 26.0 1.0
CD D:GLU177 3.4 28.8 1.0
C12 D:TD2303 3.6 26.2 1.0
C16 D:TD2303 3.6 29.5 1.0
CG D:ASN178 3.8 40.1 1.0
CG D:GLU177 3.8 25.1 1.0
OE2 D:GLU177 4.1 24.2 1.0
C17 D:TD2303 4.1 29.5 1.0
CB D:ASN178 4.2 23.5 1.0
O D:GLU177 4.5 25.1 1.0
H25 D:TD2303 4.5 29.4 1.0
NH1 D:ARG198 4.6 19.3 1.0
CB D:GLU177 4.8 20.9 1.0
C D:GLU177 4.8 26.6 1.0
OD1 D:ASN178 4.8 40.7 1.0
C9 D:TD2303 4.8 26.5 1.0
H22 D:TD2303 4.9 29.4 1.0
O D:HOH475 4.9 26.2 1.0

Fluorine binding site 6 out of 8 in 7cxd

Go back to Fluorine Binding Sites List in 7cxd
Fluorine binding site 6 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F303

b:47.5
occ:1.00
F28 D:TD2303 0.0 47.5 1.0
C26 D:TD2303 1.3 37.0 1.0
C27 D:TD2303 2.3 29.7 1.0
C25 D:TD2303 2.4 29.6 1.0
H30 D:TD2303 2.5 29.4 1.0
H29 D:TD2303 2.7 29.4 1.0
C22 D:TD2303 3.6 32.0 1.0
C24 D:TD2303 3.6 29.6 1.0
C23 D:TD2303 4.1 29.6 1.0
CD1 D:ILE249 4.5 42.2 1.0
H28 D:TD2303 4.5 29.4 1.0
C10 D:TD2303 4.8 33.5 1.0
O D:HOH425 4.8 40.9 1.0
N9 D:TD2303 5.0 37.5 1.0

Fluorine binding site 7 out of 8 in 7cxd

Go back to Fluorine Binding Sites List in 7cxd
Fluorine binding site 7 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F302

b:39.0
occ:1.00
F18 E:TD2302 0.0 39.0 1.0
C14 E:TD2302 1.3 32.5 1.0
C13 E:TD2302 2.3 29.5 1.0
C15 E:TD2302 2.4 29.6 1.0
H8 E:TD2302 2.5 29.4 1.0
ND2 E:ASN178 2.6 50.6 1.0
H24 E:TD2302 2.6 29.4 1.0
OE1 E:GLU177 3.2 30.7 1.0
CG E:ASN178 3.3 59.9 1.0
O E:HOH413 3.4 36.1 1.0
CD E:GLU177 3.4 32.6 1.0
NH2 E:ARG180 3.4 44.0 1.0
CB E:ASN178 3.5 27.7 1.0
C12 E:TD2302 3.6 28.4 1.0
CG E:GLU177 3.6 21.9 1.0
C16 E:TD2302 3.6 29.5 1.0
OE2 E:GLU177 4.1 22.6 1.0
C17 E:TD2302 4.1 29.5 1.0
OD1 E:ASN178 4.2 60.0 1.0
O E:GLU177 4.3 28.6 1.0
C E:GLU177 4.4 28.8 1.0
H25 E:TD2302 4.5 29.4 1.0
N E:ASN178 4.6 28.5 1.0
CZ E:ARG180 4.6 70.4 1.0
CB E:GLU177 4.6 23.5 1.0
CA E:ASN178 4.7 28.1 1.0
C9 E:TD2302 4.8 28.9 1.0
NH1 E:ARG198 4.8 27.7 1.0
H22 E:TD2302 4.8 29.4 1.0

Fluorine binding site 8 out of 8 in 7cxd

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Fluorine binding site 8 out of 8 in the Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Xray Structure of Rat Galectin-3 Crd in Complex with Td-139 Belonging to P121 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F302

b:47.0
occ:1.00
F28 E:TD2302 0.0 47.0 1.0
C26 E:TD2302 1.3 36.2 1.0
C27 E:TD2302 2.3 29.6 1.0
C25 E:TD2302 2.4 29.6 1.0
H30 E:TD2302 2.6 29.4 1.0
H29 E:TD2302 2.6 29.4 1.0
C22 E:TD2302 3.6 31.9 1.0
C24 E:TD2302 3.6 29.5 1.0
C23 E:TD2302 4.1 29.5 1.0
H28 E:TD2302 4.5 29.4 1.0
C10 E:TD2302 4.8 33.8 1.0
H23 E:TD2302 4.9 29.4 1.0

Reference:

A.Kumar, M.Paul, M.Panda, S.Jayaram, N.Kalidindi, H.Sale, M.Vetrichelvan, A.Gupta, A.Mathur, B.Beno, A.Regueiro-Ren, D.Cheng, M.Ramarao, K.Ghosh. Molecular Mechanism of Interspecies Differences in the Binding Affinity of TD139 to Galectin-3. Glycobiology 2021.
ISSN: ESSN 1460-2423
PubMed: 34228782
DOI: 10.1093/GLYCOB/CWAB072
Page generated: Fri Aug 2 06:18:29 2024

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