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Chlorine in PDB 7y1w: Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Enzymatic activity of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

All present enzymatic activity of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1:
6.1.1.15; 6.1.1.17;

Protein crystallography data

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1w was solved by S.Kim, I.Yoon, J.Son, S.Park, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.22 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.556, 92.147, 86.728, 90, 108.77, 90
R / Rfree (%) 22.9 / 28.9

Other elements in 7y1w:

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 (pdb code 7y1w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1w:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7y1w

Go back to Chlorine Binding Sites List in 7y1w
Chlorine binding site 1 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1602

b:108.0
occ:1.00
 CL A:F9O1602 0.0 108.0 1.0
C14 A:F9O1602 1.7 88.3 1.0
C9 A:F9O1602 2.7 69.0 1.0
C13 A:F9O1602 2.7 89.2 1.0
OE1 A:GLU1100 3.1 88.0 1.0
CL1 A:F9O1602 3.1 108.9 1.0
N2 A:F9O1602 3.2 65.0 1.0
CD A:ARG1152 3.4 51.2 1.0
CB A:GLU1100 3.8 71.5 1.0
NE A:ARG1152 3.9 57.3 1.0
C10 A:F9O1602 4.0 69.3 1.0
C12 A:F9O1602 4.0 75.3 1.0
CD1 A:PHE1097 4.0 78.0 1.0
CB A:PRO1120 4.0 45.2 1.0
CG A:PHE1097 4.1 79.5 1.0
CD A:GLU1100 4.2 92.1 1.0
CB A:PHE1097 4.3 75.5 1.0
O A:PHE1097 4.4 81.9 1.0
C8 A:F9O1602 4.5 66.7 1.0
CE1 A:PHE1097 4.5 80.8 1.0
C11 A:F9O1602 4.5 66.4 1.0
CZ A:ARG1152 4.6 64.5 1.0
CG A:GLU1100 4.6 84.3 1.0
CD2 A:PHE1097 4.6 78.6 1.0
CG A:ARG1152 4.7 54.2 1.0
NH1 A:ARG1152 4.8 70.5 1.0
CA A:PHE1097 4.8 75.1 1.0
CG A:PRO1120 4.8 51.0 1.0
O A:GLU1100 4.9 55.3 1.0
N1 A:F9O1602 4.9 63.6 1.0

Chlorine binding site 2 out of 4 in 7y1w

Go back to Chlorine Binding Sites List in 7y1w
Chlorine binding site 2 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1602

b:108.9
occ:1.00
 CL1 A:F9O1602 0.0 108.9 1.0
C13 A:F9O1602 1.7 89.2 1.0
C12 A:F9O1602 2.7 75.3 1.0
C14 A:F9O1602 2.7 88.3 1.0
CL A:F9O1602 3.1 108.0 1.0
CG A:PRO1120 3.2 51.0 1.0
CG2 A:VAL1101 3.5 53.4 1.0
CB A:PRO1120 3.6 45.2 1.0
O A:PHE1097 3.7 81.9 1.0
CB A:PHE1097 3.8 75.5 1.0
C11 A:F9O1602 4.0 66.4 1.0
C9 A:F9O1602 4.0 69.0 1.0
CG A:PHE1097 4.4 79.5 1.0
C A:PHE1097 4.4 74.6 1.0
C10 A:F9O1602 4.5 69.3 1.0
CG A:HIS1093 4.6 90.3 1.0
CD A:PRO1120 4.6 43.2 1.0
CD2 A:PHE1097 4.7 78.6 1.0
CD2 A:HIS1093 4.7 96.3 1.0
CA A:PHE1097 4.7 75.1 1.0
ND1 A:HIS1093 4.8 89.5 1.0
CB A:HIS1093 4.8 90.0 1.0
CA A:PRO1120 5.0 40.3 1.0
CB A:VAL1101 5.0 51.7 1.0

Chlorine binding site 3 out of 4 in 7y1w

Go back to Chlorine Binding Sites List in 7y1w
Chlorine binding site 3 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1602

b:91.7
occ:0.68
 CL B:F9O1602 0.0 91.7 0.7
C14 B:F9O1602 1.7 86.6 1.0
C9 B:F9O1602 2.7 78.8 1.0
C13 B:F9O1602 2.7 89.7 1.0
CL1 B:F9O1602 3.1 102.1 0.8
N2 B:F9O1602 3.2 74.7 1.0
CD B:ARG1152 3.5 47.5 1.0
OE1 B:GLU1100 3.5 111.0 1.0
CG B:ARG1152 3.6 48.0 1.0
NE B:ARG1152 3.7 57.4 1.0
CD B:GLU1100 3.9 103.9 1.0
CB B:GLU1100 4.0 70.4 1.0
C10 B:F9O1602 4.0 76.6 1.0
C12 B:F9O1602 4.0 87.5 1.0
CE1 B:PHE1097 4.2 122.8 1.0
CB B:ARG1152 4.2 61.1 1.0
CD1 B:PHE1097 4.3 122.5 1.0
OE2 B:GLU1100 4.3 105.0 1.0
CZ B:ARG1152 4.3 63.3 1.0
C8 B:F9O1602 4.5 69.0 1.0
CG B:GLU1100 4.5 84.8 1.0
C11 B:F9O1602 4.5 79.0 1.0
CZ B:PHE1097 4.7 117.5 1.0
NH1 B:ARG1152 4.7 66.5 1.0
CB B:PRO1120 4.8 47.7 1.0
CG B:PHE1097 4.8 120.8 1.0
N1 B:F9O1602 4.9 68.4 1.0

Chlorine binding site 4 out of 4 in 7y1w

Go back to Chlorine Binding Sites List in 7y1w
Chlorine binding site 4 out of 4 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1602

b:102.1
occ:0.84
 CL1 B:F9O1602 0.0 102.1 0.8
C13 B:F9O1602 1.7 89.7 1.0
C12 B:F9O1602 2.7 87.5 1.0
C14 B:F9O1602 2.7 86.6 1.0
CL B:F9O1602 3.1 91.7 0.7
CG2 B:VAL1101 3.6 65.9 1.0
CB B:PRO1120 3.7 47.7 1.0
O B:PHE1097 3.7 110.5 1.0
CG B:PRO1120 3.9 54.5 1.0
C11 B:F9O1602 4.0 79.0 1.0
C9 B:F9O1602 4.0 78.8 1.0
CB B:PHE1097 4.2 122.0 1.0
CG B:PHE1097 4.4 120.8 1.0
C10 B:F9O1602 4.5 76.6 1.0
CB B:GLU1100 4.5 70.4 1.0
C B:PHE1097 4.6 112.5 1.0
CD1 B:PHE1097 4.6 122.5 1.0
CA B:PHE1097 4.8 124.5 1.0
C B:GLU1100 4.9 72.0 1.0

Reference:

S.Kim, K.Hwang, I.Yoon. Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl-Trna Synthetase 1 To Be Published.
Page generated: Sun Jul 13 08:31:52 2025

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