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Chlorine in PDB 6ury: Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide

Enzymatic activity of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide

All present enzymatic activity of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide:
3.2.2.22;

Protein crystallography data

The structure of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide, PDB code: 6ury was solved by R.K.Harijan, X.P.Li, J.B.Bonanno, S.C.Almo, N.E.Tumer, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.14 / 1.54
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.228, 66.228, 264.571, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.5

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide (pdb code 6ury). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 16 binding sites of Chlorine where determined in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide, PDB code: 6ury:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 16 in 6ury

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Chlorine binding site 1 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl319

b:19.6
occ:1.00
 O A:HOH585 2.9 35.4 1.0
N A:GLY120 3.2 12.6 1.0
NE A:ARG125 3.2 17.8 1.0
O A:HOH520 3.4 18.7 1.0
OD1 A:ASN122 3.5 18.9 1.0
NH2 A:ARG125 3.7 20.2 1.0
CG A:ARG125 3.8 14.6 1.0
CZ A:ARG125 3.9 18.9 1.0
CA A:PHE119 3.9 11.5 1.0
CA A:GLY120 3.9 12.6 1.0
CB A:ARG125 4.0 12.4 1.0
C A:PHE119 4.1 12.2 1.0
CD A:ARG125 4.1 15.7 1.0
CB A:PHE119 4.2 12.1 1.0
O A:HOH562 4.4 27.9 1.0
O A:GLY120 4.5 12.5 1.0
C A:GLY120 4.6 11.7 1.0
CG A:ASN122 4.6 14.8 1.0
O A:HOH682 4.9 49.0 1.0
ND2 A:ASN122 4.9 15.2 1.0

Chlorine binding site 2 out of 16 in 6ury

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Chlorine binding site 2 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl320

b:16.2
occ:1.00
 O A:HOH734 3.1 25.9 1.0
O A:HOH509 3.1 14.6 1.0
O A:HOH511 3.2 16.8 1.0
NE A:ARG114 3.3 13.6 1.0
NH2 A:ARG114 3.3 12.2 1.0
CZ A:ARG114 3.7 12.6 1.0
CG2 A:THR105 3.9 13.5 1.0
CA A:THR105 3.9 12.0 1.0
N A:THR105 4.1 11.7 1.0
O A:ILE104 4.1 12.2 1.0
C A:ILE104 4.2 11.9 1.0
CE2 A:PHE92 4.3 10.8 1.0
CG1 A:ILE104 4.3 15.0 1.0
CB A:THR105 4.4 12.4 1.0
O A:HOH736 4.4 31.7 1.0
CD1 A:ILE104 4.4 15.8 1.0
CD A:ARG114 4.4 14.9 1.0
CD2 A:PHE92 4.5 11.1 1.0
OG1 A:THR116 4.6 12.3 1.0
O A:HOH573 4.7 23.9 1.0
O A:HOH755 4.7 29.9 1.0
O A:HOH739 4.9 21.7 1.0

Chlorine binding site 3 out of 16 in 6ury

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Chlorine binding site 3 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl321

b:25.3
occ:1.00
 N A:GLY15 3.1 15.7 1.0
NE2 A:HIS65 3.1 13.3 1.0
O A:HOH485 3.2 27.6 1.0
N B:GLN98 3.4 26.0 1.0
CA A:GLY15 3.5 16.0 1.0
CG B:GLN98 3.6 31.6 1.0
O A:HOH722 3.7 36.9 1.0
CE1 A:HIS65 3.7 14.2 1.0
CA B:ASN97 3.8 27.0 1.0
C B:ASN97 4.0 27.0 1.0
CB B:GLN98 4.1 29.8 1.0
O A:THR13 4.2 12.8 1.0
CD B:GLN98 4.2 32.4 1.0
C A:ALA14 4.2 14.8 1.0
C A:GLY15 4.3 15.2 1.0
CB B:ASN97 4.3 28.8 1.0
CA B:GLN98 4.3 26.4 1.0
N A:ALA16 4.3 14.7 1.0
CD2 A:HIS65 4.3 12.8 1.0
NE2 B:GLN98 4.4 32.6 1.0
CA A:ALA14 4.6 13.4 1.0
O B:HOH405 4.7 32.3 1.0
O B:HOH637 4.8 46.4 1.0
OE1 B:GLN98 4.9 34.0 1.0
N B:ASN97 5.0 25.3 1.0
ND1 A:HIS65 5.0 12.6 1.0
O B:ASP96 5.0 27.2 1.0

Chlorine binding site 4 out of 16 in 6ury

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Chlorine binding site 4 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl322

b:22.2
occ:1.00
 O A:HOH725 2.9 24.3 1.0
O A:HOH655 3.0 24.9 1.0
N A:PHE108 3.0 11.1 1.0
O A:HOH515 3.2 21.8 1.0
O A:HOH548 3.5 36.6 1.0
CA A:PHE108 3.8 10.6 1.0
CD1 A:LEU59 3.8 11.7 1.0
CD2 A:TYR6 3.8 16.9 1.0
CD1 A:PHE108 3.9 10.3 1.0
C A:LEU107 4.0 10.8 1.0
CA A:LEU107 4.0 10.6 1.0
CD2 A:LEU107 4.1 10.9 1.0
CD2 A:LEU59 4.3 11.5 1.0
CE1 A:PHE108 4.4 10.5 1.0
O A:HIS106 4.4 11.8 1.0
CE2 A:TYR6 4.4 18.2 1.0
CG A:PHE108 4.5 10.0 1.0
CG A:LEU59 4.6 10.8 1.0
CB A:LEU107 4.7 10.6 1.0
CB A:PHE108 4.8 10.4 1.0
N A:THR109 4.8 12.8 1.0
O A:HOH552 4.8 18.6 1.0
C A:PHE108 4.9 11.7 1.0
CG A:TYR6 4.9 15.5 1.0

Chlorine binding site 5 out of 16 in 6ury

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Chlorine binding site 5 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl323

b:21.9
occ:1.00
 O A:HOH565 3.0 15.5 1.0
NH1 A:ARG197 3.3 30.0 1.0
NE A:ARG197 3.4 27.1 1.0
CZ A:ARG197 3.8 28.7 1.0
CG A:PRO143 3.8 8.9 1.0
CB A:GLU138 4.1 13.8 1.0
OE1 A:GLU138 4.1 18.9 1.0
CB A:PRO143 4.3 8.7 1.0
NH2 A:ARG166 4.5 12.2 0.5
CA A:PRO143 4.5 8.8 1.0
CD A:ARG197 4.6 26.2 1.0
O2 A:EDO305 4.6 30.7 1.0
C2 A:EDO305 4.6 33.8 1.0
CD A:GLU138 4.7 18.6 1.0
OE1 A:GLU146 4.7 11.9 1.0
CD A:PRO143 4.8 8.9 1.0
CG A:GLU138 4.8 15.5 1.0
O A:GLU138 4.8 10.8 1.0
N A:PRO143 5.0 8.7 1.0

Chlorine binding site 6 out of 16 in 6ury

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Chlorine binding site 6 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl324

b:31.2
occ:1.00
 N A:ASP124 3.2 12.2 1.0
OD1 A:ASP124 3.2 23.6 1.0
CG A:ASP124 3.4 19.4 1.0
O A:HOH514 3.4 21.2 1.0
N A:TYR123 3.5 10.5 1.0
OD2 A:ASP124 3.8 22.6 1.0
CB A:ASP124 3.9 15.4 1.0
CB A:ASN122 3.9 12.9 1.0
CB A:TYR123 4.0 11.3 1.0
CA A:TYR123 4.0 11.0 1.0
C A:TYR123 4.0 11.3 1.0
CA A:ASP124 4.1 13.5 1.0
O A:HOH563 4.1 12.8 1.0
C A:ASN122 4.2 11.0 1.0
ND2 A:ASN122 4.2 15.2 1.0
O A:HOH685 4.4 38.6 1.0
CA A:ASN122 4.5 11.8 1.0
O A:HOH754 4.5 14.1 1.0
O A:HOH738 4.6 52.5 1.0
CG A:ASN122 4.6 14.8 1.0
O A:HOH476 4.7 16.3 1.0
CD2 A:TYR123 4.8 11.2 1.0
CG A:TYR123 4.8 11.6 1.0
O A:HOH574 5.0 32.8 1.0

Chlorine binding site 7 out of 16 in 6ury

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Chlorine binding site 7 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl325

b:26.4
occ:1.00
 O A:HOH707 3.1 35.5 1.0
N A:ALA199 3.1 13.4 1.0
O A:HOH579 3.2 39.1 1.0
O A:HOH723 3.3 45.9 1.0
CA A:SER198 3.7 15.6 1.0
CB A:ALA199 3.8 13.7 1.0
C A:SER198 3.9 13.9 1.0
CB A:SER198 4.0 17.9 1.0
CA A:ALA199 4.0 13.2 1.0
O A:HOH433 4.3 37.0 1.0
CG A:GLU138 4.3 15.5 1.0
OE2 A:GLU138 4.4 19.7 1.0
O A:HOH412 4.5 25.2 1.0
O A:ALA199 4.7 13.2 1.0
CD A:GLU138 4.8 18.6 1.0
C A:ALA199 4.9 12.6 1.0
O A:HOH452 4.9 33.8 1.0
O A:ARG197 4.9 22.0 1.0
N A:SER198 4.9 16.4 1.0
O A:HOH660 5.0 44.7 1.0

Chlorine binding site 8 out of 16 in 6ury

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Chlorine binding site 8 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl326

b:21.0
occ:1.00
 OD1 A:ASN136 3.2 23.5 1.0
N A:LEU133 3.2 12.7 1.0
OD1 A:ASN132 3.4 20.9 1.0
CA A:ASN132 3.6 13.1 1.0
CB A:ASN136 3.9 15.5 1.0
C A:ASN132 3.9 12.4 1.0
CG A:ASN136 3.9 18.1 1.0
CG A:LEU133 4.0 14.5 1.0
CB A:ASN132 4.0 14.2 1.0
CB A:LEU133 4.0 13.3 1.0
CG A:ASN132 4.1 17.2 1.0
CA A:LEU133 4.2 12.4 1.0
O2 A:EDO308 4.3 40.1 1.0
CD1 A:LEU133 4.5 15.7 1.0
O A:GLY131 4.5 14.6 1.0
O A:LEU133 4.6 11.6 1.0
N A:ASN132 4.8 13.6 1.0
C A:LEU133 4.9 11.8 1.0

Chlorine binding site 9 out of 16 in 6ury

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Chlorine binding site 9 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl327

b:27.1
occ:1.00
 O A:HOH422 3.1 31.4 1.0
O A:HOH486 3.1 33.2 1.0
N A:TYR243 3.2 19.2 1.0
N A:ASP244 3.8 18.6 1.0
CA A:VAL242 3.9 20.0 1.0
CA A:TYR243 4.0 19.6 1.0
CG1 A:VAL242 4.0 21.1 1.0
CB A:TYR243 4.1 20.9 1.0
C A:VAL242 4.1 18.1 1.0
CG2 A:ILE247 4.1 21.0 1.0
C A:TYR243 4.3 19.2 1.0
O A:ASP244 4.3 17.2 1.0
CD2 A:TYR243 4.3 27.4 1.0
CB A:ASP244 4.4 20.3 1.0
CB A:VAL242 4.5 20.5 1.0
CA A:ASP244 4.6 18.8 1.0
O A:SER241 4.6 21.7 1.0
CB A:ILE247 4.7 21.0 1.0
CG A:TYR243 4.7 24.4 1.0
C A:ASP244 4.9 19.0 1.0
CD1 A:ILE247 5.0 24.6 1.0
CG2 A:VAL242 5.0 21.5 1.0

Chlorine binding site 10 out of 16 in 6ury

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Chlorine binding site 10 out of 16 in the Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Ricin A Chain in Complex with Inhibitor 9-Oxo-4- Fluorenecarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl328

b:23.5
occ:1.00
 ND1 A:HIS106 3.0 14.5 1.0
CE1 A:HIS106 3.8 14.3 1.0
CB A:PRO3 4.0 17.8 1.0
CG A:HIS106 4.1 12.7 1.0
CG A:PRO3 4.2 18.6 1.0
CG2 A:ILE53 4.4 19.8 1.0
CB A:HIS106 4.4 12.5 1.0
CA A:PRO3 4.6 17.2 1.0
OD1 A:ASN54 4.9 23.0 1.0

Reference:

X.P.Li, R.K.Harijan, J.N.Kahn, V.L.Schramm, N.E.Tumer. Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes. Acs Infect Dis. 2020.
ISSN: ESSN 2373-8227
PubMed: 32428396
DOI: 10.1021/ACSINFECDIS.0C00127
Page generated: Mon Jul 29 15:58:44 2024

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