Chlorine in PDB 8i6b: Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I:
3.2.2.27;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I, PDB code: 8i6b was solved by P.Raj, A.Paul, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.49 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.16, 63.68, 45.19, 90, 112.58, 90
R / Rfree (%) 14.9 / 18.2

Other elements in 8i6b:

The structure of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I (pdb code 8i6b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I, PDB code: 8i6b:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8i6b

Go back to Chlorine Binding Sites List in 8i6b
Chlorine binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I


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 Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:33.9
occ:1.00
 NA A:NA308 2.8 23.0 1.0
O A:VAL123 3.0 8.7 1.0
O A:ALA119 3.0 8.3 1.0
O A:HOH527 3.3 22.9 1.0
CB A:PHE55 3.4 10.3 1.0
C A:VAL123 3.5 7.8 1.0
O A:HOH431 3.8 16.7 1.0
N A:LEU124 3.9 7.5 1.0
CA A:LEU124 3.9 7.8 1.0
C A:ALA119 3.9 7.0 1.0
CA A:ALA119 4.0 7.1 1.0
N A:VAL123 4.0 6.9 1.0
CG A:PHE55 4.1 10.2 1.0
C A:GLY122 4.3 7.4 1.0
CG2 A:VAL60 4.3 8.3 1.0
CA A:GLY122 4.4 8.7 1.0
CB A:ALA119 4.4 6.9 1.0
CA A:VAL123 4.4 7.3 1.0
CB A:LEU124 4.5 8.4 1.0
CD2 A:PHE55 4.7 9.9 1.0
CD1 A:PHE55 4.7 10.1 1.0
N A:GLY122 4.7 8.3 1.0
CA A:PHE55 4.7 9.7 1.0
CD1 A:LEU124 4.7 12.4 1.0
O A:ALA52 4.8 8.0 1.0
C A:PHE55 4.9 10.3 1.0
O A:GLY122 4.9 7.5 1.0

Chlorine binding site 2 out of 3 in 8i6b

Go back to Chlorine Binding Sites List in 8i6b
Chlorine binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I


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 Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:19.6
occ:1.00
 O A:HOH517 3.0 20.0 1.0
N A:ARG41 3.1 11.4 1.0
O A:HOH503 3.1 19.1 1.0
NE A:ARG133 3.2 12.9 1.0
O A:HOH673 3.6 40.8 1.0
CG A:ARG133 3.7 10.0 1.0
CB A:ARG41 3.7 14.8 1.0
CA A:ARG40 3.7 10.2 1.0
NH2 A:ARG133 3.9 15.1 1.0
C A:ARG40 3.9 10.5 1.0
CG A:ARG41 3.9 18.4 1.0
CA A:ARG41 4.0 12.4 1.0
CZ A:ARG133 4.0 13.5 1.0
CD A:ARG133 4.1 11.7 1.0
C2 A:DMS303 4.1 18.9 1.0
CB A:ARG40 4.2 9.6 1.0
CD A:PRO134 4.2 7.9 1.0
O A:ARG41 4.3 10.4 1.0
CG A:PRO134 4.5 8.7 1.0
C A:ARG41 4.6 10.1 1.0
O A:GLY39 4.6 10.8 1.0
CG A:ARG40 4.7 10.4 1.0
CB A:PRO134 4.8 8.4 1.0
O A:HOH609 4.9 23.8 1.0
N A:ARG40 5.0 9.1 1.0
N A:PRO134 5.0 8.0 1.0

Chlorine binding site 3 out of 3 in 8i6b

Go back to Chlorine Binding Sites List in 8i6b
Chlorine binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I


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 Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with 5-Hydroxy-2,4(1H,3H)-Pyrimidinedione, Form I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:37.4
occ:1.00
 OE2 A:GLU212 3.2 22.5 1.0
O A:GLU212 3.5 11.7 1.0
CA A:GLY216 3.8 15.5 1.0
CD A:GLU212 4.0 20.7 1.0
CG A:GLU212 4.0 17.9 1.0
C A:GLU212 4.2 10.8 1.0
CA A:LEU213 4.3 8.7 1.0
CD2 A:LEU213 4.3 9.2 1.0
N A:GLY216 4.4 15.2 1.0
N A:LEU213 4.5 9.0 1.0
O A:LEU213 4.8 9.9 1.0
C A:GLY216 4.9 15.9 1.0
C A:LEU213 5.0 9.1 1.0

Reference:

S.Kesharwani, P.Raj, A.Paul, K.Roy, A.Bhanot, A.Mehta, A.Gopal, U.Varshney, B.Gopal, S.Sundriyal. Crystal Structures of Non-Uracil Ring Fragments in Complex with Mycobacterium Tuberculosis Uracil Dna Glycosylase (Mtung) As A Starting Point For Novel Inhibitor Design: A Case Study with the Barbituric Acid Fragment Eur.J.Med.Chem. V. 258 15604 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115604
Page generated: Tue Jul 30 10:28:09 2024

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