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 / R_free (%)*	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

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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

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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

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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: Sun Jul 13 12:11:14 2025

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