Chlorine in PDB 3mby: Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer, PDB code: 3mby was solved by V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.84 / 2.00
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.830, 80.030, 55.420, 90.00, 107.70, 90.00
*R / R_free (%)*	19 / 24.6

Other elements in 3mby:

The structure of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer (pdb code 3mby). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer, PDB code: 3mby:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3mby

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Chlorine Binding Sites List in 3mby

Chlorine binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl343 b:36.9 occ:1.00	N	A:HIS34	3.2	29.8	1.0
	CB	A:HIS34	3.4	31.5	1.0
	CB	A:ALA32	3.4	29.0	1.0
	C	A:ALA32	3.5	31.0	1.0
	CA	A:ALA32	3.5	29.9	1.0
	N	A:LYS35	3.6	27.1	1.0
	N	A:ILE33	3.7	30.9	1.0
	CA	A:HIS34	3.7	29.2	1.0
	O	A:ALA32	3.9	30.5	1.0
	CD2	A:HIS34	4.0	36.2	1.0
	CG	A:HIS34	4.0	33.9	1.0
	C	A:HIS34	4.1	27.7	1.0
	CG	A:LYS35	4.2	25.8	1.0
	C	A:ILE33	4.3	31.5	1.0
	O	A:HOH578	4.5	33.0	1.0
	CA	A:ILE33	4.5	32.0	1.0
	CB	A:LYS35	4.6	24.3	1.0
	CA	A:LYS35	4.7	24.2	1.0
	O	T:HOH376	4.9	50.9	1.0
	O6	D:DG1	4.9	29.4	1.0
	N	A:ALA32	4.9	28.9	1.0

Chlorine binding site 2 out of 3 in 3mby

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Chlorine Binding Sites List in 3mby

Chlorine binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl344 b:44.7 occ:1.00	O	A:HOH397	2.9	44.9	1.0
	N	A:LEU82	3.3	26.6	1.0
	NH1	A:ARG89	3.4	46.1	1.0
	OE2	A:GLU86	3.4	46.3	1.0
	O	A:HOH396	3.5	42.7	1.0
	NH2	A:ARG89	3.6	47.3	1.0
	CA	A:LYS81	3.8	27.2	1.0
	CZ	A:ARG89	3.9	45.5	1.0
	C	A:LYS81	4.0	27.1	1.0
	CB	A:LEU82	4.1	28.5	1.0
	O	A:LEU82	4.1	28.4	1.0
	CA	A:LEU82	4.1	28.6	1.0
	CB	A:LEU85	4.2	26.3	1.0
	CD1	A:LEU85	4.2	25.2	1.0
	CB	A:LYS81	4.2	31.1	1.0
	CD	A:GLU86	4.5	44.6	1.0
	C	A:LEU82	4.5	29.0	1.0
	CG	A:LYS81	4.6	33.2	1.0
	O	A:GLY80	4.8	27.4	1.0
	CG	A:LEU85	4.8	23.9	1.0
	CG	A:GLU86	4.8	41.0	1.0

Chlorine binding site 3 out of 3 in 3mby

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Chlorine Binding Sites List in 3mby

Chlorine binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl345 b:34.9 occ:1.00	O	A:HOH652	2.9	39.6	1.0
	ND2	A:ASN294	3.2	22.4	1.0
	OG1	A:THR297	3.2	25.0	1.0
	O	A:HOH638	3.3	38.4	1.0
	CB	A:TYR296	3.9	22.5	1.0
	CZ	A:ARG299	3.9	39.6	1.0
	OD1	A:ASN294	3.9	22.5	1.0
	CG	A:ASN294	4.0	22.4	1.0
	NH2	A:ARG299	4.1	38.4	1.0
	CG2	A:THR297	4.1	27.0	1.0
	NH1	A:ARG299	4.2	40.8	1.0
	CD2	A:TYR296	4.2	20.9	1.0
	NE	A:ARG299	4.2	36.5	1.0
	CB	A:THR297	4.2	24.8	1.0
	CG	A:TYR296	4.5	22.7	1.0
	N	A:THR297	4.6	22.4	1.0
	CD	A:ARG299	4.7	32.5	1.0
	O	A:HOH639	4.8	41.8	1.0
	O	A:HOH518	4.8	26.5	1.0
	C	A:TYR296	5.0	20.4	1.0

Reference:

V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson. Mutagenic Conformation of 8-Oxo-7,8-Dihydro-2'-Dgtp in the Confines of A Dna Polymerase Active Site. Nat.Struct.Mol.Biol. V. 17 889 2010.
ISSN: ISSN 1545-9993
PubMed: 20526335
DOI: 10.1038/NSMB.1852

Page generated: Sun Jul 21 00:06:36 2024

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