Chlorine in PDB 3rh6: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

Enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

All present enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6 was solved by N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.77 / 2.05
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	51.060, 79.810, 55.060, 90.00, 107.68, 90.00
*R / R_free (%)*	19.5 / 26.6

Other elements in 3rh6:

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) also contains other interesting chemical elements:

Manganese	(Mn)	6 atoms
Sodium	(Na)	2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) (pdb code 3rh6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3rh6

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Chlorine Binding Sites List in 3rh6

Chlorine binding site 1 out of 3 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl348 b:44.4 occ:1.00	OG1	A:THR297	3.1	29.7	1.0
	ND2	A:ASN294	3.3	27.0	1.0
	CG2	A:THR297	3.7	36.1	1.0
	OD1	A:ASN294	3.9	26.7	1.0
	CB	A:THR297	4.0	35.2	1.0
	CG	A:ASN294	4.0	21.4	1.0
	CZ	A:ARG299	4.1	43.5	1.0
	CB	A:TYR296	4.1	30.3	1.0
	NE	A:ARG299	4.2	33.3	1.0
	NH1	A:ARG299	4.2	45.8	1.0
	CD2	A:TYR296	4.4	33.3	1.0
	CD	A:ARG299	4.5	32.5	1.0
	NH2	A:ARG299	4.5	42.9	1.0
	O	A:HOH594	4.7	47.7	1.0
	O	A:HOH373	4.7	34.9	1.0
	N	A:THR297	4.7	27.4	1.0
	CG	A:TYR296	4.7	28.5	1.0
	O	T:HOH191	4.9	35.2	1.0
	CA	A:THR297	5.0	28.4	1.0

Chlorine binding site 2 out of 3 in 3rh6

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Chlorine Binding Sites List in 3rh6

Chlorine binding site 2 out of 3 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl349 b:43.5 occ:1.00	N	A:HIS34	2.9	24.9	1.0
	CB	A:HIS34	3.1	31.5	1.0
	C	A:ALA32	3.3	25.4	1.0
	CD2	A:HIS34	3.4	37.7	1.0
	CA	A:HIS34	3.5	29.8	1.0
	N	A:LYS35	3.5	22.1	1.0
	N	A:ILE33	3.5	22.2	1.0
	CB	A:ALA32	3.5	32.6	1.0
	CA	A:ALA32	3.6	33.7	1.0
	CG	A:HIS34	3.6	35.1	1.0
	O	A:ALA32	3.7	30.0	1.0
	C	A:HIS34	4.0	26.6	1.0
	C	A:ILE33	4.0	31.1	1.0
	O	A:HOH398	4.2	37.4	1.0
	CA	A:ILE33	4.3	29.7	1.0
	CB	A:LYS35	4.6	26.6	1.0
	CA	A:LYS35	4.7	19.3	1.0
	CG2	A:ILE33	4.7	40.8	1.0
	CG	A:LYS35	4.7	25.3	1.0
	NE2	A:HIS34	4.8	41.0	1.0
	O6	D:DG1	4.8	26.3	1.0
	ND1	A:HIS34	4.9	36.2	1.0

Chlorine binding site 3 out of 3 in 3rh6

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Chlorine Binding Sites List in 3rh6

Chlorine binding site 3 out of 3 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl351 b:50.5 occ:1.00	N	A:LEU82	3.3	28.4	1.0
	NH1	A:ARG89	3.3	43.6	1.0
	O	A:HOH590	3.3	44.1	1.0
	NH2	A:ARG89	3.6	57.0	1.0
	OE2	A:GLU86	3.7	48.7	1.0
	CA	A:LYS81	3.7	33.0	1.0
	CZ	A:ARG89	3.9	51.3	1.0
	C	A:LYS81	3.9	30.8	1.0
	CD1	A:LEU85	4.0	41.1	1.0
	CB	A:LYS81	4.0	37.4	1.0
	CB	A:LEU85	4.1	33.6	1.0
	O	A:LEU82	4.2	32.3	1.0
	CA	A:LEU82	4.3	32.9	1.0
	CB	A:LEU82	4.3	33.0	1.0
	CD	A:GLU86	4.6	52.5	1.0
	C	A:LEU82	4.6	33.5	1.0
	CG	A:LEU85	4.7	37.0	1.0
	O	A:GLY80	4.8	32.1	1.0
	CG	A:GLU86	4.8	38.2	1.0
	N	A:LYS81	5.0	26.9	1.0

Reference:

N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson. Molecular Insights Into Dna Polymerase Deterrents For Ribonucleotide Insertion. J.Biol.Chem. V. 286 31650 2011.
ISSN: ISSN 0021-9258
PubMed: 21733843
DOI: 10.1074/JBC.M111.253401

Page generated: Sun Jul 21 03:41:10 2024

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