Arsenic in PDB 2gws: Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

Enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus, PDB code: 2gws was solved by M.Garcia-Diaz, A.J.Picher, K.Bebenek, L.C.Pedersen, T.A.Kunkel, L.Blanco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 2.40
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	192.374, 98.268, 104.960, 90.00, 90.00, 90.00
*R / R_free (%)*	20.9 / 25.3

Other elements in 2gws:

The structure of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	8 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus (pdb code 2gws). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 3 binding sites of Arsenic where determined in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus, PDB code: 2gws:
Jump to Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in 2gws

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Arsenic Binding Sites List in 2gws

Arsenic binding site 1 out of 3 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

Mono view

Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:As949 b:0.5 occ:1.00	AS	D:CAC949	0.0	0.5	1.0
	O2	D:CAC949	1.6	0.1	1.0
	O1	D:CAC949	1.7	0.2	1.0
	C2	D:CAC949	1.8	0.2	1.0
	C1	D:CAC949	2.0	0.9	1.0
	O6	D:DG4	3.9	43.2	1.0
	N7	D:DG4	4.1	38.7	1.0
	O	A:HOH1064	4.5	37.0	1.0
	C6	D:DG4	4.6	38.5	1.0
	C5	D:DG4	4.7	38.7	1.0

Arsenic binding site 2 out of 3 in 2gws

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Arsenic Binding Sites List in 2gws

Arsenic binding site 2 out of 3 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

Mono view

Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
H:As950 b:0.6 occ:1.00	AS	H:CAC950	0.0	0.6	1.0
	O2	H:CAC950	1.6	0.7	1.0
	O1	H:CAC950	1.7	0.3	1.0
	C2	H:CAC950	1.8	0.5	1.0
	C1	H:CAC950	2.0	0.3	1.0
	O6	L:DG4	4.5	56.7	1.0
	O6	H:DG4	4.6	50.3	1.0
	N7	H:DG4	4.7	52.0	1.0
	N7	L:DG4	4.7	57.8	1.0
	O	L:HOH56	4.8	39.7	1.0
	C5	L:DC3	4.9	55.8	1.0
	O	I:HOH953	5.0	36.0	1.0

Arsenic binding site 3 out of 3 in 2gws

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Arsenic Binding Sites List in 2gws

Arsenic binding site 3 out of 3 in the Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus

Mono view

Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Human Dna Polymerase Lambda with A G/G Mismatch in the Primer Terminus within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
J:As951 b:0.2 occ:1.00	AS	J:CAC951	0.0	0.2	1.0
	O2	J:CAC951	1.6	0.1	1.0
	O1	J:CAC951	1.7	0.9	1.0
	C2	J:CAC951	1.8	0.0	1.0
	C1	J:CAC951	2.0	0.8	1.0
	N7	J:DG2	3.9	56.6	1.0
	O6	J:DG3	4.1	50.8	1.0
	O6	J:DG2	4.1	54.5	1.0
	O	L:HOH610	4.2	41.9	1.0
	N4	L:DC2	4.5	51.5	1.0
	C5	J:DG2	4.6	55.6	1.0
	C6	J:DG2	4.7	54.3	1.0
	O6	L:DG1	4.7	48.9	1.0
	O	J:HOH459	4.8	32.9	1.0
	C8	J:DG2	4.9	57.6	1.0
	C5	J:DC1	5.0	60.9	1.0

Reference:

A.J.Picher, M.Garcia-Diaz, K.Bebenek, L.C.Pedersen, T.A.Kunkel, L.Blanco. Promiscuous Mismatch Extension By Human Dna Polymerase Lambda. Nucleic Acids Res. V. 34 3259 2006.
ISSN: ISSN 0305-1048
PubMed: 16807316
DOI: 10.1093/NAR/GKL377

Page generated: Sun Jul 6 23:08:49 2025

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