Sodium in PDB 7ktj: Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7ktj was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.86 / 1.45
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	60.02, 62.099, 118.212, 90, 90, 90
*R / R_free (%)*	16.1 / 18.4

Other elements in 7ktj:

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) (pdb code 7ktj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7ktj:

Sodium binding site 1 out of 1 in 7ktj

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Sodium Binding Sites List in 7ktj

Sodium binding site 1 out of 1 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na504 b:43.6 occ:1.00	O	A:PHE205	2.2	33.4	1.0
	O	A:HOH812	2.2	41.8	1.0
	O	A:HOH898	2.3	44.3	1.0
	O	D:HOH103	2.6	34.3	1.0
	C	A:PHE205	3.5	24.9	1.0
	O	A:HOH831	3.8	50.1	1.0
	O	A:LEU202	4.2	24.2	1.0
	CA	A:GLY206	4.2	21.6	1.0
	N	A:GLY206	4.3	20.9	1.0
	CA	A:PHE205	4.5	20.4	1.0
	CB	A:PHE205	4.6	23.3	1.0
	OP2	D:DC3	4.7	21.7	1.0
	N	A:PHE205	4.7	19.3	1.0
	OP1	D:DC3	5.0	19.3	1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6

Page generated: Mon Aug 18 10:35:28 2025

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