Sodium in PDB 4ycx: Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate

Enzymatic activity of Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate

All present enzymatic activity of Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate:
2.7.7.7;

Protein crystallography data

The structure of Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate, PDB code: 4ycx was solved by A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	22.47 / 2.10
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	60.043, 68.683, 116.830, 90.00, 90.00, 90.00
*R / R_free (%)*	20.1 / 23.4

Other elements in 4ycx:

The structure of Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate (pdb code 4ycx). 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 Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate, PDB code: 4ycx:

Sodium binding site 1 out of 1 in 4ycx

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Sodium Binding Sites List in 4ycx

Sodium binding site 1 out of 1 in the Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na702 b:49.9 occ:1.00	O	P:HOH103	2.4	30.4	1.0
	O	A:HOH977	2.4	39.1	1.0
	O	A:HOH1027	2.4	39.2	1.0
	O	A:HOH828	2.4	28.5	1.0
	O	A:HOH982	3.2	40.7	1.0
	OP1	P:DT3	3.8	27.7	1.0
	O	A:THR241	3.8	27.3	1.0
	O	P:HOH107	4.2	28.9	1.0
	O	A:ILE243	4.2	23.3	1.0
	OP2	P:DA4	4.3	25.2	1.0
	O	A:GLN242	4.6	28.4	1.0
	CA	A:PHE244	4.7	25.8	1.0
	C	A:ILE243	4.7	25.0	1.0
	C	A:GLN242	4.8	26.8	1.0
	P	P:DT3	4.9	27.3	1.0
	N	A:PHE244	4.9	25.9	1.0
	O	A:VAL246	4.9	25.5	1.0
	C	A:THR241	5.0	25.6	1.0

Reference:

A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Creative Template-Dependent Synthesis By Human Polymerase Mu. Proc.Natl.Acad.Sci.Usa V. 112 E4530 2015.
ISSN: ESSN 1091-6490
PubMed: 26240373
DOI: 10.1073/PNAS.1505798112

Page generated: Sun Aug 17 22:35:44 2025

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