Sodium in PDB 4ptf: Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G

Enzymatic activity of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G

All present enzymatic activity of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G, PDB code: 4ptf was solved by R.Jain, K.R.Rajashankar, A.Buku, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	46.81 / 2.81
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	147.293, 68.478, 149.079, 90.00, 109.60, 90.00
*R / R_free (%)*	18.3 / 24.7

Other elements in 4ptf:

The structure of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G (pdb code 4ptf). 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 Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G, PDB code: 4ptf:

Sodium binding site 1 out of 1 in 4ptf

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Sodium Binding Sites List in 4ptf

Sodium binding site 1 out of 1 in the Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Crystal Structure of Yeast Dna Polymerase Epsilon with Template G within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1205 b:26.1 occ:1.00	OP1	T:DG10	2.7	36.3	1.0
	NH1	A:ARG968	3.2	38.5	1.0
	CE	A:LYS1156	3.7	38.4	1.0
	CE1	A:PHE984	4.0	24.2	1.0
	CD	A:ARG968	4.0	27.0	1.0
	OE2	A:GLU985	4.0	32.1	1.0
	P	T:DG10	4.1	60.1	1.0
	CD1	A:PHE984	4.2	26.0	1.0
	CD1	A:ILE965	4.2	35.7	1.0
	CZ	A:ARG968	4.2	35.7	1.0
	NZ	A:LYS1156	4.2	39.7	1.0
	CD	A:LYS1156	4.4	34.0	1.0
	CB	A:LYS1156	4.5	25.6	1.0
	NE	A:ARG968	4.5	29.6	1.0
	O3'	T:DG9	4.5	52.5	1.0
	OE1	A:GLU985	4.5	33.7	1.0
	CD	A:GLU985	4.7	32.7	1.0
	CB	A:PRO956	4.7	29.2	1.0
	C5'	T:DG10	4.8	35.6	1.0
	CG2	A:ILE965	4.9	33.1	1.0
	O5'	T:DG10	4.9	30.6	1.0
	CG1	A:ILE1157	5.0	25.3	1.0

Reference:

R.Jain, K.R.Rajashankar, A.Buku, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Crystal Structure of Yeast Dna Polymerase Epsilon Catalytic Domain. Plos One V. 9 94835 2014.
ISSN: ESSN 1932-6203
PubMed: 24733111
DOI: 10.1371/JOURNAL.PONE.0094835

Page generated: Sun Aug 17 21:15:49 2025

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