Sodium in PDB 3d0p: Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex

Enzymatic activity of Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex

All present enzymatic activity of Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex:
3.1.26.4;

Protein crystallography data

The structure of Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex, PDB code: 3d0p was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	41.59 / 1.80
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	98.397, 66.660, 76.926, 90.00, 122.31, 90.00
*R / R_free (%)*	21.4 / 24.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex (pdb code 3d0p). 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 Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex, PDB code: 3d0p:

Sodium binding site 1 out of 1 in 3d0p

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Sodium Binding Sites List in 3d0p

Sodium binding site 1 out of 1 in the Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Na1 b:53.2 occ:1.00	O	C:HOH262	2.2	23.9	0.7
	O	C:HOH266	2.4	18.9	0.5
	O	C:HOH285	2.4	36.0	1.0
	O	C:LEU111	3.3	21.2	1.0
	O	C:HOH247	3.7	22.6	1.0
	N	C:HIS115	3.7	21.5	1.0
	CA	C:HIS115	4.0	22.9	1.0
	CB	C:HIS115	4.0	22.8	1.0
	O	C:HOH253	4.1	28.1	1.0
	OH	C:TYR83	4.2	26.7	1.0
	C	C:LEU111	4.2	20.5	1.0
	CB	C:VAL114	4.2	21.3	1.0
	CA	C:LEU111	4.2	20.8	1.0
	CG1	C:VAL114	4.3	22.1	1.0
	CD2	C:LEU111	4.3	24.1	1.0
	C	C:VAL114	4.3	21.4	1.0
	CB	C:ALA165	4.4	21.9	1.0
	CB	C:LEU111	4.4	20.1	1.0
	ND1	C:HIS115	4.7	29.9	1.0
	CG	C:HIS115	4.7	25.4	1.0
	CA	C:VAL114	4.8	21.4	1.0
	NH1	C:ARG118	4.9	29.8	1.0
	O	C:VAL114	4.9	21.1	1.0
	CD	C:ARG118	4.9	28.2	1.0
	CG	C:LEU111	5.0	21.6	1.0

Reference:

P.S.Pallan, M.Egli. Insights Into Rna/Dna Hybrid Recognition and Processing By Rnase H From the Crystal Structure of A Non-Specific Enzyme-Dsdna Complex. Cell Cycle V. 7 2562 2008.
ISSN: ISSN 1538-4101
PubMed: 18719385

Page generated: Sun Aug 17 14:15:33 2025

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