Sodium in PDB 4x5v: Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp

Enzymatic activity of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp

All present enzymatic activity of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp, PDB code: 4x5v was solved by M.J.Burak, K.E.Guja, M.Garcia-Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	46.99 / 2.15
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.010, 62.842, 141.507, 90.00, 90.00, 90.00
*R / R_free (%)*	21.4 / 24.5

Other elements in 4x5v:

The structure of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp (pdb code 4x5v). 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 Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp, PDB code: 4x5v:

Sodium binding site 1 out of 1 in 4x5v

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Sodium Binding Sites List in 4x5v

Sodium binding site 1 out of 1 in the Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Post-Catalytic Nick Complex of Dna Polymerase Lambda with A Templating A and Incorporated 8-Oxo-Dgmp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na601 b:79.6 occ:1.00	O4	A:CIT603	2.2	40.4	1.0
	OD1	A:ASP427	2.3	32.3	1.0
	OD2	A:ASP429	2.3	31.2	1.0
	O7	A:CIT603	2.5	44.1	1.0
	OP1	P:8OG7	2.8	24.6	0.9
	O	A:HOH741	2.8	38.6	1.0
	C5	A:CIT603	3.2	43.5	1.0
	CG	A:ASP427	3.3	29.1	1.0
	CG	A:ASP429	3.3	29.0	1.0
	C3	A:CIT603	3.5	44.8	1.0
	O6	A:CIT603	3.5	41.0	1.0
	OD1	A:ASP429	3.6	25.0	1.0
	C4	A:CIT603	3.7	42.8	1.0
	OD2	A:ASP427	3.7	35.2	1.0
	C6	A:CIT603	3.9	41.8	1.0
	O	A:ASP427	3.9	25.7	1.0
	P	P:8OG7	3.9	25.6	0.9
	CA	A:GLY416	4.1	29.1	1.0
	O5'	P:8OG7	4.1	40.9	0.9
	N	A:SER417	4.2	27.0	1.0
	O3	A:CIT603	4.2	46.7	1.0
	C5'	P:8OG7	4.3	41.0	0.9
	C	A:ASP427	4.3	25.3	1.0
	OG	A:SER417	4.4	38.9	1.0
	N	A:ASP427	4.4	29.7	1.0
	CB	A:ASP427	4.5	28.1	1.0
	OP2	P:8OG7	4.6	26.6	0.9
	CB	A:ASP429	4.6	26.3	1.0
	CA	A:ASP427	4.6	26.6	1.0
	O	A:HOH746	4.7	26.2	1.0
	C	A:GLY416	4.7	28.0	1.0
	C2	A:CIT603	4.8	49.3	1.0
	N	A:ASP429	4.8	26.2	1.0
	N	A:VAL428	5.0	23.5	1.0
	O5	A:CIT603	5.0	44.3	1.0

Reference:

M.J.Burak, K.E.Guja, M.Garcia-Diaz. Nucleotide Binding Interactions Modulate Dntp Selectivity and Facilitate 8-Oxo-Dgtp Incorporation By Dna Polymerase Lambda. Nucleic Acids Res. V. 43 8089 2015.
ISSN: ESSN 1362-4962
PubMed: 26220180
DOI: 10.1093/NAR/GKV760

Page generated: Mon Oct 7 18:58:41 2024

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