Sodium in PDB 8u0o: Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus

Enzymatic activity of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus

All present enzymatic activity of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus, PDB code: 8u0o was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, T.A.Kunkel, K.K.Chiruvella, D.A.Ramsden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	41.34 / 2.05
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	58.971, 58.971, 211.248, 90, 90, 120
*R / R_free (%)*	21.5 / 25.9

Other elements in 8u0o:

The structure of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus (pdb code 8u0o). 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 Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus, PDB code: 8u0o:

Sodium binding site 1 out of 1 in 8u0o

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Sodium Binding Sites List in 8u0o

Sodium binding site 1 out of 1 in the Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Synaptic Complex of Human Dna Polymerase Lambda Dl Variant Engaged on A Dna Double-Strand Break Containing An Unpaired 3' Primer Terminus within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na601 b:40.4 occ:1.00	O	A:SER339	2.2	45.6	1.0
	O	A:HOH755	2.4	43.6	1.0
	O	A:ALA344	2.5	42.3	1.0
	O	A:ILE341	2.5	41.4	1.0
	C	A:SER339	3.3	48.1	1.0
	C	A:ILE341	3.5	41.5	1.0
	C	A:ALA344	3.6	46.1	1.0
	O	A:HOH743	3.9	62.6	1.0
	CA	A:SER339	3.9	48.3	1.0
	N	A:ALA344	4.0	38.7	1.0
	CA	A:TRP342	4.0	35.6	1.0
	N	A:TRP342	4.1	36.4	1.0
	N	A:ILE341	4.2	46.2	1.0
	N	A:GLY343	4.2	37.4	1.0
	N	A:ASN340	4.3	47.0	1.0
	C	A:ASN340	4.3	46.1	1.0
	CA	A:ALA344	4.3	45.6	1.0
	CB	A:SER339	4.4	46.3	1.0
	CA	A:ILE341	4.5	42.0	1.0
	C	A:TRP342	4.5	35.5	1.0
	CA	A:ASN340	4.5	46.8	1.0
	N	A:GLY345	4.5	46.2	1.0
	CA	A:GLY345	4.7	39.9	1.0
	CB	A:ALA344	4.8	42.5	1.0
	O	A:ASN340	4.9	48.5	1.0
	C	A:GLY343	4.9	43.6	1.0

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, K.Bebenek, T.A.Kunkel, L.C.Pedersen. Dna Polymerase Lambda LOOP1 Variant Yields Unexpected Gain-of-Function Capabilities in Nonhomologous End-Joining. Dna Repair (Amst) V. 136 03645 2024.
ISSN: ISSN 1568-7856
PubMed: 38428373
DOI: 10.1016/J.DNAREP.2024.103645

Page generated: Wed Oct 9 13:46:31 2024

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