Sodium in PDB 4qzg: Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair

Enzymatic activity of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair

All present enzymatic activity of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair:
2.7.7.31;

Protein crystallography data

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qzg was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	42.48 / 2.75
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	56.992, 70.851, 114.893, 90.00, 96.16, 90.00
*R / R_free (%)*	18.8 / 20.8

Other elements in 4qzg:

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair (pdb code 4qzg). 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 Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qzg:

Sodium binding site 1 out of 1 in 4qzg

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Sodium Binding Sites List in 4qzg

Sodium binding site 1 out of 1 in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-C Base Pair within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na603 b:76.0 occ:1.00	OP1	U:DA5	2.4	81.1	1.0
	O	A:THR253	2.5	68.8	1.0
	O	A:VAL258	2.9	67.5	1.0
	O	A:VAL255	2.9	63.0	1.0
	P	U:DA5	3.4	81.2	1.0
	OP2	U:DA5	3.5	80.1	1.0
	C	A:THR253	3.6	67.7	1.0
	C	A:VAL255	3.8	61.6	1.0
	C	A:VAL258	3.9	68.1	1.0
	CA	A:THR253	4.2	64.7	1.0
	N	A:VAL258	4.2	62.2	1.0
	CA	A:PHE256	4.3	57.2	1.0
	N	A:PHE256	4.4	58.5	1.0
	N	A:GLY257	4.4	63.4	1.0
	O5'	U:DA5	4.4	79.1	1.0
	CB	A:THR253	4.4	66.1	1.0
	N	A:VAL255	4.5	56.4	1.0
	CA	A:VAL258	4.6	63.4	1.0
	O3'	U:DA4	4.7	84.4	1.0
	N	A:SER254	4.7	62.3	1.0
	C	A:SER254	4.7	62.3	1.0
	C	A:PHE256	4.8	64.8	1.0
	CA	A:VAL255	4.9	55.5	1.0
	N	A:GLY259	4.9	65.8	1.0
	CA	A:SER254	5.0	60.6	1.0

Reference:

J.Gouge, S.Rosario, F.Romain, F.Poitevin, P.Beguin, M.Delarue. Structural Basis For A Novel Mechanism of Dna Bridging and Alignment in Eukaryotic Dsb Dna Repair. Embo J. V. 34 1126 2015.
ISSN: ISSN 0261-4189
PubMed: 25762590
DOI: 10.15252/EMBJ.201489643

Page generated: Mon Oct 7 18:08:18 2024

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