Sodium in PDB 4khn: Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase

Enzymatic activity of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase

All present enzymatic activity of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase, PDB code: 4khn was solved by K.E.Guja, A.Jacewicz, A.Trzemecka, D.Plochocka, E.Yakubovskaya, A.Bebenek, M.Garcia-Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.33 / 2.55
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	74.258, 119.353, 148.031, 90.00, 91.64, 90.00
*R / R_free (%)*	16.8 / 21.1

Other elements in 4khn:

The structure of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase (pdb code 4khn). 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 Ternary Complex of the D714A Mutant of RB69 Dna Polymerase, PDB code: 4khn:

Sodium binding site 1 out of 1 in 4khn

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Sodium Binding Sites List in 4khn

Sodium binding site 1 out of 1 in the Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase

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 Ternary Complex of the D714A Mutant of RB69 Dna Polymerase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1010 b:46.0 occ:1.00	OD2	A:ASP621	2.4	47.5	1.0
	OP1	D:DC115	2.7	45.5	1.0
	OH	A:TYR619	2.7	25.8	1.0
	O3'	D:DA114	2.8	39.5	1.0
	P	D:DC115	3.3	41.4	1.0
	CG	A:ASP621	3.4	44.8	1.0
	CB	A:ASP621	3.5	38.1	1.0
	CA	A:LYS706	3.6	31.6	1.0
	CZ	A:TYR619	3.6	25.3	1.0
	C5'	D:DC115	3.7	40.1	1.0
	CE2	A:TYR619	3.7	24.2	1.0
	CE1	A:TYR708	3.7	28.3	1.0
	CG	A:LYS706	3.7	35.6	1.0
	CB	A:LYS706	4.0	31.1	1.0
	O5'	D:DC115	4.0	42.3	1.0
	N	A:LYS706	4.1	31.5	1.0
	C3'	D:DA114	4.1	34.6	1.0
	OH	A:TYR708	4.3	34.9	1.0
	C4'	D:DA114	4.3	33.6	1.0
	CZ	A:TYR708	4.5	31.1	1.0
	OD1	A:ASP621	4.5	40.0	1.0
	C	A:LYS706	4.6	32.2	1.0
	CD	A:LYS706	4.6	37.9	1.0
	OP2	D:DC115	4.7	48.8	1.0
	CD1	A:TYR708	4.7	30.3	1.0
	CE1	A:TYR619	4.9	21.1	1.0
	O4'	D:DA114	4.9	34.9	1.0
	O	A:LYS706	5.0	33.6	1.0
	C2'	D:DA114	5.0	30.5	1.0

Reference:

A.Jacewicz, A.Trzemecka, K.E.Guja, D.Plochocka, E.Yakubovskaya, A.Bebenek, M.Garcia-Diaz. A Remote Palm Domain Residue of RB69 Dna Polymerase Is Critical For Enzyme Activity and Influences the Conformation of the Active Site. Plos One V. 8 76700 2013.
ISSN: ESSN 1932-6203
PubMed: 24116139
DOI: 10.1371/JOURNAL.PONE.0076700

Page generated: Mon Oct 7 16:29:15 2024

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