Calcium in PDB 5u2s: Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+.

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+.

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+.:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+., PDB code: 5u2s was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.03 / 2.30
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	54.630, 79.450, 55.170, 90.00, 106.66, 90.00
*R / R_free (%)*	23 / 28.4

Other elements in 5u2s:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+. also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+. (pdb code 5u2s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+., PDB code: 5u2s:

Calcium binding site 1 out of 1 in 5u2s

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Calcium Binding Sites List in 5u2s

Calcium binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+.

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate Incoming (-)3TC-Tp and CA2+. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca402 b:64.0 occ:1.00	O2A	A:1RZ401	2.2	68.9	1.0
	OD1	A:ASP190	2.4	33.0	1.0
	O3G	A:1RZ401	2.4	62.1	1.0
	OD2	A:ASP192	2.5	45.6	1.0
	O	A:HOH507	2.8	42.6	1.0
	O3B	A:1RZ401	2.9	59.9	1.0
	OD1	A:ASP192	3.1	35.0	1.0
	CG	A:ASP192	3.2	38.3	1.0
	PG	A:1RZ401	3.3	59.9	1.0
	CG	A:ASP190	3.5	29.0	1.0
	PA	A:1RZ401	3.6	68.1	1.0
	PB	A:1RZ401	3.7	58.9	1.0
	O2B	A:1RZ401	3.7	59.9	1.0
	O	P:HOH101	3.8	41.7	1.0
	O3A	A:1RZ401	3.8	62.6	1.0
	OD2	A:ASP190	3.9	29.6	1.0
	O2C	A:1RZ401	4.1	63.2	1.0
	O	A:ASP190	4.3	29.2	1.0
	O5'	A:1RZ401	4.4	73.8	1.0
	O1G	A:1RZ401	4.5	66.8	1.0
	CA	A:GLY179	4.5	40.4	1.0
	N	A:ASP190	4.5	29.8	1.0
	NA	A:NA412	4.6	37.6	1.0
	C	A:ASP190	4.6	31.3	1.0
	CB	A:ASP192	4.6	33.8	1.0
	CB	A:ASP190	4.7	29.8	1.0
	O1A	A:1RZ401	4.8	67.6	1.0
	OG	A:SER180	4.8	43.0	1.0
	CA	A:ASP190	4.9	30.4	1.0
	N	A:SER180	4.9	45.7	1.0
	O	A:HOH531	4.9	13.0	0.5
	N	A:ASP192	4.9	30.5	1.0

Reference:

R.Vyas, A.J.Reed, A.T.Raper, W.J.Zahurancik, P.C.Wallenmeyer, Z.Suo. Structural Basis For the D-Stereoselectivity of Human Dna Polymerase Beta. Nucleic Acids Res. V. 45 6228 2017.
ISSN: ESSN 1362-4962
PubMed: 28402499
DOI: 10.1093/NAR/GKX252

Page generated: Mon Jul 15 11:26:32 2024

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