Sodium in PDB 6cr6: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue, PDB code: 6cr6 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.85 / 2.10
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	49.141, 79.236, 55.539, 90.00, 106.69, 90.00
*R / R_free (%)*	21.6 / 29.3

Other elements in 6cr6:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue (pdb code 6cr6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue, PDB code: 6cr6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6cr6

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Sodium Binding Sites List in 6cr6

Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
P:Na101 b:37.0 occ:1.00	O	A:THR101	2.3	32.7	1.0
	O	A:ILE106	2.3	34.6	1.0
	OP1	P:DG9	2.4	35.8	1.0
	O	A:VAL103	2.5	32.0	1.0
	O	P:HOH206	2.5	36.4	1.0
	O	P:HOH211	2.7	42.9	1.0
	P	P:DG9	3.3	37.2	1.0
	C	A:VAL103	3.3	36.7	1.0
	OP2	P:DG9	3.4	40.7	1.0
	C	A:THR101	3.4	33.7	1.0
	C	A:ILE106	3.4	34.2	1.0
	N	A:ILE106	3.7	30.7	1.0
	CA	A:SER104	3.9	38.2	1.0
	N	A:GLY105	3.9	35.5	1.0
	N	A:SER104	4.0	34.9	1.0
	CA	A:THR101	4.1	35.6	1.0
	N	A:VAL103	4.1	35.1	1.0
	CA	A:ILE106	4.1	32.2	1.0
	C	A:ARG102	4.2	36.2	1.0
	C	A:SER104	4.3	34.8	1.0
	O3'	P:DC8	4.3	33.8	1.0
	CA	A:VAL103	4.4	33.6	1.0
	N	A:ARG102	4.4	33.3	1.0
	N	A:GLY107	4.4	33.0	1.0
	O5'	P:DG9	4.5	35.1	1.0
	O	A:ARG102	4.5	40.3	1.0
	CA	A:ARG102	4.5	35.1	1.0
	C	A:GLY105	4.6	34.9	1.0
	CB	A:ILE106	4.6	36.5	1.0
	CB	A:THR101	4.6	36.7	1.0
	CA	A:GLY107	4.7	34.5	1.0
	CA	A:GLY105	4.8	35.5	1.0
	O	A:LEU100	4.9	30.1	1.0

Sodium binding site 2 out of 3 in 6cr6

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Sodium Binding Sites List in 6cr6

Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Na101 b:52.3 occ:1.00	OP1	D:DC3	2.3	47.1	1.0
	O	A:VAL65	2.4	51.5	1.0
	O	A:LYS60	2.5	52.7	1.0
	O	A:LEU62	2.7	49.5	1.0
	C	A:VAL65	3.4	49.2	1.0
	P	D:DC3	3.4	61.3	1.0
	C	A:LYS60	3.6	52.6	1.0
	OP2	D:DC3	3.8	55.4	1.0
	C	A:LEU62	3.8	45.1	1.0
	N	A:VAL65	3.8	48.7	1.0
	CA	A:VAL65	4.1	48.1	1.0
	CG	A:LYS60	4.2	53.2	1.0
	N	A:GLY64	4.2	45.5	1.0
	CA	A:LYS60	4.2	48.2	1.0
	C	A:LYS61	4.4	55.0	1.0
	CA	A:PRO63	4.4	43.5	1.0
	N	A:GLY66	4.4	49.1	1.0
	N	A:LEU62	4.4	53.2	1.0
	O	A:LYS61	4.5	55.5	1.0
	O3'	D:DT2	4.5	54.2	1.0
	O5'	D:DC3	4.5	56.9	1.0
	N	A:PRO63	4.5	42.5	1.0
	CB	A:VAL65	4.5	49.3	1.0
	N	A:LYS61	4.6	48.6	1.0
	C	A:PRO63	4.7	46.0	1.0
	CA	A:GLY66	4.7	51.1	1.0
	CA	A:LEU62	4.8	46.6	1.0
	CA	A:LYS61	4.8	50.2	1.0
	C	A:GLY64	4.8	52.9	1.0
	CB	A:LYS60	4.8	52.5	1.0
	NZ	A:LYS60	4.9	55.7	1.0

Sodium binding site 3 out of 3 in 6cr6

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Sodium Binding Sites List in 6cr6

Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Ch-CH3, Beta, Gamma Datp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na403 b:45.0 occ:1.00	OD2	A:ASP256	2.2	42.2	1.0
	OD2	A:ASP190	2.2	39.8	1.0
	OD1	A:ASP192	2.2	28.7	1.0
	O1A	A:HGV401	2.9	27.2	1.0
	CG	A:ASP190	3.1	37.0	1.0
	C3'	P:DOC10	3.2	38.2	1.0
	CG	A:ASP256	3.3	37.8	1.0
	CG	A:ASP192	3.3	32.2	1.0
	OD1	A:ASP190	3.4	32.0	1.0
	C4'	P:DOC10	3.5	40.4	1.0
	C5'	P:DOC10	3.5	40.7	1.0
	OD2	A:ASP192	3.8	31.6	1.0
	MG	A:MG402	3.9	29.6	1.0
	PA	A:HGV401	3.9	31.0	1.0
	CB	A:ASP256	3.9	32.4	1.0
	O5'	A:HGV401	4.1	31.1	1.0
	O5'	P:DOC10	4.1	45.5	1.0
	OD1	A:ASP256	4.2	36.3	1.0
	O2A	A:HGV401	4.3	26.7	1.0
	CB	A:ASP190	4.4	29.2	1.0
	C2'	P:DOC10	4.4	33.4	1.0
	C5'	A:HGV401	4.5	29.8	1.0
	NH2	A:ARG254	4.6	35.5	1.0
	CB	A:ASP192	4.6	27.7	1.0
	O	A:MET191	4.8	30.1	1.0
	OP1	P:DOC10	4.8	42.2	1.0
	O4'	P:DOC10	4.9	34.8	1.0
	N	A:ASP256	5.0	26.7	1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418

Page generated: Tue Oct 8 06:40:11 2024

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