Sodium in PDB 6g2q: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp 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 Chcl (S-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6g2q 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)*	22.63 / 2.15
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	48.397, 76.851, 54.544, 90.00, 103.81, 90.00
*R / R_free (%)*	19.6 / 26

Other elements in 6g2q:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

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 Chcl (S-Isomer), Beta, Gamma Dttp Analogue (pdb code 6g2q). 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 Chcl (S-Isomer), Beta, Gamma Dttp Analogue, PDB code: 6g2q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6g2q

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Sodium Binding Sites List in 6g2q

Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp 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 Chcl (S-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
P:Na101 b:36.7 occ:1.00	O	A:THR101	2.5	29.6	1.0
	OP1	P:DG9	2.5	27.6	1.0
	O	A:HOH593	2.6	42.6	1.0
	O	A:VAL103	2.6	25.3	1.0
	O	A:HOH604	3.2	34.3	1.0
	C	A:VAL103	3.4	28.1	1.0
	O	A:ILE106	3.4	25.1	1.0
	P	P:DG9	3.6	28.0	1.0
	C	A:THR101	3.6	26.6	1.0
	CA	A:SER104	3.7	26.9	1.0
	OP2	P:DG9	3.7	25.2	1.0
	N	A:SER104	3.9	28.8	1.0
	N	A:GLY105	4.0	24.4	1.0
	C	A:ARG102	4.0	28.6	1.0
	N	A:VAL103	4.1	30.8	1.0
	O	A:ARG102	4.1	27.9	1.0
	C	A:SER104	4.3	26.3	1.0
	N	A:ILE106	4.3	21.0	1.0
	CA	A:VAL103	4.4	27.9	1.0
	C	A:ILE106	4.4	25.8	1.0
	CA	A:ARG102	4.4	29.3	1.0
	CA	A:THR101	4.5	27.3	1.0
	N	A:ARG102	4.5	27.7	1.0
	O3'	P:DC8	4.6	26.6	1.0
	O5'	P:DG9	4.8	27.3	1.0
	CA	A:ILE106	4.9	24.5	1.0
	CB	A:SER104	4.9	28.6	1.0

Sodium binding site 2 out of 3 in 6g2q

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Sodium Binding Sites List in 6g2q

Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp 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 Chcl (S-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na404 b:55.4 occ:1.00	O	A:LYS60	2.6	40.3	1.0
	O	A:VAL65	2.8	44.4	1.0
	O	A:LEU62	3.6	45.8	1.0
	OP2	D:DC3	3.6	43.4	1.0
	OP1	D:DC3	3.7	51.5	1.0
	C	A:LYS60	3.8	44.5	1.0
	C	A:VAL65	4.0	41.8	1.0
	P	D:DC3	4.2	44.8	1.0
	CG	A:LYS60	4.2	42.4	1.0
	CA	A:LYS60	4.5	39.8	1.0
	C	A:LEU62	4.6	41.4	1.0
	N	A:VAL65	4.7	39.7	1.0
	C	A:LYS61	4.7	43.0	1.0
	N	A:LYS61	4.8	40.3	1.0
	N	A:GLY66	4.9	37.6	1.0
	CA	A:VAL65	4.9	38.6	1.0
	CA	A:LYS61	4.9	40.1	1.0
	CA	A:GLY66	4.9	36.6	1.0
	N	A:LEU62	4.9	43.4	1.0
	CB	A:LYS60	4.9	40.9	1.0

Sodium binding site 3 out of 3 in 6g2q

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Sodium Binding Sites List in 6g2q

Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (S-Isomer), Beta, Gamma Dttp 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 Chcl (S-Isomer), Beta, Gamma Dttp Analogue within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na405 b:51.8 occ:1.00	OD2	A:ASP190	2.2	37.4	1.0
	OD1	A:ASP192	2.4	32.0	1.0
	C3'	P:DOC10	2.7	34.9	1.0
	O1A	A:EJH401	2.8	33.3	1.0
	C4'	P:DOC10	3.2	34.6	1.0
	C5'	P:DOC10	3.2	35.2	1.0
	CG	A:ASP190	3.3	34.6	1.0
	CG	A:ASP192	3.5	36.5	1.0
	PA	A:EJH401	3.7	29.7	1.0
	O5'	A:EJH401	3.7	29.5	1.0
	OD1	A:ASP190	3.7	32.8	1.0
	OD2	A:ASP192	3.9	30.7	1.0
	O5'	P:DOC10	3.9	31.6	1.0
	CB	A:ASP256	4.0	31.6	1.0
	MG	A:MG402	4.0	35.7	1.0
	C5'	A:EJH401	4.1	30.4	1.0
	O2A	A:EJH401	4.1	34.1	1.0
	C2'	P:DOC10	4.1	31.2	1.0
	OD2	A:ASP256	4.2	30.1	1.0
	O	A:HOH541	4.4	34.9	1.0
	OP1	P:DOC10	4.4	39.2	1.0
	CB	A:ASP190	4.6	30.0	1.0
	O4'	P:DOC10	4.6	30.6	1.0
	CG	A:ASP256	4.6	32.8	1.0
	NH1	A:ARG254	4.7	40.9	1.0
	P	P:DOC10	4.7	34.9	1.0
	CB	A:ASP192	4.8	29.1	1.0
	CE1	A:PHE272	5.0	29.6	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 08:53:33 2024

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