Manganese in PDB 4r66: Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta

Enzymatic activity of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta

All present enzymatic activity of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta, PDB code: 4r66 was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	21.65 / 2.25
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	54.960, 79.196, 54.874, 90.00, 92.86, 90.00
*R / R_free (%)*	18.1 / 24.7

Other elements in 4r66:

The structure of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta (pdb code 4r66). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta, PDB code: 4r66:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4r66

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Manganese Binding Sites List in 4r66

Manganese binding site 1 out of 4 in the Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn402 b:28.4 occ:1.00	O2B	A:DUP401	2.1	29.4	1.0
	O2A	A:DUP401	2.1	32.1	1.0
	OD2	A:ASP192	2.2	25.6	1.0
	OD1	A:ASP190	2.2	22.4	1.0
	O3G	A:DUP401	2.3	25.3	1.0
	O	A:HOH551	2.3	29.4	1.0
	CG	A:ASP192	3.2	25.4	1.0
	PB	A:DUP401	3.2	31.4	1.0
	CG	A:ASP190	3.4	23.9	1.0
	PG	A:DUP401	3.4	22.9	1.0
	PA	A:DUP401	3.4	30.8	1.0
	OD1	A:ASP192	3.5	30.7	1.0
	MN	A:MN403	3.5	41.4	1.0
	O3B	A:DUP401	3.7	31.9	1.0
	N3A	A:DUP401	3.8	28.4	1.0
	OD2	A:ASP190	3.8	30.1	1.0
	O1G	A:DUP401	3.9	36.4	1.0
	O	A:ASP190	4.0	26.8	1.0
	O	A:HOH602	4.2	33.9	1.0
	C5'	A:DUP401	4.3	38.8	1.0
	O	A:HOH537	4.3	19.7	1.0
	O5'	A:DUP401	4.4	43.1	1.0
	N	A:SER180	4.4	27.2	1.0
	C	A:ASP190	4.4	25.0	1.0
	N	A:ASP190	4.4	19.8	1.0
	O1A	A:DUP401	4.4	41.7	1.0
	CA	A:GLY179	4.4	23.1	1.0
	OG	A:SER180	4.4	31.7	1.0
	CB	A:ASP192	4.6	22.5	1.0
	O1B	A:DUP401	4.6	27.3	1.0
	CB	A:ASP190	4.6	19.1	1.0
	CA	A:ASP190	4.7	22.5	1.0
	O2G	A:DUP401	4.8	31.6	1.0
	N	A:ASP192	4.9	18.0	1.0

Manganese binding site 2 out of 4 in 4r66

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Manganese Binding Sites List in 4r66

Manganese binding site 2 out of 4 in the Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn403 b:41.4 occ:1.00	O2A	A:DUP401	2.2	32.1	1.0
	OD2	A:ASP190	2.3	30.1	1.0
	OD1	A:ASP192	2.4	30.7	1.0
	CG	A:ASP190	3.1	23.9	1.0
	OD1	A:ASP190	3.3	22.4	1.0
	PA	A:DUP401	3.3	30.8	1.0
	O1A	A:DUP401	3.3	41.7	1.0
	CG	A:ASP192	3.4	25.4	1.0
	MN	A:MN402	3.5	28.4	1.0
	OD2	A:ASP192	3.6	25.6	1.0
	O5'	A:DUP401	3.8	43.1	1.0
	O	A:HOH602	4.1	33.9	1.0
	OD2	A:ASP256	4.2	37.9	1.0
	C5'	P:DC10	4.2	37.2	1.0
	C3'	P:DC10	4.2	41.5	1.0
	O3G	A:DUP401	4.4	25.3	1.0
	O	P:HOH112	4.5	32.4	1.0
	C5'	A:DUP401	4.5	38.8	1.0
	CB	A:ASP190	4.6	19.1	1.0
	CB	A:ASP192	4.7	22.5	1.0
	C4'	P:DC10	4.8	36.6	1.0
	N3A	A:DUP401	4.8	28.4	1.0
	O2B	A:DUP401	4.8	29.4	1.0
	O3'	P:DC10	4.9	52.7	1.0

Manganese binding site 3 out of 4 in 4r66

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Manganese Binding Sites List in 4r66

Manganese binding site 3 out of 4 in the Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
T:Mn101 b:76.7 occ:1.00	O	P:HOH132	2.4	35.8	1.0
	O	P:HOH127	2.6	42.9	1.0
	O	P:HOH131	2.8	41.9	1.0
	N7	T:DA14	3.5	24.2	1.0
	O	T:HOH222	3.8	28.4	1.0
	N7	T:DG15	3.9	25.4	1.0
	O6	T:DG15	3.9	20.7	1.0
	O	P:HOH107	4.0	25.8	1.0
	C8	T:DA14	4.0	27.1	1.0
	C5	T:DA14	4.4	24.8	1.0
	N4	T:DC16	4.6	26.6	1.0
	C5	T:DG15	4.6	17.5	1.0
	C6	T:DG15	4.6	18.8	1.0
	N6	T:DA14	4.8	19.4	1.0
	C8	T:DG15	4.9	17.7	1.0
	OP2	T:DA14	5.0	26.9	1.0

Manganese binding site 4 out of 4 in 4r66

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Manganese Binding Sites List in 4r66

Manganese binding site 4 out of 4 in the Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ternary Complex Crystal Structure of E295K Mutant of Dna Polymerase Beta within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mn101 b:34.5 occ:1.00	O	D:HOH235	2.2	34.6	1.0
	O	D:HOH216	2.2	38.0	1.0
	O	D:HOH221	2.3	26.7	1.0
	N7	D:DG4	2.5	20.5	1.0
	C8	D:DG4	3.3	24.0	1.0
	C5	D:DG4	3.6	21.1	1.0
	O	D:HOH229	3.9	28.2	1.0
	O6	D:DG4	4.0	23.9	1.0
	O	D:HOH206	4.1	24.0	1.0
	C6	D:DG4	4.2	24.1	1.0
	O6	D:DG5	4.5	25.8	1.0
	N9	D:DG4	4.5	24.6	1.0
	C4	D:DG4	4.7	21.9	1.0
	C6	D:DC3	4.7	19.2	1.0
	C2'	D:DC3	4.8	26.0	1.0
	C5	D:DC3	5.0	14.0	1.0

Reference:

W.A.Beard, D.D.Shock, V.K.Batra, R.Prasad, S.H.Wilson. Substrate-Induced Dna Polymerase Beta Activation. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25261471
DOI: 10.1074/JBC.M114.607432

Page generated: Sat Oct 5 21:06:19 2024

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