Magnesium in PDB 2pfq: Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal

Enzymatic activity of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal

All present enzymatic activity of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal:
2.7.7.7;

Protein crystallography data

The structure of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal, PDB code: 2pfq was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 2.10
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.091, 63.485, 139.775, 90.00, 90.00, 90.00
*R / R_free (%)*	25.6 / 28.7

Other elements in 2pfq:

The structure of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Sodium	(Na)	2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal (pdb code 2pfq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal, PDB code: 2pfq:

Magnesium binding site 1 out of 1 in 2pfq

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Magnesium Binding Sites List in 2pfq

Magnesium binding site 1 out of 1 in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1294 b:38.4 occ:0.25	MN	A:MN1296	0.1	45.2	0.8
	O2B	A:DCP1438	1.9	26.2	0.2
	O11	A:PPV1439	2.0	49.9	0.8
	O2A	A:DCP1438	2.0	27.2	0.2
	O2G	A:DCP1438	2.0	29.1	0.2
	O12	A:PPV1439	2.0	54.0	0.8
	OD1	A:ASP427	2.0	36.1	0.2
	O	A:HOH1602	2.0	46.9	1.0
	OD1	A:ASP427	2.1	24.3	0.5
	OD2	A:ASP429	2.1	40.0	0.2
	OD2	A:ASP429	2.2	27.8	0.8
	OP1	P:DC7	2.2	28.7	0.8
	PB	A:DCP1438	2.9	27.9	0.2
	P1	A:PPV1439	3.0	52.1	0.8
	PA	A:DCP1438	3.1	27.0	0.2
	CG	A:ASP427	3.1	24.9	0.5
	P2	A:PPV1439	3.1	54.9	0.8
	O21	A:PPV1439	3.2	53.6	0.8
	O3A	A:DCP1438	3.2	28.4	0.2
	PG	A:DCP1438	3.2	30.1	0.2
	CG	A:ASP427	3.2	36.6	0.2
	CG	A:ASP429	3.2	29.1	0.8
	CG	A:ASP429	3.2	40.3	0.2
	OPP	A:PPV1439	3.3	53.6	0.8
	O3B	A:DCP1438	3.3	28.7	0.2
	OD1	A:ASP429	3.6	33.1	0.8
	MN	A:MN1297	3.6	42.5	0.8
	P	P:DC7	3.6	33.0	0.8
	OD2	A:ASP427	3.6	25.0	0.5
	NA	A:NA1295	3.7	30.1	0.2
	OD1	A:ASP429	3.7	41.3	0.2
	OD2	A:ASP427	3.7	36.9	0.2
	O32	A:PPV1439	3.8	53.5	0.8
	O3G	A:DCP1438	3.9	28.6	0.2
	O5'	P:DC7	4.0	31.4	0.8
	C5'	A:DCP1438	4.0	29.5	0.2
	C5'	P:DC7	4.0	33.0	0.8
	O	A:ASP427	4.0	36.6	0.2
	O5'	A:DCP1438	4.1	27.9	0.2
	O	A:ASP427	4.2	22.7	0.5
	O31	A:PPV1439	4.2	50.6	0.8
	O1B	A:DCP1438	4.3	26.7	0.2
	O1A	A:DCP1438	4.3	27.2	0.2
	C	A:ASP427	4.3	36.5	0.2
	N	A:ASP427	4.4	35.7	0.2
	CB	A:ASP427	4.4	36.0	0.2
	CB	A:ASP427	4.4	22.9	0.5
	N	A:ASP427	4.4	24.0	0.5
	O1G	A:DCP1438	4.4	28.4	0.2
	O22	A:PPV1439	4.4	53.1	0.8
	C	A:ASP427	4.4	22.6	0.5
	O	A:HOH1493	4.5	33.0	1.0
	OP2	P:DC7	4.5	33.8	0.8
	CB	A:ASP429	4.5	40.2	0.2
	CB	A:ASP429	4.5	28.4	0.8
	N	A:SER417	4.6	31.8	1.0
	CA	A:GLY416	4.6	31.9	1.0
	CA	A:ASP427	4.6	36.2	0.2
	O	P:HOH299	4.6	39.8	1.0
	OG	A:SER417	4.7	27.7	1.0
	CA	A:ASP427	4.7	22.8	0.5
	O3'	P:DC6	4.7	27.4	0.8
	N	A:ASP429	4.9	28.5	0.8
	N	A:ASP429	4.9	38.8	0.2
N	A:VAL428	5.0	37.6	1.0

Reference:

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Role of the Catalytic Metal During Polymerization By Dna Polymerase Lambda. Dna Repair V. 6 1333 2007.
ISSN: ISSN 1568-7864
PubMed: 17475573
DOI: 10.1016/J.DNAREP.2007.03.005

Page generated: Sun Aug 10 12:54:33 2025

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