Magnesium in PDB 4c8m: Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2)

Enzymatic activity of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2)

All present enzymatic activity of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2):
2.7.7.7;

Protein crystallography data

The structure of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2), PDB code: 4c8m was solved by K.Betz, D.A.Malyshev, T.Lavergne, W.Welte, K.Diederichs, F.E.Romesberg, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.236 / 1.57
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	65.374, 101.456, 204.543, 90.00, 90.00, 90.00
*R / R_free (%)*	17.85 / 20.71

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2) (pdb code 4c8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2), PDB code: 4c8m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4c8m

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Magnesium Binding Sites List in 4c8m

Magnesium binding site 1 out of 2 in the Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg1112 b:66.6 occ:0.87	O	B:HOH2115	2.2	43.1	0.9
	O	B:HOH2116	2.2	49.0	0.9
	O	B:HOH2118	2.2	53.2	0.9
	O	B:HOH2117	2.2	57.1	0.9
	O	B:HOH2113	2.2	67.7	0.9
	O	B:HOH2114	2.2	44.2	0.9
	H12	C:GOL1217	3.3	80.7	1.0
	HO1	C:GOL1217	3.7	70.7	1.0
	C1	C:GOL1217	4.2	67.3	1.0
	O	B:HOH2005	4.2	52.1	1.0
	H5	B:DC106	4.2	50.1	1.0
	N7	B:DG107	4.2	43.1	1.0
	O6	B:DG108	4.2	45.5	1.0
	H41	C:DC209	4.3	57.3	1.0
	O1	C:GOL1217	4.3	58.9	1.0
	H42	C:DC209	4.3	57.3	1.0
	H11	C:GOL1217	4.4	80.7	1.0
	O6	B:DG107	4.5	40.6	1.0
	C5	B:DC106	4.5	41.7	1.0
	H6	B:DC106	4.6	49.8	1.0
	N4	C:DC209	4.7	47.7	1.0
	C6	B:DC106	4.7	41.5	1.0
	H2'	B:DC106	4.9	60.2	1.0

Magnesium binding site 2 out of 2 in 4c8m

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Magnesium Binding Sites List in 4c8m

Magnesium binding site 2 out of 2 in the Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Aritificial Base Pair D5SICS-Dnam at the Postinsertion Site (Sequence Context 2) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg1216 b:58.9 occ:1.00	O	C:HOH2221	2.2	44.5	1.0
	O	C:HOH2216	2.2	77.6	1.0
	O	C:HOH2220	2.2	55.3	1.0
	O	C:HOH2218	2.2	57.7	1.0
	O	C:HOH2219	2.2	49.6	1.0
	O	C:HOH2217	2.2	43.6	1.0
	N7	C:DG213	4.1	38.1	1.0
	O6	C:DG213	4.2	38.1	1.0
	H42	B:DC103	4.2	53.7	1.0
	H73	C:DT212	4.3	46.9	1.0
	H41	B:DC103	4.3	53.7	1.0
	O6	C:DG214	4.3	36.1	1.0
	O6	B:DG102	4.3	44.1	1.0
	O	B:HOH2001	4.4	53.6	1.0
	N4	B:DC103	4.6	44.8	1.0
	O	C:HOH2010	4.6	43.0	1.0
	C5	C:DG213	4.8	36.8	1.0
	C6	C:DG213	4.8	38.4	1.0

Reference:

K.Betz, D.A.Malyshev, T.Lavergne, W.Welte, K.Diederichs, F.E.Romesberg, A.Marx. Structural Insights Into Dna Replication Without Hydrogen Bonds. J.Am.Chem.Soc. V. 135 18637 2013.
ISSN: ISSN 0002-7863
PubMed: 24283923
DOI: 10.1021/JA409609J

Page generated: Thu Aug 15 16:45:41 2024

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