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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 / Rfree (%) 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

Go back to 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

Go back to 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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