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Magnesium in PDB 4c8l: Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1)

Enzymatic activity of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1)

All present enzymatic activity of Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1):
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 Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1), PDB code: 4c8l 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) 48.394 / 1.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 65.614, 100.543, 204.341, 90.00, 90.00, 90.00
R / Rfree (%) 18.86 / 21.38

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 Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1) (pdb code 4c8l). 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 Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1), PDB code: 4c8l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4c8l

Go back to Magnesium Binding Sites List in 4c8l
Magnesium binding site 1 out of 2 in the Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1)


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 Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1841

b:72.2
occ:1.00
 OP1 B:DG110 2.2 46.4 1.0
H5' B:DG110 2.4 39.0 1.0
O A:HOH2129 2.8 35.8 1.0
H5'' B:DG110 2.9 39.0 1.0
HA A:GLU537 2.9 45.5 1.0
C5' B:DG110 3.0 32.5 1.0
O A:HOH2128 3.0 47.0 1.0
P B:DG110 3.1 46.6 1.0
HD3 A:LYS540 3.2 42.9 1.0
O3' B:DC109 3.3 40.7 1.0
O A:HOH2130 3.3 46.4 1.0
HG3 A:GLU537 3.4 59.4 1.0
O5' B:DG110 3.4 36.1 1.0
HD2 A:LYS540 3.6 42.9 1.0
HB2 A:GLU537 3.7 50.2 1.0
CA A:GLU537 3.8 37.9 1.0
CD A:LYS540 3.9 35.8 1.0
HB3 A:LYS540 4.0 38.7 1.0
CB A:GLU537 4.1 41.8 1.0
CG A:GLU537 4.1 49.5 1.0
H4' B:DC109 4.1 44.2 1.0
C4' B:DG110 4.4 30.1 1.0
C3' B:DC109 4.4 37.9 1.0
O A:GLU537 4.4 32.9 1.0
H4' B:DG110 4.5 36.0 1.0
OP2 B:DG110 4.6 42.6 1.0
OE2 A:GLU537 4.6 63.9 1.0
H3' B:DC109 4.6 45.5 1.0
C A:GLU537 4.6 34.5 1.0
HE2 A:LYS540 4.7 43.6 1.0
CB A:LYS540 4.7 32.3 1.0
HB2 A:LYS540 4.7 38.7 1.0
CD A:GLU537 4.7 60.5 1.0
N A:GLU537 4.8 38.3 1.0
C4' B:DC109 4.8 36.9 1.0
HG2 A:GLU537 4.9 59.4 1.0
CG A:LYS540 4.9 34.5 1.0
O4' B:DG110 4.9 30.8 1.0
CE A:LYS540 4.9 36.4 1.0

Magnesium binding site 2 out of 2 in 4c8l

Go back to Magnesium Binding Sites List in 4c8l
Magnesium binding site 2 out of 2 in the Binary Complex of the Large Fragment of Dna Polymerase I From Thermus Aquaticus with the Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1)


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 Artificial Base Pair Dnam- D5SICS at the Postinsertion Site (Sequence Context 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1113

b:67.3
occ:0.86
 O B:HOH2008 2.2 42.9 0.9
O B:HOH2026 2.2 50.6 0.9
O B:HOH2025 2.2 51.9 0.9
O B:HOH2006 2.2 46.1 0.9
O B:HOH2027 2.2 54.5 0.9
O B:HOH2012 3.4 48.5 1.0
H5 B:DC106 3.9 56.6 1.0
O B:HOH2007 4.0 52.6 1.0
O1 C:SO41216 4.2 62.7 0.7
C5 B:DC106 4.2 47.2 1.0
O4 C:SO41216 4.2 64.3 0.7
N7 B:DG107 4.3 45.8 1.0
H6 B:DC106 4.4 57.2 1.0
O6 B:DG108 4.4 41.0 1.0
H41 C:DC209 4.4 40.7 1.0
H42 C:DC209 4.4 40.7 1.0
C6 B:DC106 4.5 47.6 1.0
O6 B:DG107 4.5 41.1 1.0
H2' B:DC106 4.7 62.7 1.0
N4 C:DC209 4.8 33.9 1.0
S C:SO41216 4.9 65.7 0.7
O C:HOH2011 4.9 51.0 1.0
C4 B:DC106 5.0 45.5 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 16:45:30 2024

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