Atomistry » Magnesium » PDB 4c2z-4cfv » 4c8l
Atomistry »
  Magnesium »
    PDB 4c2z-4cfv »
      4c8l »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy