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Magnesium in PDB 4c8k: Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp

Enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp

All present enzymatic activity of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp, PDB code: 4c8k 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) 48.637 / 2.17
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.039, 115.039, 91.106, 90.00, 90.00, 120.00
R / Rfree (%) 18.11 / 22.14

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp (pdb code 4c8k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp, PDB code: 4c8k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4c8k

Go back to Magnesium Binding Sites List in 4c8k
Magnesium binding site 1 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1835

b:72.5
occ:1.00
 O A:HOH2111 2.1 53.2 1.0
O A:HOH2085 2.1 62.3 1.0
O A:HOH2086 2.1 62.9 1.0
O2B A:BMR1834 2.1 80.0 1.0
O1A A:BMR1834 2.3 76.5 1.0
O3C A:BMR1834 2.4 79.9 1.0
PB A:BMR1834 3.4 80.7 1.0
HH22 A:ARG587 3.5 93.8 1.0
PC A:BMR1834 3.6 80.0 1.0
PA A:BMR1834 3.6 76.9 1.0
O3B A:BMR1834 3.7 79.0 1.0
O3A A:BMR1834 3.9 62.0 1.0
O A:HOH2105 4.0 57.9 1.0
H5'A A:BMR1834 4.1 88.3 1.0
O2C A:BMR1834 4.3 79.0 1.0
NH2 A:ARG587 4.3 78.2 1.0
HH12 A:ARG587 4.6 94.8 1.0
H5' A:BMR1834 4.6 88.3 1.0
O2A A:BMR1834 4.6 77.8 1.0
HH21 A:ARG587 4.7 93.8 1.0
O1B A:BMR1834 4.7 82.2 1.0
O5' A:BMR1834 4.7 75.2 1.0
C5' A:BMR1834 4.7 73.6 1.0
O1C A:BMR1834 4.8 79.3 1.0
HZ2 A:LYS663 4.8 97.0 1.0

Magnesium binding site 2 out of 2 in 4c8k

Go back to Magnesium Binding Sites List in 4c8k
Magnesium binding site 2 out of 2 in the Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Partially Closed Complex with the Artificial Base Pair D5SICS-Dnamtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1113

b:76.2
occ:1.00
 O B:HOH2018 2.2 57.1 1.0
O B:HOH2004 2.2 52.9 1.0
O B:HOH2016 2.2 55.0 1.0
O B:HOH2017 2.2 69.5 1.0
O B:HOH2005 2.2 40.8 1.0
O B:HOH2008 2.2 47.9 1.0
O6 B:DG108 4.0 41.9 1.0
O C:HOH2005 4.2 44.1 1.0
H41 C:DC209 4.2 44.0 1.0
H42 C:DC209 4.3 44.0 1.0
O6 B:DG107 4.4 36.4 1.0
O C:HOH2004 4.4 40.0 1.0
N7 B:DG107 4.4 39.6 1.0
H5 B:DC106 4.5 39.8 1.0
N4 C:DC209 4.6 36.7 1.0
C5 B:DC106 5.0 33.2 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: Mon Dec 14 09:16:41 2020

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