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Magnesium in PDB 6fbc: Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.

Enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.

All present enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.:
2.7.7.7;

Protein crystallography data

The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer., PDB code: 6fbc was solved by H.M.Kropp, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 1.54
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.230, 109.230, 90.700, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 20.9

Other elements in 6fbc:

The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. (pdb code 6fbc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer., PDB code: 6fbc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6fbc

Go back to Magnesium Binding Sites List in 6fbc
Magnesium binding site 1 out of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:22.5
occ:1.00
 OE2 A:GLU462 1.9 44.0 1.0
OE2 A:GLU466 2.0 43.1 0.6
O A:HOH1100 2.2 45.3 1.0
O A:HOH1177 2.3 33.0 1.0
HH12 A:ARG593 2.9 52.5 1.0
CD A:GLU462 3.0 41.6 1.0
CD A:GLU466 3.1 44.2 0.6
HG2 A:GLU462 3.1 46.0 1.0
CG A:GLU462 3.4 38.4 1.0
HG3 A:GLU462 3.5 46.0 1.0
OE1 A:GLU466 3.5 42.3 0.6
NH1 A:ARG593 3.7 43.7 1.0
HH11 A:ARG593 3.8 52.5 1.0
OE1 A:GLU462 4.1 36.7 1.0
HG3 A:GLU466 4.1 55.5 0.4
CG A:GLU466 4.3 43.6 0.6
O A:HOH1196 4.4 57.7 1.0
HG2 A:GLU466 4.4 52.3 0.6
OE2 A:GLU466 4.5 44.4 0.4
HG3 A:GLU466 4.5 52.3 0.6
HH22 A:ARG593 4.5 55.1 1.0
CZ A:ARG593 4.8 43.7 1.0
CB A:GLU462 4.9 32.9 1.0
CG A:GLU466 5.0 46.3 0.4

Magnesium binding site 2 out of 2 in 6fbc

Go back to Magnesium Binding Sites List in 6fbc
Magnesium binding site 2 out of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification at the 3'-Terminus of the Primer. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:30.1
occ:0.95
 O B:HOH312 2.0 24.1 1.0
O B:HOH335 2.0 40.9 1.0
O B:HOH315 2.1 23.9 1.0
O B:HOH303 2.2 31.3 1.0
O B:HOH336 2.3 42.1 1.0
O C:HOH446 2.3 47.5 1.0
O6 B:DG108 4.0 22.8 1.0
O C:HOH414 4.1 35.0 1.0
O C:HOH440 4.2 34.9 1.0
H42 C:DC209 4.3 27.2 1.0
H41 C:DC209 4.3 27.2 1.0
O B:HOH308 4.3 27.9 1.0
N7 B:DG107 4.3 21.2 1.0
O6 B:DG107 4.3 19.6 1.0
O B:HOH330 4.4 37.0 1.0
H5 B:DC106 4.4 25.2 1.0
N4 C:DC209 4.6 22.7 1.0
O B:HOH329 4.6 41.4 1.0
O B:HOH323 4.7 40.5 1.0
C5 B:DC106 4.8 21.0 1.0

Reference:

H.M.Kropp, S.L.Durr, C.Peter, K.Diederichs, A.Marx. Snapshots of A Modified Nucleotide Moving Through the Confines of A Dna Polymerase. Proc. Natl. Acad. Sci. V. 115 9992 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30224478
DOI: 10.1073/PNAS.1811518115
Page generated: Tue Oct 1 00:18:01 2024

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