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Magnesium in PDB 6fbd: Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide.

Enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide.

All present enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide.:
2.7.7.7;

Protein crystallography data

The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide., PDB code: 6fbd 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) 47.08 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.964, 109.964, 91.165, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 23.3

Other elements in 6fbd:

The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide. 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 Upstream at the Second Primer Nucleotide. (pdb code 6fbd). 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 Upstream at the Second Primer Nucleotide., PDB code: 6fbd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6fbd

Go back to Magnesium Binding Sites List in 6fbd
Magnesium binding site 1 out of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide.


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 Upstream at the Second Primer Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:38.9
occ:1.00
 O B:HOH311 2.0 39.1 1.0
O B:HOH305 2.1 40.5 1.0
O B:HOH313 2.1 44.6 1.0
O C:HOH430 2.1 46.7 1.0
O B:HOH314 2.2 45.8 1.0
O B:HOH304 2.3 42.7 1.0
O6 B:DG108 4.0 35.3 1.0
O C:HOH419 4.0 44.5 1.0
O C:HOH423 4.1 40.2 1.0
H5 B:DC106 4.2 36.1 1.0
H42 C:DC209 4.2 46.5 1.0
H41 C:DC209 4.3 46.5 1.0
O6 B:DG107 4.3 31.8 1.0
N7 B:DG107 4.5 35.8 1.0
N4 C:DC209 4.6 38.8 1.0
C5 B:DC106 4.7 30.1 1.0

Magnesium binding site 2 out of 2 in 6fbd

Go back to Magnesium Binding Sites List in 6fbd
Magnesium binding site 2 out of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Second Primer Nucleotide.


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 Upstream at the Second Primer Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:53.7
occ:1.00
 O C:HOH426 2.0 54.4 1.0
O C:HOH425 2.2 52.5 1.0
O C:HOH422 2.2 51.3 1.0
O C:HOH432 2.3 64.7 1.0
O C:HOH416 2.3 88.5 1.0
N7 C:DG205 2.7 39.1 1.0
O C:HOH431 3.4 64.8 1.0
C8 C:DG205 3.4 39.6 1.0
H8 C:DG205 3.5 47.5 1.0
C5 C:DG205 3.7 39.2 1.0
O C:HOH429 3.7 89.0 1.0
O6 C:DG205 4.0 41.5 1.0
C6 C:DG205 4.2 40.5 1.0
N7 C:DG206 4.3 34.1 1.0
H3' C:DC204 4.5 53.9 1.0
OP2 C:DG205 4.5 36.6 1.0
C5 C:DC204 4.6 48.9 1.0
N9 C:DG205 4.6 39.8 1.0
O6 C:DG206 4.7 32.8 1.0
H5 C:DC204 4.7 58.7 1.0
C4 C:DC204 4.7 47.0 1.0
C4 C:DG205 4.8 39.0 1.0
C6 C:DC204 4.9 48.1 1.0
HH22 A:ARG677 5.0 77.6 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 00:18:23 2024

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