Atomistry » Magnesium » PDB 6f5p-6fcd » 6fbd
Atomistry »
  Magnesium »
    PDB 6f5p-6fcd »
      6fbd »

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

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