Atomistry » Manganese » PDB 6f4q-6fxr » 6fbc
Atomistry »
  Manganese »
    PDB 6f4q-6fxr »
      6fbc »

Manganese 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:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6fbc

Go back to Manganese Binding Sites List in 6fbc
Manganese 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 Manganese with other atoms in the Mn 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:Mn903

b:22.2
occ:1.00
H3 B:D4B112 2.0 25.5 1.0
OD2 A:ASP610 2.1 25.8 1.0
OD1 A:ASP785 2.1 21.6 1.0
O A:HOH1003 2.2 23.3 1.0
O1A A:XG4901 2.2 19.6 1.0
O3' B:D4B112 2.3 21.2 1.0
O A:HOH1129 2.4 27.7 1.0
CG A:ASP785 3.1 20.6 1.0
CG A:ASP610 3.1 26.1 1.0
H5'B B:D4B112 3.3 22.1 1.0
H3' B:D4B112 3.4 26.8 1.0
PA A:XG4901 3.4 22.6 1.0
C3' B:D4B112 3.4 22.4 1.0
HB2 A:GLU786 3.4 32.0 1.0
OD2 A:ASP785 3.4 22.2 1.0
OD1 A:ASP610 3.5 26.6 1.0
MN A:MN904 3.6 20.4 0.9
O2A A:XG4901 3.7 24.0 1.0
H5'A A:XG4901 3.8 19.2 1.0
O A:HOH1118 3.9 28.8 1.0
HZ1 A:LYS831 3.9 45.0 1.0
O5' A:XG4901 3.9 18.7 1.0
HZ2 A:LYS831 4.0 45.0 1.0
H A:ASP785 4.0 22.8 1.0
HB3 A:GLU786 4.1 32.0 1.0
H5' A:XG4901 4.1 19.2 1.0
C5' B:D4B112 4.2 18.4 1.0
OE1 A:GLU786 4.2 28.8 1.0
CB A:GLU786 4.2 26.6 1.0
C5' A:XG4901 4.2 16.0 1.0
C4' B:D4B112 4.2 21.8 1.0
O A:VAL783 4.2 21.8 1.0
NZ A:LYS831 4.3 37.5 1.0
HH22 A:ARG660 4.4 59.6 0.5
CB A:ASP610 4.4 25.7 1.0
H4' B:D4B112 4.4 26.2 1.0
HB2 A:ASP610 4.5 30.9 1.0
CB A:ASP785 4.5 22.2 1.0
C A:ASP785 4.6 21.0 1.0
HZ3 A:LYS831 4.6 45.0 1.0
O1 B:D4B112 4.7 21.8 1.0
C2' B:D4B112 4.7 23.4 1.0
O A:ASP785 4.7 20.6 1.0
O3G A:XG4901 4.7 21.9 1.0
N A:ASP785 4.8 19.0 1.0
N A:GLU786 4.8 20.4 1.0
N3A A:XG4901 4.8 21.3 1.0
H2'B B:D4B112 4.8 28.1 1.0
HB3 A:ASP785 4.8 26.7 1.0
CA A:ASP785 4.8 19.4 1.0
O A:HOH1010 4.9 42.1 1.0
HA A:ASP610 4.9 27.3 1.0
HB A:VAL783 4.9 26.1 1.0
H2'A B:D4B112 5.0 28.1 1.0

Manganese binding site 2 out of 2 in 6fbc

Go back to Manganese Binding Sites List in 6fbc
Manganese 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 Manganese with other atoms in the Mn 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
A:Mn904

b:20.4
occ:0.92
OD2 A:ASP785 2.0 22.2 1.0
O3G A:XG4901 2.1 21.9 1.0
OD1 A:ASP610 2.1 26.6 1.0
O A:TYR611 2.1 26.0 1.0
O1A A:XG4901 2.3 19.6 1.0
O1B A:XG4901 2.3 22.3 1.0
CG A:ASP785 3.1 20.6 1.0
CG A:ASP610 3.1 26.1 1.0
PB A:XG4901 3.2 24.0 1.0
H5' A:XG4901 3.2 19.2 1.0
C A:TYR611 3.3 29.2 1.0
PG A:XG4901 3.5 24.9 1.0
PA A:XG4901 3.5 22.6 1.0
OD2 A:ASP610 3.5 25.8 1.0
OD1 A:ASP785 3.5 21.6 1.0
MN A:MN903 3.6 22.2 1.0
N3A A:XG4901 3.6 21.3 1.0
O3B A:XG4901 3.7 22.8 1.0
O A:HOH1118 3.8 28.8 1.0
H A:GLN613 3.9 32.4 1.0
N A:TYR611 4.0 22.9 1.0
H A:TYR611 4.0 27.5 1.0
O A:HOH1209 4.0 26.1 1.0
H A:ILE614 4.0 33.0 1.0
HG22 A:ILE614 4.0 31.9 1.0
HA A:SER612 4.0 34.6 1.0
HB2 A:TYR611 4.1 27.6 1.0
C5' A:XG4901 4.1 16.0 1.0
H3 B:D4B112 4.1 25.5 1.0
CA A:TYR611 4.2 26.7 1.0
O5' A:XG4901 4.2 18.7 1.0
HB A:ILE614 4.3 32.2 1.0
C A:ASP610 4.3 23.6 1.0
N A:SER612 4.4 27.0 1.0
N A:GLN613 4.4 27.0 1.0
O1G A:XG4901 4.4 28.5 1.0
CB A:ASP610 4.4 25.7 1.0
CB A:ASP785 4.4 22.2 1.0
HB2 A:ASP785 4.4 26.7 1.0
H5'A A:XG4901 4.5 19.2 1.0
O2G A:XG4901 4.5 24.6 1.0
CA A:SER612 4.5 28.9 1.0
HN3A A:XG4901 4.5 25.6 1.0
CB A:TYR611 4.6 23.0 1.0
O2A A:XG4901 4.6 24.0 1.0
HG21 A:ILE614 4.6 31.9 1.0
O2B A:XG4901 4.6 24.2 1.0
HB3 A:ASP610 4.6 30.9 1.0
C A:SER612 4.7 27.6 1.0
CG2 A:ILE614 4.7 26.6 1.0
HB3 A:TYR611 4.8 27.6 1.0
N A:ILE614 4.8 27.5 1.0
O A:ASP610 4.8 30.8 1.0
HB3 A:ASP785 4.8 26.7 1.0
CA A:ASP610 4.9 22.8 1.0
O A:ASP785 4.9 20.6 1.0
O A:HOH1129 4.9 27.7 1.0
HA A:ASP610 4.9 27.3 1.0
CB A:ILE614 4.9 26.9 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: Sun Oct 6 04:35:23 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy