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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: Tue Dec 15 04:53:20 2020

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