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Manganese in PDB 6fbe: Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Third Primer Nucleotide.

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

All present enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Third 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 Third Primer Nucleotide., PDB code: 6fbe 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) 46.97 / 1.59
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.480, 108.480, 90.309, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 20.3

Other elements in 6fbe:

The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Third Primer Nucleotide. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Third Primer Nucleotide. (pdb code 6fbe). 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 Upstream at the Third Primer Nucleotide., PDB code: 6fbe:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6fbe

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


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 Upstream at the Third Primer Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:23.3
occ:0.92
OD1 A:ASP785 2.1 23.4 1.0
OD2 A:ASP610 2.2 25.9 1.0
O A:HOH1014 2.2 26.2 1.0
O A:HOH1119 2.2 32.1 1.0
O3' B:DC112 2.2 22.3 1.0
O1A A:XG4904 2.3 21.5 1.0
CG A:ASP785 3.1 25.5 1.0
CG A:ASP610 3.1 29.4 1.0
HB2 A:GLU786 3.4 27.2 0.9
C3' B:DC112 3.4 31.5 1.0
PA A:XG4904 3.4 25.2 1.0
OD2 A:ASP785 3.4 22.4 1.0
OD1 A:ASP610 3.5 25.3 1.0
H3' B:DC112 3.5 37.9 1.0
MN A:MN902 3.6 24.2 1.0
O2A A:XG4904 3.7 27.7 1.0
H5'' B:DC112 3.7 25.5 1.0
H5'A A:XG4904 3.8 29.6 1.0
O A:HOH1260 4.0 31.0 1.0
O5' A:XG4904 4.0 21.5 1.0
H5' A:XG4904 4.1 29.6 1.0
H A:ASP785 4.1 22.1 1.0
HZ3 A:LYS831 4.1 93.6 1.0
H4' B:DC112 4.2 26.3 1.0
C4' B:DC112 4.2 21.9 1.0
C5' A:XG4904 4.2 24.7 1.0
HB3 A:GLU786 4.2 27.2 0.9
CB A:GLU786 4.2 22.6 0.9
OE1 A:GLU786 4.3 27.0 0.9
C5' B:DC112 4.3 21.2 1.0
O A:VAL783 4.4 20.5 1.0
CB A:ASP610 4.5 27.2 1.0
CB A:ASP785 4.5 20.4 1.0
C A:ASP785 4.5 22.3 1.0
HB2 A:ASP610 4.5 32.7 1.0
C2' B:DC112 4.6 37.7 1.0
O A:ASP785 4.6 22.2 1.0
H2'' B:DC112 4.7 45.3 1.0
HZ1 A:LYS831 4.7 93.6 1.0
O3G A:XG4904 4.7 24.0 1.0
N A:GLU786 4.8 20.9 0.9
N A:ASP785 4.8 18.4 1.0
NZ A:LYS831 4.8 78.0 1.0
CA A:ASP785 4.8 22.4 1.0
N3A A:XG4904 4.8 35.4 1.0
HB3 A:ASP785 4.8 24.6 1.0
H2' B:DC112 4.9 45.3 1.0
O5' B:DC112 4.9 22.1 1.0
HA A:ASP610 4.9 27.6 1.0

Manganese binding site 2 out of 2 in 6fbe

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


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 Upstream at the Third Primer Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:24.2
occ:1.00
OD2 A:ASP785 2.1 22.4 1.0
O A:TYR611 2.1 25.4 1.0
O3G A:XG4904 2.1 24.0 1.0
OD1 A:ASP610 2.1 25.3 1.0
O1B A:XG4904 2.2 25.1 1.0
O1A A:XG4904 2.3 21.5 1.0
CG A:ASP785 3.2 25.5 1.0
CG A:ASP610 3.2 29.4 1.0
H5' A:XG4904 3.2 29.6 1.0
PB A:XG4904 3.2 28.8 1.0
C A:TYR611 3.3 26.5 1.0
PG A:XG4904 3.4 30.7 1.0
PA A:XG4904 3.5 25.2 1.0
OD1 A:ASP785 3.6 23.4 1.0
MN A:MN901 3.6 23.3 0.9
OD2 A:ASP610 3.6 25.9 1.0
N3A A:XG4904 3.6 35.4 1.0
O3B A:XG4904 3.6 28.5 1.0
H A:GLN613 3.8 34.9 1.0
O A:HOH1260 3.9 31.0 1.0
O A:HOH1235 4.0 29.1 1.0
N A:TYR611 4.0 21.6 1.0
HA A:SER612 4.0 36.2 1.0
H A:TYR611 4.0 25.8 1.0
H A:ILE614 4.0 33.6 1.0
HG22 A:ILE614 4.1 30.8 1.0
HB2 A:TYR611 4.1 28.4 1.0
C5' A:XG4904 4.1 24.7 1.0
CA A:TYR611 4.1 22.6 1.0
O1G A:XG4904 4.3 30.7 1.0
O5' A:XG4904 4.3 21.5 1.0
N A:SER612 4.3 26.4 1.0
N A:GLN613 4.3 29.1 1.0
C A:ASP610 4.4 22.9 1.0
HB2 A:ASP785 4.4 24.6 1.0
HB A:ILE614 4.4 36.7 1.0
CB A:ASP785 4.4 20.4 1.0
H5'A A:XG4904 4.5 29.6 1.0
CB A:ASP610 4.5 27.2 1.0
CA A:SER612 4.5 30.2 1.0
O2G A:XG4904 4.5 29.9 1.0
HN3A A:XG4904 4.6 42.6 1.0
CB A:TYR611 4.6 23.7 1.0
O2B A:XG4904 4.6 25.4 1.0
O2A A:XG4904 4.6 27.7 1.0
C A:SER612 4.6 26.9 1.0
HB3 A:ASP610 4.7 32.7 1.0
O A:HOH1119 4.7 32.1 1.0
HB3 A:TYR611 4.7 28.4 1.0
HG21 A:ILE614 4.8 30.8 1.0
CG2 A:ILE614 4.8 25.6 1.0
N A:ILE614 4.8 28.0 1.0
O A:ASP610 4.8 25.8 1.0
O A:ASP785 4.8 22.2 1.0
HB3 A:ASP785 4.9 24.6 1.0
CA A:ASP610 4.9 22.9 1.0
HA A:ASP610 4.9 27.6 1.0
O3' B:DC112 5.0 22.3 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 04:53:22 2020

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