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Manganese 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:

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 Upstream at the Second Primer Nucleotide. (pdb code 6fbd). 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 Second Primer Nucleotide., PDB code: 6fbd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6fbd

Go back to Manganese Binding Sites List in 6fbd
Manganese 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 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 Second Primer Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:31.9
occ:0.63
 O A:HOH1012 2.0 38.7 1.0
O1A A:XG4903 2.1 40.8 1.0
O A:HOH1003 2.1 27.2 0.7
OD1 A:ASP785 2.1 55.1 1.0
OD2 A:ASP610 2.1 60.5 1.0
OE1 A:GLU786 2.2 57.5 0.3
O3' B:DC112 2.2 64.2 1.0
CG A:ASP610 3.0 56.6 1.0
CG A:ASP785 3.1 53.1 1.0
HG2 A:GLU786 3.1 61.5 0.3
CD A:GLU786 3.2 55.7 0.3
PA A:XG4903 3.2 52.5 1.0
HZ2 A:LYS831 3.3 85.0 1.0
OD1 A:ASP610 3.3 61.6 1.0
OD2 A:ASP785 3.3 59.4 1.0
HB2 A:GLU786 3.3 59.9 0.7
C3' B:DC112 3.3 59.1 1.0
H3' B:DC112 3.4 70.9 1.0
H5'' B:DC112 3.5 62.1 1.0
O2A A:XG4903 3.5 48.0 1.0
HB3 A:GLU786 3.5 60.2 0.3
CG A:GLU786 3.6 51.2 0.3
MN A:MN902 3.7 36.4 0.6
H5'A A:XG4903 3.7 56.5 1.0
O5' A:XG4903 3.9 48.1 1.0
OE1 A:GLU786 3.9 54.0 0.7
H4' B:DC112 3.9 66.2 1.0
HB3 A:GLU786 3.9 59.9 0.7
C4' B:DC112 4.0 55.1 1.0
CB A:GLU786 4.1 49.9 0.7
CB A:GLU786 4.1 50.2 0.3
C5' B:DC112 4.1 51.8 1.0
NZ A:LYS831 4.1 70.8 1.0
H5' A:XG4903 4.2 56.5 1.0
C5' A:XG4903 4.2 47.1 1.0
OE2 A:GLU786 4.3 53.7 0.3
H A:ASP785 4.3 47.1 1.0
HZ3 A:LYS831 4.4 85.0 1.0
CB A:ASP610 4.4 48.6 1.0
HG3 A:GLU786 4.4 61.5 0.3
CB A:ASP785 4.4 44.6 1.0
HB2 A:ASP610 4.5 58.3 1.0
O A:VAL783 4.5 45.8 1.0
C A:ASP785 4.5 44.6 1.0
O A:ASP785 4.6 45.9 1.0
C2' B:DC112 4.6 55.3 1.0
HZ1 A:LYS831 4.6 85.0 1.0
H2'' B:DC112 4.6 66.4 1.0
N3A A:XG4903 4.6 51.2 1.0
O5' B:DC112 4.7 45.9 1.0
HE3 A:LYS831 4.7 83.4 1.0
HB3 A:ASP785 4.7 53.5 1.0
HB2 A:GLU786 4.8 60.2 0.3
O3G A:XG4903 4.8 40.4 1.0
N A:GLU786 4.8 44.5 0.3
N A:GLU786 4.8 44.0 0.7
CD A:GLU786 4.8 53.5 0.7
CE A:LYS831 4.9 69.5 1.0
HE2 A:LYS831 4.9 83.4 1.0
HB A:VAL783 4.9 54.8 1.0
CA A:ASP785 4.9 44.7 1.0
H2' B:DC112 4.9 66.4 1.0
HA A:ASP610 4.9 51.1 1.0
H5' B:DC112 4.9 62.1 1.0
N A:ASP785 5.0 39.3 1.0
HB3 A:ASP610 5.0 58.3 1.0

Manganese binding site 2 out of 2 in 6fbd

Go back to Manganese Binding Sites List in 6fbd
Manganese 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 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 Second Primer Nucleotide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:36.4
occ:0.63
 O A:TYR611 2.1 61.3 1.0
OD2 A:ASP785 2.1 59.4 1.0
OD1 A:ASP610 2.1 61.6 1.0
O3G A:XG4903 2.1 40.4 1.0
O1B A:XG4903 2.2 50.8 1.0
O1A A:XG4903 2.3 40.8 1.0
PB A:XG4903 3.0 53.6 1.0
H5' A:XG4903 3.1 56.5 1.0
CG A:ASP610 3.2 56.6 1.0
CG A:ASP785 3.3 53.1 1.0
PA A:XG4903 3.3 52.5 1.0
C A:TYR611 3.3 56.7 1.0
N3A A:XG4903 3.3 51.2 1.0
PG A:XG4903 3.4 53.6 1.0
O3B A:XG4903 3.4 54.1 1.0
MN A:MN901 3.7 31.9 0.6
OD2 A:ASP610 3.7 60.5 1.0
OD1 A:ASP785 3.8 55.1 1.0
HA A:SER612 3.8 68.9 1.0
H A:GLN613 3.8 63.2 1.0
O A:HOH1022 3.9 43.7 1.0
HG22 A:ILE614 3.9 57.5 1.0
C5' A:XG4903 3.9 47.1 1.0
H A:ILE614 4.1 50.1 1.0
N A:TYR611 4.1 44.8 1.0
H A:TYR611 4.1 53.8 1.0
O5' A:XG4903 4.1 48.1 1.0
CA A:TYR611 4.2 49.0 1.0
HN3A A:XG4903 4.2 61.4 1.0
HB2 A:TYR611 4.2 55.3 1.0
H5'A A:XG4903 4.3 56.5 1.0
O1G A:XG4903 4.3 53.6 1.0
N A:SER612 4.3 58.0 1.0
N A:GLN613 4.3 52.7 1.0
CA A:SER612 4.4 57.5 1.0
O2G A:XG4903 4.4 49.2 1.0
HB2 A:ASP785 4.4 53.5 1.0
O2B A:XG4903 4.5 52.1 1.0
C A:ASP610 4.5 45.2 1.0
CB A:ASP785 4.5 44.6 1.0
CB A:ASP610 4.5 48.6 1.0
HB A:ILE614 4.5 55.8 1.0
O2A A:XG4903 4.6 48.0 1.0
O A:HOH1012 4.6 38.7 1.0
HB3 A:ASP610 4.6 58.3 1.0
C A:SER612 4.6 53.6 1.0
CG2 A:ILE614 4.7 47.9 1.0
HG21 A:ILE614 4.7 57.5 1.0
CB A:TYR611 4.7 46.1 1.0
O3' B:DC112 4.7 64.2 1.0
O A:ASP785 4.8 45.9 1.0
HO3' A:XG4903 4.9 58.1 1.0
N A:ILE614 4.9 41.7 1.0
HB3 A:TYR611 4.9 55.3 1.0
HB3 A:ASP785 4.9 53.5 1.0
O A:ASP610 4.9 47.1 1.0
CA A:ASP610 5.0 42.6 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: Sun Oct 6 04:35:34 2024

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