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

All present enzymatic activity of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Fourth Primer Nucleotide.:
2.7.7.7;

The structure of Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Fourth Primer Nucleotide., PDB code: 6fbf 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)	47.33 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.310, 109.310, 91.123, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.6

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

Manganese binding site 1 out of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Fourth 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 Fourth Primer Nucleotide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn901 b:32.2 occ:1.00 OD1 A:ASP785 2.1 33.6 1.0 OD2 A:ASP610 2.2 32.7 1.0 O A:HOH1026 2.2 30.1 1.0 O A:HOH1045 2.2 33.6 1.0 O1A A:XG4903 2.2 36.6 1.0 O3' B:DC112 2.3 34.7 1.0 CG A:ASP610 3.1 32.1 1.0 CG A:ASP785 3.1 32.2 1.0 OD1 A:ASP610 3.3 33.7 1.0 PA A:XG4903 3.3 33.2 1.0 OD2 A:ASP785 3.4 35.0 1.0 HB2 A:GLU786 3.4 44.3 1.0 C3' B:DC112 3.5 41.6 1.0 O2A A:XG4903 3.5 33.0 1.0 H3' B:DC112 3.5 49.9 1.0 MN A:MN902 3.6 33.2 1.0 H5'' B:DC112 3.6 45.1 1.0 H5' A:XG4903 3.7 38.6 1.0 O A:HOH1148 3.9 35.5 1.0 O5' A:XG4903 3.9 33.1 1.0 H5'A A:XG4903 4.0 38.6 1.0 C5' A:XG4903 4.1 32.2 1.0 H A:ASP785 4.2 35.5 1.0 HB3 A:GLU786 4.2 44.3 1.0 H4' B:DC112 4.2 43.2 1.0 C4' B:DC112 4.2 36.0 1.0 CB A:GLU786 4.2 36.9 1.0 OE1 A:GLU786 4.3 38.1 1.0 C5' B:DC112 4.3 37.6 1.0 O A:VAL783 4.3 31.6 1.0 CB A:ASP610 4.4 32.5 1.0 CB A:ASP785 4.5 31.5 1.0 HB2 A:ASP610 4.5 38.9 1.0 C A:ASP785 4.6 31.0 1.0 C2' B:DC112 4.7 32.8 1.0 O5' B:DC112 4.7 34.1 1.0 N3A A:XG4903 4.7 33.4 1.0 O A:ASP785 4.7 31.3 1.0 HB A:VAL783 4.7 39.2 1.0 O1G A:XG4903 4.8 34.6 1.0 N A:GLU786 4.8 35.8 1.0 H2'' B:DC112 4.8 39.4 1.0 N A:ASP785 4.9 29.6 1.0 HB3 A:ASP785 4.9 37.8 1.0 CA A:ASP785 4.9 30.6 1.0 O1B A:XG4903 4.9 34.7 1.0 HA A:ASP610 4.9 38.9 1.0 H2' B:DC112 5.0 39.4 1.0 OP1 B:DC112 5.0 45.8 1.0

Manganese binding site 2 out of 2 in the Klentaq Dna Polymerase Processing A Modified Primer - Bearing the Modification Upstream at the Fourth 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 Fourth Primer Nucleotide. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn902 b:33.2 occ:1.00 O1B A:XG4903 2.1 34.7 1.0 O A:TYR611 2.1 41.5 1.0 O1G A:XG4903 2.1 34.6 1.0 OD1 A:ASP610 2.1 33.7 1.0 OD2 A:ASP785 2.1 35.0 1.0 O1A A:XG4903 2.2 36.6 1.0 PB A:XG4903 3.1 30.4 1.0 H5'A A:XG4903 3.2 38.6 1.0 CG A:ASP785 3.2 32.2 1.0 CG A:ASP610 3.2 32.1 1.0 C A:TYR611 3.3 39.6 1.0 PG A:XG4903 3.4 32.1 1.0 PA A:XG4903 3.5 33.2 1.0 O3B A:XG4903 3.5 33.7 1.0 N3A A:XG4903 3.6 33.4 1.0 MN A:MN901 3.6 32.2 1.0 OD1 A:ASP785 3.7 33.6 1.0 OD2 A:ASP610 3.7 32.7 1.0 H A:GLN613 3.8 45.2 1.0 HA A:SER612 3.8 52.0 1.0 O A:HOH1067 3.9 26.6 1.0 O A:HOH1148 3.9 35.5 1.0 HG22 A:ILE614 3.9 39.9 1.0 H A:ILE614 4.0 41.4 1.0 N A:TYR611 4.1 37.1 1.0 HB2 A:TYR611 4.1 45.7 1.0 C5' A:XG4903 4.1 32.2 1.0 H A:TYR611 4.1 44.6 1.0 CA A:TYR611 4.2 38.6 1.0 N A:SER612 4.3 43.0 1.0 N A:GLN613 4.3 37.7 1.0 O5' A:XG4903 4.3 33.1 1.0 O2G A:XG4903 4.4 34.6 1.0 O3G A:XG4903 4.4 32.0 1.0 C A:ASP610 4.4 32.9 1.0 HB A:ILE614 4.4 40.7 1.0 CA A:SER612 4.4 43.3 1.0 H5' A:XG4903 4.4 38.6 1.0 O2B A:XG4903 4.4 30.2 1.0 HB2 A:ASP785 4.5 37.8 1.0 O2A A:XG4903 4.5 33.0 1.0 CB A:ASP785 4.5 31.5 1.0 CB A:ASP610 4.5 32.5 1.0 HN3A A:XG4903 4.5 40.0 1.0 CB A:TYR611 4.6 38.1 1.0 HG21 A:ILE614 4.6 39.9 1.0 C A:SER612 4.6 42.5 1.0 CG2 A:ILE614 4.7 33.2 1.0 HB3 A:ASP610 4.7 38.9 1.0 O A:HOH1045 4.7 33.6 1.0 HB3 A:TYR611 4.7 45.7 1.0 O A:ASP610 4.8 33.6 1.0 N A:ILE614 4.8 34.5 1.0 HZ2 A:LYS663 4.8 54.0 1.0 HZ3 A:LYS663 4.9 54.0 1.0 HB3 A:ASP785 4.9 37.8 1.0 CA A:ASP610 4.9 32.4 1.0 HA A:ASP610 5.0 38.9 1.0 O A:ASP785 5.0 31.3 1.0 O3' B:DC112 5.0 34.7 1.0

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