Manganese in PDB 6fbi: Klentaq Dna Polymerase in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site

All present enzymatic activity of Klentaq Dna Polymerase in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site:
2.7.7.7;

The structure of Klentaq Dna Polymerase in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site, PDB code: 6fbi 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)	47.53 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.770, 109.770, 91.460, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 23.5

The binding sites of Manganese atom in the Klentaq Dna Polymerase in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site (pdb code 6fbi). 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 in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site, PDB code: 6fbi:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Klentaq Dna Polymerase in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site


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 in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn902 b:28.0 occ:0.55 O A:HOH1001 1.6 25.6 1.0 OD1 A:ASP785 1.8 55.2 1.0 OD2 A:ASP610 2.1 63.0 1.0 O A:HOH1044 2.1 26.2 1.0 O1A A:XG4901 2.2 35.0 1.0 O3' B:DC112 2.3 44.6 1.0 CG A:ASP785 2.8 52.5 1.0 CG A:ASP610 3.0 59.9 1.0 OD2 A:ASP785 3.2 59.7 1.0 OD1 A:ASP610 3.3 66.0 1.0 C3' B:DC112 3.4 45.4 1.0 PA A:XG4901 3.4 38.2 1.0 HB2 A:GLU786 3.4 50.6 1.0 MN A:MN903 3.5 29.3 0.7 H3' B:DC112 3.5 54.5 1.0 O2A A:XG4901 3.6 37.8 1.0 H5'' B:DC112 3.7 53.1 1.0 H5'A A:XG4901 3.7 46.7 1.0 HZ1 A:LYS831 3.9 65.8 1.0 HZ3 A:LYS831 3.9 65.8 1.0 H A:ASP785 3.9 46.2 1.0 O5' A:XG4901 4.0 38.4 1.0 O A:HOH1139 4.0 36.6 1.0 H5' A:XG4901 4.0 46.7 1.0 HB3 A:GLU786 4.1 50.6 1.0 H4' B:DC112 4.1 53.9 1.0 C5' A:XG4901 4.1 38.9 1.0 CB A:ASP785 4.2 45.4 1.0 C4' B:DC112 4.2 44.9 1.0 CB A:GLU786 4.2 42.1 1.0 OE1 A:GLU786 4.3 45.8 1.0 NZ A:LYS831 4.3 54.9 1.0 C A:ASP785 4.3 39.6 1.0 O A:VAL783 4.3 37.9 1.0 O A:ASP785 4.4 40.3 1.0 CB A:ASP610 4.4 53.9 1.0 C5' B:DC112 4.4 44.3 1.0 HB2 A:ASP610 4.4 64.6 1.0 HB3 A:ASP785 4.5 54.5 1.0 HZ2 A:LYS831 4.5 65.8 1.0 CA A:ASP785 4.6 40.4 1.0 N A:GLU786 4.6 37.5 1.0 N A:ASP785 4.6 38.5 1.0 C2' B:DC112 4.6 44.6 1.0 H2'' B:DC112 4.7 53.5 1.0 O3G A:XG4901 4.8 34.6 1.0 N3A A:XG4901 4.8 39.7 1.0 O1B A:XG4901 4.8 34.7 1.0 HB2 A:ASP785 4.8 54.5 1.0 HA A:ASP610 4.8 51.4 1.0 H2' B:DC112 4.9 53.5 1.0 O5' B:DC112 4.9 41.5 1.0 CA A:GLU786 4.9 39.5 1.0 H A:GLU786 4.9 45.0 1.0 HB3 A:ASP610 5.0 64.6 1.0

Manganese binding site 2 out of 2 in the Klentaq Dna Polymerase in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site


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 in A Closed, Ternary Complex with Dgpnhpp Bound in the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn903 b:29.3 occ:0.67 O1B A:XG4901 2.0 34.7 1.0 OD2 A:ASP785 2.0 59.7 1.0 OD1 A:ASP610 2.1 66.0 1.0 O A:TYR611 2.2 66.4 1.0 O3G A:XG4901 2.2 34.6 1.0 O1A A:XG4901 2.2 35.0 1.0 CG A:ASP785 3.1 52.5 1.0 H5' A:XG4901 3.2 46.7 1.0 CG A:ASP610 3.2 59.9 1.0 PB A:XG4901 3.2 39.1 1.0 C A:TYR611 3.4 60.1 1.0 PA A:XG4901 3.4 38.2 1.0 MN A:MN902 3.5 28.0 0.6 OD1 A:ASP785 3.5 55.2 1.0 PG A:XG4901 3.5 40.0 1.0 OD2 A:ASP610 3.6 63.0 1.0 N3A A:XG4901 3.6 39.7 1.0 O3B A:XG4901 3.7 40.2 1.0 O A:HOH1042 3.7 35.2 1.0 HG22 A:ILE614 3.9 50.3 1.0 H A:ILE614 4.0 57.7 1.0 N A:TYR611 4.0 47.5 1.0 H A:GLN613 4.0 66.4 1.0 C5' A:XG4901 4.0 38.9 1.0 HA A:SER612 4.0 69.8 1.0 H A:TYR611 4.1 56.9 1.0 HB2 A:TYR611 4.1 60.0 1.0 O A:HOH1139 4.1 36.6 1.0 O A:HOH1001 4.2 25.6 1.0 CA A:TYR611 4.2 53.3 1.0 O5' A:XG4901 4.3 38.4 1.0 HB A:ILE614 4.3 53.7 1.0 H5'A A:XG4901 4.3 46.7 1.0 CB A:ASP785 4.3 45.4 1.0 HB2 A:ASP785 4.4 54.5 1.0 O2B A:XG4901 4.4 40.2 1.0 N A:SER612 4.4 58.9 1.0 C A:ASP610 4.4 49.3 1.0 N A:GLN613 4.4 55.3 1.0 O2G A:XG4901 4.4 38.8 1.0 O1G A:XG4901 4.5 42.3 1.0 CB A:ASP610 4.5 53.9 1.0 O2A A:XG4901 4.5 37.8 1.0 HN3A A:XG4901 4.5 47.6 1.0 CA A:SER612 4.6 58.2 1.0 HG21 A:ILE614 4.6 50.3 1.0 CB A:TYR611 4.6 50.0 1.0 CG2 A:ILE614 4.6 42.0 1.0 HB3 A:ASP610 4.7 64.6 1.0 C A:SER612 4.7 55.3 1.0 O A:ASP785 4.7 40.3 1.0 N A:ILE614 4.7 48.1 1.0 HB3 A:ASP785 4.8 54.5 1.0 HB3 A:TYR611 4.8 60.0 1.0 O A:ASP610 4.8 50.6 1.0 CB A:ILE614 4.9 44.8 1.0 O3' B:DC112 4.9 44.6 1.0 CA A:ASP610 4.9 42.8 1.0 HA A:ASP610 4.9 51.4 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