Manganese in PDB 5omf: Closed, Ternary Structure of Kod Dna Polymerase

All present enzymatic activity of Closed, Ternary Structure of Kod Dna Polymerase:
2.7.7.7;

The structure of Closed, Ternary Structure of Kod Dna Polymerase, PDB code: 5omf was solved by H.M.Kropp, K.Betz, J.Wirth, K.Diederichs, A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.27 / 2.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.909, 147.559, 71.142, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.4

The structure of Closed, Ternary Structure of Kod Dna Polymerase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Closed, Ternary Structure of Kod Dna Polymerase (pdb code 5omf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Closed, Ternary Structure of Kod Dna Polymerase, PDB code: 5omf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Closed, Ternary Structure of Kod Dna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Closed, Ternary Structure of Kod Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:46.1 occ:1.00 OE2 A:GLU580 2.0 64.9 1.0 OD2 A:ASP404 2.2 40.7 1.0 O2G A:DTP810 2.2 37.3 1.0 O A:HOH913 2.4 39.2 1.0 O A:HOH928 2.4 31.3 1.0 O A:HOH992 2.5 36.7 1.0 HOG2 A:DTP810 2.8 44.7 1.0 HB3 A:ASP404 3.0 37.3 1.0 HOG3 A:DTP810 3.0 38.1 1.0 CG A:ASP404 3.1 24.6 1.0 CD A:GLU580 3.1 47.8 1.0 PG A:DTP810 3.2 28.8 1.0 O3G A:DTP810 3.3 31.8 1.0 MN A:MN802 3.4 30.9 1.0 OE1 A:GLU580 3.5 49.8 1.0 CB A:ASP404 3.5 31.1 1.0 O A:PHE405 3.8 35.4 1.0 O1G A:DTP810 3.8 27.2 1.0 HB2 A:ASP404 4.1 37.3 1.0 OD1 A:ASP404 4.1 33.2 1.0 O1A A:DTP810 4.2 37.0 1.0 OE1 A:GLU578 4.3 42.0 1.0 O A:HOH1095 4.4 41.5 1.0 CG A:GLU580 4.4 47.8 1.0 HB2 A:GLU580 4.4 55.1 1.0 HA A:ARG406 4.5 35.9 1.0 HG3 A:GLU580 4.5 57.4 1.0 O3B A:DTP810 4.6 30.0 1.0 O A:ASP404 4.6 30.5 1.0 C A:ASP404 4.6 34.5 1.0 HZ1 A:LYS487 4.6 74.8 1.0 O A:HOH938 4.7 33.1 1.0 CA A:ASP404 4.7 32.2 1.0 HE2 A:TYR402 4.7 57.7 1.0 C A:PHE405 4.7 38.3 1.0 HB2 A:GLU578 4.8 42.7 1.0 HH22 A:ARG460 4.8 47.1 1.0 MG A:MG807 4.9 32.9 1.0 CB A:GLU580 4.9 45.9 1.0 O1B A:DTP810 4.9 33.5 1.0

Manganese binding site 2 out of 2 in the Closed, Ternary Structure of Kod Dna Polymerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Closed, Ternary Structure of Kod Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:30.9 occ:1.00 HOG2 A:DTP810 1.3 44.7 1.0 OD2 A:ASP542 2.0 34.4 1.0 OD2 A:ASP404 2.1 40.7 1.0 O2G A:DTP810 2.1 37.3 1.0 O1B A:DTP810 2.2 33.5 1.0 O A:PHE405 2.2 35.4 1.0 O1A A:DTP810 2.3 37.0 1.0 CG A:ASP404 3.0 24.6 1.0 CG A:ASP542 3.1 30.8 1.0 H5'2 A:DTP810 3.1 50.5 1.0 PB A:DTP810 3.2 30.6 1.0 PA A:DTP810 3.4 31.3 1.0 OD1 A:ASP404 3.4 33.2 1.0 C A:PHE405 3.4 38.3 1.0 MN A:MN801 3.4 46.1 1.0 MG A:MG807 3.4 32.9 1.0 PG A:DTP810 3.4 28.8 1.0 OD1 A:ASP542 3.5 33.1 1.0 O3A A:DTP810 3.5 23.8 1.0 O3B A:DTP810 3.7 30.0 1.0 H A:PHE405 3.9 38.7 1.0 N A:PHE405 4.0 32.2 1.0 H A:LEU408 4.0 48.8 1.0 H A:SER407 4.0 40.2 1.0 HB2 A:PHE405 4.0 51.9 1.0 O A:HOH913 4.1 39.2 1.0 C5' A:DTP810 4.1 42.1 1.0 CA A:PHE405 4.2 30.0 1.0 HA A:ARG406 4.2 35.9 1.0 O5' A:DTP810 4.2 33.6 1.0 O1G A:DTP810 4.2 27.2 1.0 O A:HOH992 4.2 36.7 1.0 CB A:ASP404 4.3 31.1 1.0 HB2 A:LEU408 4.4 34.1 1.0 CB A:ASP542 4.4 44.7 1.0 HB2 A:ASP542 4.4 53.7 1.0 N A:SER407 4.4 33.5 1.0 N A:ARG406 4.4 31.8 1.0 H5'1 A:DTP810 4.4 50.5 1.0 C A:ASP404 4.5 34.5 1.0 HB3 A:ASP404 4.5 37.3 1.0 CB A:PHE405 4.5 43.3 1.0 O3G A:DTP810 4.5 31.8 1.0 HOG3 A:DTP810 4.6 38.1 1.0 O2A A:DTP810 4.6 33.7 1.0 O2B A:DTP810 4.6 27.5 1.0 O A:HOH1095 4.7 41.5 1.0 CA A:ARG406 4.7 29.9 1.0 HB3 A:PHE405 4.7 51.9 1.0 N A:LEU408 4.8 40.6 1.0 C A:ARG406 4.8 28.1 1.0 O A:ASP542 4.8 32.6 1.0 HB3 A:ASP542 4.8 53.7 1.0 HA A:SER407 4.9 40.1 1.0 CA A:ASP404 4.9 32.2 1.0 HA A:ASP404 5.0 38.7 1.0

H.M.Kropp, K.Betz, J.Wirth, K.Diederichs, A.Marx. Crystal Structures of Ternary Complexes of Archaeal B-Family Dna Polymerases. Plos One V. 12 88005 2017.
ISSN: ESSN 1932-6203
PubMed: 29211756
DOI: 10.1371/JOURNAL.PONE.0188005