Manganese in PDB 4kls: Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min

All present enzymatic activity of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min, PDB code: 4kls was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.13 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.920, 78.607, 55.034, 90.00, 112.88, 90.00
R / Rfree (%)	22.6 / 28.5

The structure of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Manganese atom in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min (pdb code 4kls). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min, PDB code: 4kls:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn405 b:22.6 occ:0.60 O2A A:DTP401 2.1 12.0 0.6 OD1 A:ASP192 2.1 29.7 1.0 O P:HOH229 2.2 33.8 0.6 O A:HOH549 2.2 33.4 1.0 OD2 A:ASP256 2.3 34.8 1.0 OD2 A:ASP190 2.4 28.5 1.0 OP2 P:DA11 2.9 40.8 0.4 CG A:ASP192 3.2 30.6 1.0 PA A:DTP401 3.3 36.8 0.6 CG A:ASP256 3.4 31.2 1.0 CG A:ASP190 3.4 30.6 1.0 O1A A:DTP401 3.5 34.1 0.6 OD2 A:ASP192 3.6 25.1 1.0 P P:DA11 3.7 43.0 0.4 MN A:MN406 3.7 40.7 1.0 OD1 A:ASP190 3.7 29.1 1.0 O5' P:DA11 3.7 41.2 0.4 O3' P:DC10 3.8 52.0 0.6 O5' A:DTP401 3.8 41.0 0.6 O A:HOH529 3.8 31.4 1.0 O3' P:DC10 4.1 52.0 0.4 CB A:ASP256 4.1 23.1 1.0 C3' P:DC10 4.1 46.5 0.4 C3' P:DC10 4.3 46.5 0.6 C5' P:DC10 4.3 39.2 0.4 C5' P:DA11 4.4 41.6 0.4 OD1 A:ASP256 4.4 24.3 1.0 C5' P:DC10 4.4 39.2 0.6 CB A:ASP192 4.5 20.9 1.0 C5' A:DTP401 4.5 42.6 0.6 C4' P:DC10 4.5 39.3 0.4 OP1 P:DC10 4.7 29.0 0.6 OP1 P:DC10 4.7 29.0 0.4 C4' P:DC10 4.7 39.3 0.6 CB A:ASP190 4.8 24.1 1.0 O5' P:DC10 4.9 33.7 0.6 O5' P:DC10 4.9 33.7 0.4 O3A A:DTP401 4.9 37.2 0.6 O2G A:DTP401 5.0 41.7 0.6

Manganese binding site 2 out of 3 in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn406 b:40.7 occ:1.00 OD1 A:ASP190 2.0 29.1 1.0 O2B A:DTP401 2.0 34.8 0.6 OD2 A:ASP192 2.2 25.1 1.0 O2A A:DTP401 2.3 12.0 0.6 O2G A:DTP401 2.3 41.7 0.6 O11 A:PPV402 2.4 40.6 0.4 O A:HOH556 2.5 39.6 1.0 O32 A:PPV402 2.5 38.0 0.4 CG A:ASP190 3.0 30.6 1.0 CG A:ASP192 3.1 30.6 1.0 PA A:DTP401 3.2 36.8 0.6 PB A:DTP401 3.2 47.7 0.6 OD2 A:ASP190 3.4 28.5 1.0 OD1 A:ASP192 3.4 29.7 1.0 P2 A:PPV402 3.4 43.0 0.4 O12 A:PPV402 3.4 32.6 0.4 O3A A:DTP401 3.5 37.2 0.6 PG A:DTP401 3.6 40.6 0.6 P1 A:PPV402 3.6 40.8 0.4 MN A:MN405 3.7 22.6 0.6 O3B A:DTP401 3.9 48.8 0.6 O A:ASP190 3.9 31.2 1.0 O1G A:DTP401 4.0 41.7 0.6 OPP A:PPV402 4.0 48.1 0.4 O31 A:PPV402 4.0 41.5 0.4 C5' A:DTP401 4.2 42.6 0.6 C A:ASP190 4.2 22.2 1.0 C5' P:DA11 4.3 41.6 0.4 O1A A:DTP401 4.3 34.1 0.6 CB A:ASP190 4.3 24.1 1.0 O5' A:DTP401 4.3 41.0 0.6 N A:ASP190 4.4 25.2 1.0 CB A:ASP192 4.4 20.9 1.0 O A:HOH511 4.5 22.8 1.0 O1B A:DTP401 4.5 39.6 0.6 CA A:ASP190 4.6 22.5 1.0 O5' P:DA11 4.7 41.2 0.4 N A:MET191 4.7 27.7 1.0 N A:ASP192 4.7 23.8 1.0 OG A:SER180 4.7 34.8 1.0 O22 A:PPV402 4.8 37.5 0.4 O A:HOH549 4.8 33.4 1.0 O3G A:DTP401 4.8 43.2 0.6 O21 A:PPV402 4.8 43.0 0.4 N A:SER180 4.9 38.8 1.0 O P:HOH229 4.9 33.8 0.6 CA A:GLY179 4.9 40.3 1.0 C A:MET191 5.0 25.7 1.0

Manganese binding site 3 out of 3 in the Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta Mismatched Reactant Complex with MN2+, 10 Min within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:69.5 occ:1.00 O P:HOH211 2.2 40.7 1.0 O P:HOH216 2.2 47.1 1.0 O P:HOH217 2.2 61.2 1.0 N7 P:DG4 2.6 29.0 1.0 C8 P:DG4 3.4 37.7 1.0 C5 P:DG4 3.7 29.7 1.0 O6 P:DG4 3.9 31.4 1.0 N6 P:DA5 3.9 26.8 1.0 O T:HOH124 3.9 39.1 1.0 C6 P:DG4 4.2 28.8 1.0 C2' P:DT3 4.3 40.5 1.0 OP2 P:DG4 4.4 35.9 1.0 N9 P:DG4 4.6 28.5 1.0 C4 P:DG4 4.7 31.4 1.0 N7 P:DA5 4.9 33.0 1.0 C6 P:DA5 4.9 30.9 1.0

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048