Manganese in PDB 4klh: Dna Polymerase Beta Matched Product Complex with MN2+, 40 S

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MN2+, 40 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MN2+, 40 S, PDB code: 4klh 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)	25.09 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.900, 80.200, 55.100, 90.00, 107.90, 90.00
R / Rfree (%)	20.5 / 26.9

The structure of Dna Polymerase Beta Matched Product Complex with MN2+, 40 S also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Manganese atom in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 S (pdb code 4klh). 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 Matched Product Complex with MN2+, 40 S, PDB code: 4klh:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 S


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 Matched Product Complex with MN2+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:28.6 occ:0.75 O P:HOH201 2.2 30.4 1.0 OP2 P:DC11 2.2 18.1 1.0 O A:HOH503 2.2 32.6 1.0 O P:HOH202 2.2 34.2 1.0 O A:HOH504 2.2 27.2 1.0 O12 A:PPV403 2.3 28.1 1.0 P P:DC11 3.2 24.8 1.0 O P:HOH209 3.5 30.7 1.0 OP1 P:DC11 3.7 22.0 1.0 O5' P:DC11 3.7 19.3 1.0 P2 A:PPV403 3.7 20.5 1.0 O11 A:PPV403 4.0 26.9 1.0 O21 A:PPV403 4.0 27.0 1.0 OPP A:PPV403 4.1 24.1 1.0 O A:HOH508 4.2 22.6 1.0 P1 A:PPV403 4.3 27.4 1.0 O A:HOH501 4.4 17.4 1.0 MN A:MN402 4.5 21.7 1.0 O22 A:PPV403 4.5 22.6 1.0 O3' P:DC10 4.6 25.4 1.0 O32 A:PPV403 4.6 17.5 1.0 C5' P:DC11 4.9 17.3 1.0

Manganese binding site 2 out of 3 in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 S


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 Matched Product Complex with MN2+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:21.4 occ:1.00 OD1 A:ASP192 2.1 16.9 1.0 OD2 A:ASP256 2.1 22.5 1.0 OD2 A:ASP190 2.2 25.2 1.0 O A:HOH501 2.2 17.4 1.0 OP1 P:DC11 2.2 22.0 1.0 O3' P:DC10 2.7 25.4 1.0 CG A:ASP190 2.9 25.7 1.0 P P:DC11 3.0 24.8 1.0 OD1 A:ASP190 3.0 21.7 1.0 CG A:ASP192 3.1 19.4 1.0 CG A:ASP256 3.2 19.2 1.0 MN A:MN402 3.5 21.7 1.0 OD2 A:ASP192 3.5 19.7 1.0 CB A:ASP256 3.7 20.2 1.0 OP2 P:DC11 3.9 18.1 1.0 C3' P:DC10 4.0 18.0 1.0 C4' P:DC10 4.2 20.3 1.0 O5' P:DC11 4.2 19.3 1.0 C5' P:DC10 4.3 22.2 1.0 OD1 A:ASP256 4.3 17.9 1.0 CB A:ASP190 4.4 20.2 1.0 CB A:ASP192 4.4 18.0 1.0 C5' P:DC11 4.5 17.3 1.0 NH2 A:ARG254 4.6 18.3 1.0 O A:MET191 4.7 20.8 1.0 O P:HOH202 4.7 34.2 1.0 OP1 P:DC10 4.8 24.3 1.0 N A:ASP256 4.9 20.3 1.0 C A:MET191 4.9 16.5 1.0 O5' P:DC10 4.9 21.9 1.0 CA A:ASP192 4.9 18.5 1.0 CA A:ASP256 4.9 16.9 1.0

Manganese binding site 3 out of 3 in the Dna Polymerase Beta Matched Product Complex with MN2+, 40 S


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 Matched Product Complex with MN2+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:21.7 occ:1.00 O A:HOH502 2.0 24.4 1.0 O32 A:PPV403 2.1 17.5 1.0 OD2 A:ASP192 2.1 19.7 1.0 OD1 A:ASP190 2.1 21.7 1.0 OP1 P:DC11 2.2 22.0 1.0 O11 A:PPV403 2.3 26.9 1.0 P2 A:PPV403 3.1 20.5 1.0 O12 A:PPV403 3.1 28.1 1.0 CG A:ASP192 3.1 19.4 1.0 CG A:ASP190 3.3 25.7 1.0 OD1 A:ASP192 3.4 16.9 1.0 MN A:MN401 3.5 21.4 1.0 P P:DC11 3.5 24.8 1.0 P1 A:PPV403 3.6 27.4 1.0 OPP A:PPV403 3.7 24.1 1.0 OD2 A:ASP190 3.9 25.2 1.0 O5' P:DC11 4.0 19.3 1.0 C5' P:DC11 4.1 17.3 1.0 O P:HOH202 4.2 34.2 1.0 O A:ASP190 4.2 20.6 1.0 O A:HOH501 4.3 17.4 1.0 O31 A:PPV403 4.3 24.9 1.0 OP2 P:DC11 4.4 18.1 1.0 O22 A:PPV403 4.4 22.6 1.0 N A:ASP190 4.4 17.4 1.0 C A:ASP190 4.4 15.5 1.0 O A:HOH510 4.4 23.2 1.0 CB A:ASP192 4.5 18.0 1.0 CB A:ASP190 4.5 20.2 1.0 MN P:MN101 4.5 28.6 0.8 CA A:GLY179 4.5 20.8 1.0 O3' P:DC10 4.6 25.4 1.0 O21 A:PPV403 4.7 27.0 1.0 CA A:ASP190 4.7 16.8 1.0 N A:SER180 4.7 22.5 1.0 N A:ASP192 4.9 17.7 1.0 OG A:SER180 5.0 23.5 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