Manganese in PDB 2pfq: Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal

All present enzymatic activity of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal:
2.7.7.7;

The structure of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal, PDB code: 2pfq was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.091, 63.485, 139.775, 90.00, 90.00, 90.00
R / Rfree (%)	25.6 / 28.7

The structure of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Manganese atom in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal (pdb code 2pfq). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal, PDB code: 2pfq:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1296 b:45.2 occ:0.75 MG A:MG1294 0.1 38.4 0.2 OD1 A:ASP427 1.9 36.1 0.2 O2B A:DCP1438 2.0 26.2 0.2 OD1 A:ASP427 2.0 24.3 0.5 O2A A:DCP1438 2.0 27.2 0.2 OD2 A:ASP429 2.0 40.0 0.2 O A:HOH1602 2.0 46.9 1.0 O11 A:PPV1439 2.1 49.9 0.8 OD2 A:ASP429 2.1 27.8 0.8 O2G A:DCP1438 2.1 29.1 0.2 O12 A:PPV1439 2.1 54.0 0.8 OP1 P:DC7 2.2 28.7 0.8 PB A:DCP1438 3.0 27.9 0.2 CG A:ASP427 3.1 24.9 0.5 P1 A:PPV1439 3.1 52.1 0.8 CG A:ASP427 3.1 36.6 0.2 CG A:ASP429 3.1 29.1 0.8 CG A:ASP429 3.1 40.3 0.2 PA A:DCP1438 3.2 27.0 0.2 P2 A:PPV1439 3.3 54.9 0.8 O21 A:PPV1439 3.3 53.6 0.8 O3A A:DCP1438 3.3 28.4 0.2 PG A:DCP1438 3.3 30.1 0.2 OPP A:PPV1439 3.4 53.6 0.8 O3B A:DCP1438 3.5 28.7 0.2 OD1 A:ASP429 3.5 33.1 0.8 OD2 A:ASP427 3.5 25.0 0.5 MN A:MN1297 3.5 42.5 0.8 P P:DC7 3.6 33.0 0.8 NA A:NA1295 3.6 30.1 0.2 OD1 A:ASP429 3.6 41.3 0.2 OD2 A:ASP427 3.6 36.9 0.2 O32 A:PPV1439 3.9 53.5 0.8 O A:ASP427 4.0 36.6 0.2 O3G A:DCP1438 4.0 28.6 0.2 O5' P:DC7 4.0 31.4 0.8 C5' A:DCP1438 4.0 29.5 0.2 C5' P:DC7 4.0 33.0 0.8 O5' A:DCP1438 4.1 27.9 0.2 O A:ASP427 4.2 22.7 0.5 C A:ASP427 4.3 36.5 0.2 CB A:ASP427 4.3 22.9 0.5 CB A:ASP427 4.3 36.0 0.2 C A:ASP427 4.3 22.6 0.5 O1A A:DCP1438 4.3 27.2 0.2 O31 A:PPV1439 4.4 50.6 0.8 N A:ASP427 4.4 35.7 0.2 O1B A:DCP1438 4.4 26.7 0.2 N A:ASP427 4.4 24.0 0.5 CB A:ASP429 4.4 40.2 0.2 O A:HOH1493 4.4 33.0 1.0 CB A:ASP429 4.4 28.4 0.8 O1G A:DCP1438 4.5 28.4 0.2 O22 A:PPV1439 4.5 53.1 0.8 OP2 P:DC7 4.5 33.8 0.8 CA A:ASP427 4.6 36.2 0.2 CA A:GLY416 4.6 31.9 1.0 N A:SER417 4.6 31.8 1.0 CA A:ASP427 4.6 22.8 0.5 O P:HOH299 4.6 39.8 1.0 O3' P:DC6 4.7 27.4 0.8 OG A:SER417 4.7 27.7 1.0 N A:ASP429 4.8 28.5 0.8 N A:ASP429 4.8 38.8 0.2 N A:VAL428 4.9 37.6 1.0

Manganese binding site 2 out of 2 in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1297 b:42.5 occ:0.75 NA A:NA1295 0.2 30.1 0.2 OP1 P:DC7 1.9 28.7 0.8 OD1 A:ASP490 2.0 35.6 0.8 OD2 A:ASP427 2.1 25.0 0.5 O3' P:DC6 2.2 27.4 0.8 O P:HOH299 2.2 39.8 1.0 OD2 A:ASP427 2.2 36.9 0.2 OD1 A:ASP429 2.2 33.1 0.8 OD1 A:ASP429 2.3 41.3 0.2 P P:DC7 2.4 33.0 0.8 O2A A:DCP1438 2.4 27.2 0.2 OD1 A:ASP490 2.4 34.8 0.2 O3' P:DC6 2.7 27.4 0.2 CG A:ASP427 3.0 36.6 0.2 CG A:ASP427 3.0 24.9 0.5 CG A:ASP490 3.1 35.0 0.8 OD1 A:ASP427 3.1 36.1 0.2 CG A:ASP490 3.2 34.2 0.2 CG A:ASP429 3.2 40.3 0.2 CG A:ASP429 3.3 29.1 0.8 OP2 P:DC7 3.3 33.8 0.8 OD1 A:ASP427 3.4 24.3 0.5 OD2 A:ASP429 3.4 40.0 0.2 C3' P:DC6 3.4 22.3 0.8 PA A:DCP1438 3.5 27.0 0.2 MN A:MN1296 3.5 45.2 0.8 OD2 A:ASP429 3.6 27.8 0.8 MG A:MG1294 3.6 38.4 0.2 O5' P:DC7 3.7 31.4 0.8 C3' P:DC6 3.8 24.1 0.2 CB A:ASP490 3.8 32.8 0.2 C4' P:DC6 3.8 25.0 0.8 CB A:ASP490 3.8 31.2 0.8 O1A A:DCP1438 3.9 27.2 0.2 OD2 A:ASP490 3.9 36.7 0.8 O5' A:DCP1438 4.0 27.9 0.2 OD2 A:ASP490 4.0 34.9 0.2 C5' A:DCP1438 4.0 29.5 0.2 C5' P:DC6 4.0 25.8 0.8 C5' P:DC7 4.1 33.0 0.8 O A:HOH1530 4.1 58.2 1.0 CB A:ASP427 4.3 36.0 0.2 C5' P:DC6 4.4 24.1 0.2 CB A:ASP427 4.4 22.9 0.5 C4' P:DC6 4.4 23.5 0.2 C2' P:DC6 4.6 24.2 0.8 O12 A:PPV1439 4.6 54.0 0.8 CB A:ASP429 4.6 28.4 0.8 CB A:ASP429 4.6 40.2 0.2 O5' P:DC6 4.7 25.8 0.8 O5' P:DC6 4.7 25.0 0.2 O2G A:DCP1438 4.7 29.1 0.2 NH2 A:ARG488 4.8 26.3 1.0 O21 A:PPV1439 4.8 53.6 0.8 O3A A:DCP1438 4.8 28.4 0.2 O2B A:DCP1438 4.8 26.2 0.2 OP1 P:DC6 4.8 25.4 0.2 O11 A:PPV1439 4.8 49.9 0.8 OP1 P:DC6 4.8 24.6 0.8

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Role of the Catalytic Metal During Polymerization By Dna Polymerase Lambda. Dna Repair V. 6 1333 2007.
ISSN: ISSN 1568-7864
PubMed: 17475573
DOI: 10.1016/J.DNAREP.2007.03.005