Sodium 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
Manganese	(Mn)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Manganese Promotes Catalysis in A Dna Polymerase Lambda-Dna Crystal, PDB code: 2pfq:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na1295 b:30.1 occ:0.25 MN A:MN1297 0.2 42.5 0.8 OP1 P:DC7 1.9 28.7 0.8 OD1 A:ASP490 2.0 35.6 0.8 O3' P:DC6 2.0 27.4 0.8 OD1 A:ASP429 2.2 33.1 0.8 OD2 A:ASP427 2.3 25.0 0.5 OD1 A:ASP429 2.3 41.3 0.2 P P:DC7 2.3 33.0 0.8 O P:HOH299 2.3 39.8 1.0 OD1 A:ASP490 2.4 34.8 0.2 OD2 A:ASP427 2.4 36.9 0.2 O2A A:DCP1438 2.5 27.2 0.2 O3' P:DC6 2.5 27.4 0.2 CG A:ASP490 3.0 35.0 0.8 CG A:ASP427 3.2 36.6 0.2 CG A:ASP490 3.2 34.2 0.2 CG A:ASP429 3.2 40.3 0.2 CG A:ASP427 3.2 24.9 0.5 CG A:ASP429 3.2 29.1 0.8 OP2 P:DC7 3.3 33.8 0.8 C3' P:DC6 3.3 22.3 0.8 OD1 A:ASP427 3.3 36.1 0.2 OD2 A:ASP429 3.5 40.0 0.2 PA A:DCP1438 3.5 27.0 0.2 OD1 A:ASP427 3.5 24.3 0.5 OD2 A:ASP429 3.6 27.8 0.8 O5' P:DC7 3.6 31.4 0.8 MN A:MN1296 3.6 45.2 0.8 C3' P:DC6 3.7 24.1 0.2 MG A:MG1294 3.7 38.4 0.2 C4' P:DC6 3.7 25.0 0.8 CB A:ASP490 3.8 32.8 0.2 CB A:ASP490 3.8 31.2 0.8 O5' A:DCP1438 3.9 27.9 0.2 O1A A:DCP1438 3.9 27.2 0.2 OD2 A:ASP490 3.9 36.7 0.8 C5' A:DCP1438 3.9 29.5 0.2 C5' P:DC6 4.0 25.8 0.8 C5' P:DC7 4.0 33.0 0.8 OD2 A:ASP490 4.0 34.9 0.2 C5' P:DC6 4.3 24.1 0.2 C4' P:DC6 4.3 23.5 0.2 O A:HOH1530 4.3 58.2 1.0 C2' P:DC6 4.4 24.2 0.8 CB A:ASP427 4.5 36.0 0.2 CB A:ASP427 4.6 22.9 0.5 CB A:ASP429 4.6 28.4 0.8 O5' P:DC6 4.6 25.8 0.8 CB A:ASP429 4.6 40.2 0.2 O5' P:DC6 4.6 25.0 0.2 O12 A:PPV1439 4.7 54.0 0.8 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 NH2 A:ARG488 4.8 26.3 1.0 OP1 P:DC6 4.8 25.4 0.2 O11 A:PPV1439 4.8 49.9 0.8 O2G A:DCP1438 4.9 29.1 0.2 OP1 P:DC6 4.9 24.6 0.8 C2' P:DC6 4.9 22.9 0.2

Sodium 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 Sodium with other atoms in the Na 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:Na1 b:15.2 occ:1.00 O A:ALA344 2.3 14.8 1.0 OP1 P:DA5 2.4 15.8 1.0 O A:SER339 2.4 22.6 1.0 O A:ILE341 2.4 16.0 1.0 O A:HOH1452 2.5 24.6 1.0 C A:ILE341 3.4 17.8 1.0 C A:ALA344 3.4 14.2 1.0 P P:DA5 3.5 19.6 1.0 C A:SER339 3.5 24.3 1.0 OP2 P:DA5 3.7 21.7 1.0 N A:ALA344 3.8 15.3 1.0 N A:ILE341 3.9 18.9 1.0 O A:HOH1471 3.9 33.0 1.0 CA A:TRP342 4.0 14.1 1.0 N A:TRP342 4.0 18.4 1.0 N A:GLY343 4.1 12.6 1.0 CA A:ALA344 4.1 18.2 1.0 C A:ASN340 4.2 19.8 1.0 CA A:ILE341 4.3 19.0 1.0 C A:TRP342 4.3 13.9 1.0 CA A:SER339 4.4 27.8 1.0 N A:ASN340 4.4 23.3 1.0 O A:HOH1485 4.4 33.1 1.0 N A:GLY345 4.5 11.8 1.0 O3' P:DT4 4.5 15.9 1.0 CA A:ASN340 4.5 19.7 1.0 CB A:ALA344 4.6 16.1 1.0 O5' P:DA5 4.7 20.1 1.0 O A:HOH1482 4.7 39.2 1.0 CA A:GLY345 4.7 14.5 1.0 O A:HOH1463 4.7 29.0 1.0 C A:GLY343 4.7 17.4 1.0 O A:ASN340 4.9 21.0 1.0

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