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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 2pfq:

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

Sodium Binding Sites:

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 2pfq

Go back to Sodium Binding Sites List in 2pfq
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 2pfq

Go back to Sodium Binding Sites List in 2pfq
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

Reference:

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
Page generated: Tue Dec 15 05:53:57 2020

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