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Sodium in PDB 2pfn: Na in the Active Site of Dna Polymerase Lambda

Enzymatic activity of Na in the Active Site of Dna Polymerase Lambda

All present enzymatic activity of Na in the Active Site of Dna Polymerase Lambda:
2.7.7.7;

Protein crystallography data

The structure of Na in the Active Site of Dna Polymerase Lambda, PDB code: 2pfn 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.082, 61.557, 140.532, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 23.2

Other elements in 2pfn:

The structure of Na in the Active Site of Dna Polymerase Lambda also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Na in the Active Site of Dna Polymerase Lambda (pdb code 2pfn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Na in the Active Site of Dna Polymerase Lambda, PDB code: 2pfn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 2pfn

Go back to Sodium Binding Sites List in 2pfn
Sodium binding site 1 out of 5 in the Na in the Active Site of Dna Polymerase Lambda


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Na in the Active Site of Dna Polymerase Lambda within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na604

b:54.6
occ:1.00
 O A:HOH1063 2.4 27.6 1.0
O A:HOH1114 2.6 55.3 1.0
O P:HOH614 3.6 31.7 1.0
OP1 P:DA5 3.7 19.0 1.0
OP2 P:DC6 3.8 25.1 1.0
O5' P:DA5 3.9 20.4 1.0
CD1 A:TRP342 3.9 24.3 1.0
O P:HOH628 4.0 51.8 1.0
O A:HOH972 4.0 42.5 1.0
O A:HOH1033 4.1 44.4 1.0
NA A:NA602 4.1 21.5 1.0
P P:DA5 4.2 20.0 1.0
NE1 A:TRP342 4.2 21.7 1.0
P P:DC6 4.4 23.4 1.0
O3' P:DA5 4.4 23.6 1.0
C3' P:DA5 4.4 21.8 1.0
C5' P:DA5 4.5 19.0 1.0
OP1 P:DC6 4.5 23.9 1.0
O P:HOH616 4.5 28.8 1.0
O A:HOH1066 4.5 50.3 1.0
OP2 P:DA5 4.5 19.1 1.0
CG A:TRP342 4.6 21.4 1.0
O P:HOH629 4.7 59.0 1.0
O P:HOH630 4.7 46.5 1.0
CA A:TRP342 4.8 20.1 1.0
CE2 A:TRP342 5.0 20.4 1.0

Sodium binding site 2 out of 5 in 2pfn

Go back to Sodium Binding Sites List in 2pfn
Sodium binding site 2 out of 5 in the Na in the Active Site of Dna Polymerase Lambda


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Na in the Active Site of Dna Polymerase Lambda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na951

b:29.2
occ:1.00
 OD1 A:ASP427 2.1 30.3 1.0
OD1 A:ASP429 2.2 19.5 1.0
O2A A:DUP952 2.3 20.0 1.0
OD2 A:ASP490 2.3 25.8 1.0
O A:HOH1045 2.5 36.0 1.0
CG A:ASP427 3.0 29.1 1.0
CG A:ASP490 3.1 27.3 1.0
CG A:ASP429 3.2 24.3 1.0
OD2 A:ASP427 3.2 26.7 1.0
O3' P:DC6 3.2 29.3 1.0
PA A:DUP952 3.4 21.7 1.0
MG A:MG950 3.4 25.6 1.0
C3' P:DC6 3.5 25.8 1.0
OD2 A:ASP429 3.6 24.8 1.0
CB A:ASP490 3.7 24.3 1.0
O5' A:DUP952 3.8 21.4 1.0
O1A A:DUP952 3.8 23.2 1.0
OD1 A:ASP490 4.0 27.1 1.0
C5' A:DUP952 4.0 23.6 1.0
O A:HOH961 4.3 30.9 1.0
CB A:ASP427 4.4 26.8 1.0
CB A:ASP429 4.5 23.8 1.0
C4' P:DC6 4.5 22.8 1.0
C5' P:DC6 4.6 23.7 1.0
C2' P:DC6 4.7 23.9 1.0
O5' P:DC6 4.7 24.2 1.0
O3G A:DUP952 4.8 22.9 1.0
NH2 A:ARG488 4.8 27.0 1.0
N3A A:DUP952 4.8 24.0 1.0
O2B A:DUP952 4.9 21.8 1.0
OP1 P:DC6 5.0 23.9 1.0

Sodium binding site 3 out of 5 in 2pfn

Go back to Sodium Binding Sites List in 2pfn
Sodium binding site 3 out of 5 in the Na in the Active Site of Dna Polymerase Lambda


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Na in the Active Site of Dna Polymerase Lambda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na600

b:37.4
occ:1.00
 O A:HOH1050 2.4 43.8 1.0
O A:SER463 2.4 32.3 1.0
O T:HOH42 2.5 54.5 1.0
O A:HOH1007 2.5 37.0 1.0
O A:HOH1003 2.5 37.3 1.0
C A:SER463 3.5 31.4 1.0
OP1 T:DT10 3.8 27.6 1.0
O A:HOH1100 4.1 55.9 1.0
OE1 A:GLU466 4.2 57.9 1.0
N A:GLU465 4.3 38.2 1.0
N A:GLN464 4.4 33.0 1.0
CA A:GLN464 4.4 35.2 1.0
CA A:SER463 4.4 30.5 1.0
CB A:SER463 4.4 29.8 1.0
N A:SER463 4.6 28.5 1.0
OP2 T:DT10 4.6 30.7 1.0
P T:DT10 4.7 29.1 1.0
OE2 A:GLU465 4.7 42.4 1.0
C A:GLN464 4.9 35.7 1.0

Sodium binding site 4 out of 5 in 2pfn

Go back to Sodium Binding Sites List in 2pfn
Sodium binding site 4 out of 5 in the Na in the Active Site of Dna Polymerase Lambda


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Na in the Active Site of Dna Polymerase Lambda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:21.5
occ:1.00
 OP1 P:DA5 2.3 19.0 1.0
O A:ALA344 2.3 22.2 1.0
O A:SER339 2.3 23.0 1.0
O A:ILE341 2.4 18.2 1.0
O A:HOH1063 2.5 27.6 1.0
O P:HOH616 2.9 28.8 1.0
P P:DA5 3.3 20.0 1.0
C A:SER339 3.3 23.4 1.0
C A:ILE341 3.4 20.6 1.0
C A:ALA344 3.4 20.1 1.0
OP2 P:DA5 3.6 19.1 1.0
N A:ALA344 3.6 19.9 1.0
N A:GLY343 3.8 19.6 1.0
CA A:TRP342 3.9 20.1 1.0
N A:ILE341 4.0 20.7 1.0
N A:TRP342 4.0 20.5 1.0
CA A:ALA344 4.1 19.1 1.0
CA A:SER339 4.1 24.4 1.0
NA P:NA604 4.1 54.6 1.0
C A:ASN340 4.2 23.0 1.0
C A:TRP342 4.2 18.7 1.0
O A:HOH1066 4.3 50.3 1.0
O3' P:DT4 4.3 18.7 1.0
N A:ASN340 4.3 23.0 1.0
CA A:ASN340 4.4 24.0 1.0
CA A:ILE341 4.4 20.3 1.0
N A:GLY345 4.4 17.4 1.0
O5' P:DA5 4.5 20.4 1.0
C A:GLY343 4.6 19.1 1.0
CB A:ALA344 4.6 17.8 1.0
O A:HOH1033 4.6 44.4 1.0
CA A:GLY345 4.7 19.5 1.0
CB A:SER339 4.7 25.4 1.0
CA A:GLY343 4.8 19.9 1.0
O A:ASN340 4.8 21.8 1.0
O A:HOH972 4.9 42.5 1.0

Sodium binding site 5 out of 5 in 2pfn

Go back to Sodium Binding Sites List in 2pfn
Sodium binding site 5 out of 5 in the Na in the Active Site of Dna Polymerase Lambda


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Na in the Active Site of Dna Polymerase Lambda within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:45.5
occ:0.40
 O A:HOH1089 2.4 60.5 1.0
O A:SER301 2.5 79.3 1.0
O A:ILE302 2.6 72.6 1.0
C A:ILE302 2.8 72.9 1.0
O A:CYS300 2.8 83.9 1.0
N A:PRO303 2.8 71.5 1.0
CA A:PRO303 2.9 70.3 1.0
C A:SER301 3.1 79.1 1.0
OP1 D:DC3 3.3 51.5 1.0
N A:ILE302 3.7 76.8 1.0
CA A:ILE302 3.8 74.5 1.0
C A:CYS300 3.8 83.5 1.0
CB A:PRO303 3.9 70.4 1.0
CD A:PRO303 3.9 70.9 1.0
C A:PRO303 3.9 69.0 1.0
CA A:SER301 4.0 80.6 1.0
O A:ILE305 4.2 65.5 1.0
N A:GLY304 4.2 67.8 1.0
N A:SER301 4.3 82.3 1.0
P D:DC3 4.6 51.8 1.0
CG A:PRO303 4.6 70.8 1.0
N A:ILE305 4.7 65.2 1.0
O A:ALA299 4.9 85.6 1.0
OP2 D:DC3 4.9 52.5 1.0
O A:PRO303 4.9 68.2 1.0
CA A:CYS300 5.0 84.2 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: Mon Oct 7 03:41:12 2024

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