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Sodium in PDB 2pfp: Dna Polymerase Lambda in Complex with Dna and Dctp

Enzymatic activity of Dna Polymerase Lambda in Complex with Dna and Dctp

All present enzymatic activity of Dna Polymerase Lambda in Complex with Dna and Dctp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda in Complex with Dna and Dctp, PDB code: 2pfp 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 (°) 55.893, 62.853, 140.570, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.5

Other elements in 2pfp:

The structure of Dna Polymerase Lambda in Complex with Dna and Dctp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 5 in 2pfp

Go back to Sodium Binding Sites List in 2pfp
Sodium binding site 1 out of 5 in the Dna Polymerase Lambda in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Lambda in Complex with Dna and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:70.2
occ:1.00
 OP2 D:DG1 2.4 54.8 1.0
P D:DG1 3.6 56.2 1.0
NH2 A:ARG308 3.6 78.8 1.0
NZ A:LYS324 3.7 71.9 1.0
OP1 D:DG1 3.9 53.2 1.0
OP3 D:DG1 4.2 55.3 1.0
OH A:TYR267 4.3 41.0 1.0
NH1 A:ARG275 4.7 53.2 1.0
CZ A:ARG275 4.7 50.0 1.0
O5' D:DG1 4.8 52.6 1.0
CZ A:ARG308 4.9 77.9 1.0
CE A:LYS324 4.9 72.1 1.0
NH2 A:ARG275 5.0 50.0 1.0

Sodium binding site 2 out of 5 in 2pfp

Go back to Sodium Binding Sites List in 2pfp
Sodium binding site 2 out of 5 in the Dna Polymerase Lambda in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Lambda in Complex with Dna and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na751

b:59.0
occ:1.00
 OD2 A:ASP427 2.2 36.5 1.0
OD1 A:ASP429 2.4 26.9 1.0
O2A A:DCP755 2.5 27.2 1.0
OD1 A:ASP490 2.6 30.4 1.0
CG A:ASP427 3.0 35.4 1.0
OD1 A:ASP427 3.1 37.5 1.0
O3' P:DC6 3.2 28.9 1.0
PA A:DCP755 3.3 28.7 1.0
CG A:ASP490 3.4 31.9 1.0
CG A:ASP429 3.4 30.2 1.0
C3' P:DC6 3.5 26.9 1.0
O5' A:DCP755 3.6 26.8 1.0
MG A:MG750 3.7 32.0 1.0
O1A A:DCP755 3.7 27.8 1.0
OD2 A:ASP429 3.8 28.3 1.0
C5' A:DCP755 3.9 27.9 1.0
CB A:ASP490 4.0 26.3 1.0
O A:HOH829 4.1 44.7 1.0
OD2 A:ASP490 4.2 31.4 1.0
CB A:ASP427 4.4 33.1 1.0
C4' P:DC6 4.5 24.8 1.0
NH2 A:ARG488 4.6 24.4 1.0
C5' P:DC6 4.6 23.5 1.0
C2' P:DC6 4.7 25.3 1.0
O3A A:DCP755 4.7 30.1 1.0
CB A:ASP429 4.8 29.9 1.0
O5' P:DC6 4.8 24.3 1.0
O2G A:DCP755 4.9 37.2 1.0
OP1 P:DC6 4.9 18.9 1.0
O2B A:DCP755 4.9 23.6 1.0

Sodium binding site 3 out of 5 in 2pfp

Go back to Sodium Binding Sites List in 2pfp
Sodium binding site 3 out of 5 in the Dna Polymerase Lambda in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Lambda in Complex with Dna and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na752

b:19.8
occ:1.00
 O A:ALA344 2.3 20.8 1.0
O A:SER339 2.4 21.7 1.0
OP1 P:DA5 2.4 20.1 1.0
O A:ILE341 2.4 18.5 1.0
O P:HOH10 2.4 26.3 1.0
O P:HOH30 2.6 25.1 1.0
C A:SER339 3.4 22.2 1.0
C A:ILE341 3.4 18.7 1.0
C A:ALA344 3.4 20.7 1.0
P P:DA5 3.5 21.5 1.0
OP2 P:DA5 3.7 21.5 1.0
N A:ALA344 3.7 19.5 1.0
O P:HOH26 3.8 34.2 1.0
N A:ILE341 3.9 17.5 1.0
O A:HOH887 4.0 50.6 1.0
N A:GLY343 4.0 20.1 1.0
CA A:TRP342 4.0 19.7 1.0
N A:TRP342 4.1 19.6 1.0
CA A:SER339 4.1 24.0 1.0
CA A:ALA344 4.1 20.8 1.0
C A:ASN340 4.2 19.9 1.0
N A:ASN340 4.3 21.9 1.0
C A:TRP342 4.4 20.8 1.0
CA A:ILE341 4.4 19.6 1.0
O3' P:DT4 4.4 22.4 1.0
CA A:ASN340 4.4 20.9 1.0
N A:GLY345 4.5 20.2 1.0
CB A:ALA344 4.5 17.3 1.0
O A:HOH820 4.6 37.9 1.0
O5' P:DA5 4.7 23.8 1.0
CB A:SER339 4.7 25.1 1.0
CA A:GLY345 4.7 20.5 1.0
C A:GLY343 4.7 20.2 1.0
O A:ASN340 4.8 21.4 1.0
CA A:GLY343 4.9 19.9 1.0

Sodium binding site 4 out of 5 in 2pfp

Go back to Sodium Binding Sites List in 2pfp
Sodium binding site 4 out of 5 in the Dna Polymerase Lambda in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna Polymerase Lambda in Complex with Dna and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na753

b:34.6
occ:1.00
 O A:SER463 2.0 34.1 1.0
O A:HOH987 2.5 49.8 1.0
O A:HOH766 2.5 35.7 1.0
O A:HOH781 2.6 40.6 1.0
O T:HOH42 2.7 44.1 1.0
O A:HOH895 2.9 51.6 1.0
C A:SER463 3.2 35.5 1.0
OP1 T:DT10 3.7 29.5 1.0
O A:HOH901 3.9 54.5 1.0
N A:GLN464 4.1 36.9 1.0
CA A:GLN464 4.1 37.1 1.0
OE2 A:GLU466 4.2 61.8 1.0
CA A:SER463 4.2 34.4 1.0
N A:GLU465 4.2 38.4 1.0
CB A:SER463 4.3 34.3 1.0
N A:SER463 4.4 32.2 1.0
OP2 T:DT10 4.5 30.3 1.0
P T:DT10 4.6 29.0 1.0
OE1 A:GLU466 4.7 63.0 1.0
C A:GLN464 4.7 37.6 1.0
CD A:GLU466 4.9 60.1 1.0
OE2 A:GLU465 4.9 42.0 1.0

Sodium binding site 5 out of 5 in 2pfp

Go back to Sodium Binding Sites List in 2pfp
Sodium binding site 5 out of 5 in the Dna Polymerase Lambda in Complex with Dna and Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dna Polymerase Lambda in Complex with Dna and Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na754

b:41.4
occ:0.50
 O A:ILE302 2.2 71.7 1.0
O A:CYS300 2.5 77.3 1.0
C A:ILE302 2.6 71.5 1.0
O A:HOH992 2.6 57.3 1.0
O A:HOH788 2.8 52.7 1.0
N A:PRO303 3.1 70.5 1.0
N A:ILE302 3.3 73.2 1.0
CA A:PRO303 3.4 69.2 1.0
CA A:ILE302 3.5 72.5 1.0
C A:SER301 3.5 74.1 1.0
O A:ILE305 3.5 66.4 1.0
O A:HOH989 3.6 55.7 1.0
C A:CYS300 3.6 76.7 1.0
OP1 D:DC3 3.7 50.6 1.0
O A:SER301 3.8 73.7 1.0
C A:PRO303 4.1 68.0 1.0
CA A:SER301 4.2 75.1 1.0
CD A:PRO303 4.2 70.2 1.0
N A:GLY304 4.2 66.9 1.0
N A:SER301 4.3 75.9 1.0
N A:ILE305 4.4 65.6 1.0
OP2 D:DC3 4.4 50.0 1.0
O A:ALA299 4.5 79.5 1.0
C A:ILE305 4.6 65.5 1.0
CG A:PRO303 4.6 70.0 1.0
CB A:PRO303 4.6 69.3 1.0
P D:DC3 4.6 51.6 1.0
CA A:CYS300 4.7 77.2 1.0
CB A:ILE302 4.7 72.7 1.0
CA A:ILE305 4.9 65.7 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 03:41:19 2024

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