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Sodium in PDB 3pnc: Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site

Enzymatic activity of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site

All present enzymatic activity of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site, PDB code: 3pnc was solved by K.Bebenek, 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) 22.44 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.161, 62.254, 139.834, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.6

Other elements in 3pnc:

The structure of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site (pdb code 3pnc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site, PDB code: 3pnc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3pnc

Go back to Sodium Binding Sites List in 3pnc
Sodium binding site 1 out of 3 in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2

b:21.5
occ:1.00
 OD2 A:ASP429 2.2 20.1 1.0
OD1 A:ASP427 2.2 22.1 1.0
O2A A:1GC1 2.2 16.8 1.0
OD2 A:ASP490 2.4 20.4 1.0
CG A:ASP427 2.9 20.9 1.0
OD2 A:ASP427 3.0 17.2 1.0
CG A:ASP429 3.2 20.6 1.0
PA A:1GC1 3.3 19.8 1.0
CG A:ASP490 3.3 20.4 1.0
MG A:MG576 3.4 18.5 1.0
O3' B:DG6 3.4 22.6 1.0
OD1 A:ASP429 3.5 19.7 1.0
O1A A:1GC1 3.6 19.1 1.0
C3' B:DG6 3.6 20.0 1.0
N A:TRS577 3.7 36.5 1.0
O5' A:1GC1 3.8 18.3 1.0
CB A:ASP490 3.9 17.6 1.0
C5' A:1GC1 3.9 18.6 1.0
OD1 A:ASP490 4.2 23.0 1.0
CB A:ASP427 4.3 17.3 1.0
CB A:ASP429 4.5 20.7 1.0
O1 A:TRS577 4.6 36.0 1.0
C4' B:DG6 4.6 18.9 1.0
O1G A:1GC1 4.7 19.1 1.0
NH2 A:ARG488 4.7 20.0 1.0
C2' B:DG6 4.7 20.0 1.0
O2B A:1GC1 4.8 18.4 1.0
C5' B:DG6 4.8 16.7 1.0
C3A A:1GC1 4.8 20.8 1.0
O5' B:DG6 4.8 19.7 1.0
OP1 B:DG6 5.0 16.5 1.0
O A:VAL428 5.0 21.1 1.0

Sodium binding site 2 out of 3 in 3pnc

Go back to Sodium Binding Sites List in 3pnc
Sodium binding site 2 out of 3 in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:18.8
occ:1.00
 O A:ALA344 2.3 18.0 1.0
O A:HOH3 2.3 23.1 1.0
OP1 B:DA5 2.4 17.8 1.0
O A:SER339 2.4 19.6 1.0
O A:ILE341 2.5 20.0 1.0
O B:HOH8 2.6 24.1 1.0
C A:ILE341 3.4 19.7 1.0
C A:ALA344 3.4 18.2 1.0
C A:SER339 3.4 19.6 1.0
O A:HOH121 3.4 36.0 1.0
P B:DA5 3.5 19.4 1.0
N A:ALA344 3.7 18.5 1.0
OP2 B:DA5 3.7 16.6 1.0
N A:GLY343 3.9 19.6 1.0
CA A:TRP342 3.9 18.1 1.0
O B:HOH9 4.0 37.5 1.0
N A:ILE341 4.0 17.2 1.0
N A:TRP342 4.0 20.2 1.0
CA A:ALA344 4.1 19.0 1.0
CA A:SER339 4.2 19.7 1.0
C A:TRP342 4.3 17.9 1.0
C A:ASN340 4.3 18.8 1.0
N A:ASN340 4.4 18.9 1.0
O3' B:DT4 4.4 19.9 1.0
CA A:ILE341 4.4 19.4 1.0
N A:GLY345 4.5 16.9 1.0
CA A:ASN340 4.5 19.2 1.0
CB A:ALA344 4.6 19.2 1.0
C A:GLY343 4.6 19.0 1.0
O5' B:DA5 4.7 19.5 1.0
CB A:SER339 4.7 19.0 1.0
CA A:GLY345 4.7 18.5 1.0
O A:ASN340 4.8 18.0 1.0
CA A:GLY343 4.8 18.1 1.0
O B:HOH211 4.9 50.7 1.0
O A:HOH603 4.9 45.6 1.0

Sodium binding site 3 out of 3 in 3pnc

Go back to Sodium Binding Sites List in 3pnc
Sodium binding site 3 out of 3 in the Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Crystal Structure of A Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus and Sodium at Catalytic Metal Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na7

b:52.0
occ:1.00
 O B:HOH42 2.4 63.7 1.0
O B:HOH54 2.4 27.5 1.0
O A:HOH64 2.6 34.0 1.0
N7 B:DG6 2.6 20.0 1.0
O6 A:1GC1 2.8 20.0 1.0
O A:HOH44 2.9 32.9 1.0
C8 B:DG6 3.5 20.0 1.0
C5 B:DG6 3.7 21.0 1.0
C6 A:1GC1 3.8 19.8 1.0
O6 B:DG6 3.9 21.2 1.0
N7 A:1GC1 4.1 18.0 1.0
C6 B:DG6 4.2 22.4 1.0
N7 B:DA5 4.2 19.1 1.0
C5 A:1GC1 4.3 18.1 1.0
N4 C:DC5 4.4 21.4 1.0
C8 B:DA5 4.4 19.6 1.0
O B:HOH160 4.4 41.1 1.0
C5 B:DA5 4.4 18.7 1.0
O B:HOH110 4.6 34.1 1.0
O B:HOH92 4.7 34.5 1.0
N9 B:DA5 4.7 21.2 1.0
N9 B:DG6 4.7 19.3 1.0
C4 B:DA5 4.7 20.9 1.0
O C:HOH37 4.7 32.1 1.0
O B:HOH212 4.8 41.6 1.0
C4 B:DG6 4.8 19.4 1.0
C2' B:DA5 4.9 21.5 1.0
C6 B:DA5 5.0 19.9 1.0
N1 A:1GC1 5.0 19.3 1.0

Reference:

K.Bebenek, L.C.Pedersen, T.A.Kunkel. Replication Infidelity Via A Mismatch with Watson-Crick Geometry. Proc.Natl.Acad.Sci.Usa V. 108 1862 2011.
ISSN: ISSN 0027-8424
PubMed: 21233421
DOI: 10.1073/PNAS.1012825108
Page generated: Mon Oct 7 12:21:20 2024

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