Atomistry » Sodium » PDB 3pkk-3pzs » 3pnc
Atomistry »
  Sodium »
    PDB 3pkk-3pzs »
      3pnc »

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: Tue Dec 15 06:21:50 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy