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Sodium in PDB 3pmn: Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

Enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site

All present enzymatic activity of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn 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) 25.27 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.390, 62.417, 139.881, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.3

Other elements in 3pmn:

The structure of Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site (pdb code 3pmn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site, PDB code: 3pmn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3pmn

Go back to Sodium Binding Sites List in 3pmn
Sodium binding site 1 out of 2 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active 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 Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5

b:24.1
occ:1.00
O A:HOH580 2.3 30.1 1.0
O A:ALA344 2.3 22.0 1.0
O A:SER339 2.4 22.9 1.0
OP1 C:DA5 2.4 21.1 1.0
O C:HOH10 2.4 24.9 1.0
O A:ILE341 2.5 24.0 1.0
C A:ALA344 3.4 20.7 1.0
C A:SER339 3.4 23.9 1.0
C A:ILE341 3.4 22.4 1.0
P C:DA5 3.5 23.1 1.0
O A:HOH79 3.6 36.3 1.0
OP2 C:DA5 3.7 20.9 1.0
N A:ALA344 3.7 18.4 1.0
CA A:TRP342 3.9 22.1 1.0
N A:GLY343 3.9 21.8 1.0
O C:HOH9 4.0 33.8 1.0
N A:ILE341 4.0 21.0 1.0
N A:TRP342 4.0 23.1 1.0
CA A:ALA344 4.1 21.3 1.0
CA A:SER339 4.1 24.2 1.0
C A:ASN340 4.3 22.8 1.0
C A:TRP342 4.3 22.3 1.0
O3' C:DT4 4.4 21.6 1.0
N A:ASN340 4.4 22.9 1.0
CA A:ILE341 4.4 22.4 1.0
N A:GLY345 4.5 21.9 1.0
CA A:ASN340 4.5 24.1 1.0
CB A:ALA344 4.5 19.6 1.0
CB A:SER339 4.6 24.5 1.0
C A:GLY343 4.7 21.2 1.0
CA A:GLY345 4.7 22.5 1.0
O5' C:DA5 4.7 23.4 1.0
O A:ASN340 4.9 23.6 1.0
CA A:GLY343 4.9 20.8 1.0
O C:HOH57 4.9 39.0 1.0

Sodium binding site 2 out of 2 in 3pmn

Go back to Sodium Binding Sites List in 3pmn
Sodium binding site 2 out of 2 in the Ternary Crystal Structure of Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active 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 Polymerase Lambda Variant with A Gt Mispair at the Primer Terminus with MN2+ in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na10

b:67.9
occ:1.00
O A:HOH632 2.3 54.3 1.0
O A:CYS300 2.6 69.2 1.0
O A:ILE305 2.6 56.0 1.0
OP1 D:DC3 3.1 45.3 1.0
O A:ILE302 3.3 63.6 1.0
OP2 D:DC3 3.4 45.8 1.0
C A:ILE305 3.7 56.0 1.0
C A:CYS300 3.7 69.2 1.0
P D:DC3 3.7 47.6 1.0
C A:ILE302 4.2 63.9 1.0
N A:ILE305 4.4 55.4 1.0
CA A:GLY306 4.4 56.5 1.0
CA A:CYS300 4.4 70.1 1.0
N A:GLY306 4.4 56.1 1.0
O A:SER301 4.5 67.7 1.0
CA A:PRO303 4.6 61.2 1.0
CA A:ILE305 4.6 55.2 1.0
C A:SER301 4.6 67.4 1.0
N A:GLY304 4.7 58.7 1.0
N A:PRO303 4.8 62.5 1.0
N A:SER301 4.8 68.3 1.0
O3' D:DC2 4.8 46.1 1.0
N A:ILE302 4.9 66.2 1.0
O5' D:DC3 4.9 44.8 1.0
CB A:CYS300 5.0 70.2 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

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