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Sodium in PDB 3upq: Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.

Enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.

All present enzymatic activity of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T., PDB code: 3upq was solved by R.A.Gosavi, A.F.Moon, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.44 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.975, 63.660, 139.970, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.4

Other elements in 3upq:

The structure of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. (pdb code 3upq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T., PDB code: 3upq:

Sodium binding site 1 out of 1 in 3upq

Go back to Sodium Binding Sites List in 3upq
Sodium binding site 1 out of 1 in the Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Pre-Catalytic Ternary Complex of Polymerase Lambda with An Ratp Analog Opposite A Templating T. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4

b:24.8
occ:1.00
 O A:HOH578 2.4 32.5 1.0
O A:SER339 2.4 16.0 1.0
OP1 P:DA5 2.5 18.1 1.0
O A:ALA344 2.6 17.1 1.0
O P:HOH50 2.6 25.1 1.0
O A:ILE341 2.6 15.2 1.0
C A:ILE341 3.5 16.7 1.0
P P:DA5 3.5 19.3 1.0
C A:SER339 3.6 14.9 1.0
C A:ALA344 3.6 15.9 1.0
OP2 P:DA5 3.7 16.4 1.0
N A:ALA344 3.8 15.0 1.0
N A:GLY343 3.9 14.9 1.0
CA A:TRP342 3.9 17.1 1.0
O P:HOH47 3.9 35.1 1.0
N A:TRP342 4.0 16.4 1.0
N A:ILE341 4.2 14.0 1.0
C A:TRP342 4.3 18.2 1.0
CA A:ALA344 4.3 15.8 1.0
C A:ASN340 4.3 16.0 1.0
CA A:SER339 4.4 15.5 1.0
N A:ASN340 4.4 17.7 1.0
CA A:ASN340 4.5 17.5 1.0
O3' P:DT4 4.5 16.1 1.0
CA A:ILE341 4.5 11.5 1.0
N A:GLY345 4.7 13.9 1.0
C A:GLY343 4.7 18.1 1.0
O5' P:DA5 4.8 15.1 1.0
O A:ASN340 4.8 16.2 1.0
CB A:ALA344 4.8 18.6 1.0
CA A:GLY343 4.8 16.2 1.0
CA A:GLY345 4.9 17.5 1.0
CB A:SER339 5.0 20.8 1.0

Reference:

R.A.Gosavi, A.F.Moon, T.A.Kunkel, L.C.Pedersen, K.Bebenek. The Catalytic Cycle For Ribonucleotide Incorporation By Human Dna Pol Lambda Nucleic Acids Res. V. 40 7518 2012.
ISSN: ISSN 0305-1048
PubMed: 22584622
DOI: 10.1093/NAR/GKS413
Page generated: Tue Dec 15 06:27:24 2020

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