Sodium in PDB 9ewb: Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex:
2.7.7.7;

The structure of Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 9ewb was solved by A.Nourisson, A.Haouz, S.Missoury, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.83 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.28, 62.51, 140.22, 90, 90, 90
R / Rfree (%)	20.4 / 22.5

The structure of Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex (pdb code 9ewb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 9ewb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex


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 I493R, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:31.2 occ:1.00 O A:ALA344 2.2 33.2 1.0 O A:SER339 2.3 30.9 1.0 O A:HOH842 2.3 43.2 1.0 O A:ILE341 2.4 34.3 1.0 OP1 G:DA5 2.5 34.0 1.0 O G:HOH103 2.9 39.6 1.0 H A:ALA344 3.1 37.5 1.0 C A:SER339 3.3 32.0 1.0 C A:ALA344 3.3 32.2 1.0 C A:ILE341 3.3 35.1 1.0 HA A:TRP342 3.4 40.0 1.0 H A:GLY343 3.6 39.2 1.0 P G:DA5 3.6 36.1 1.0 HA A:SER339 3.6 42.1 1.0 N A:ALA344 3.7 31.3 1.0 OP2 G:DA5 3.8 33.7 1.0 HA2 A:GLY345 3.9 40.5 1.0 O A:HOH779 4.0 42.0 1.0 HB3 A:ALA344 4.0 38.8 1.0 N A:ILE341 4.0 30.3 1.0 HB2 A:SER339 4.0 42.9 1.0 HA A:ASN340 4.0 40.3 1.0 CA A:SER339 4.0 35.1 1.0 H A:ILE341 4.0 36.4 1.0 N A:GLY343 4.0 32.7 1.0 CA A:ALA344 4.0 32.1 1.0 N A:TRP342 4.1 35.0 1.0 CA A:TRP342 4.1 33.3 1.0 C A:ASN340 4.2 32.8 1.0 N A:ASN340 4.2 33.2 1.0 O G:HOH121 4.3 53.1 1.0 CA A:ILE341 4.3 33.3 1.0 H11 A:EDO606 4.3 105.1 1.0 CA A:ASN340 4.3 33.6 1.0 N A:GLY345 4.4 33.1 1.0 O A:HOH829 4.4 67.9 1.0 C A:TRP342 4.4 31.0 1.0 O3' G:DT4 4.5 32.2 1.0 CB A:ALA344 4.5 32.3 1.0 CB A:SER339 4.5 35.8 1.0 CA A:GLY345 4.6 33.7 1.0 C A:GLY343 4.7 31.7 1.0 HB A:ILE341 4.7 38.1 1.0 O A:ASN340 4.7 32.7 1.0 O5' G:DA5 4.8 33.4 1.0 H A:TRP342 4.8 42.0 1.0 CA A:GLY343 4.9 31.6 1.0 HA A:ALA344 4.9 38.5 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex


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 I493R, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:68.2 occ:1.00 O A:ILE302 2.3 113.1 1.0 O A:CYS300 2.6 102.6 1.0 O A:ILE305 3.0 82.2 1.0 HA A:PRO303 3.2 121.8 1.0 C A:ILE302 3.2 121.2 1.0 OP1 H:DC3 3.2 74.2 1.0 H A:ILE305 3.3 92.7 1.0 C A:CYS300 3.6 101.5 1.0 N A:ILE302 3.7 119.2 1.0 C A:SER301 3.8 92.7 1.0 N A:PRO303 3.8 102.8 1.0 CA A:PRO303 3.9 101.5 1.0 H A:GLY304 3.9 100.0 1.0 H A:ILE302 3.9 143.0 1.0 HB A:ILE305 3.9 97.9 1.0 O A:SER301 4.0 93.7 1.0 C A:ILE305 4.1 74.7 1.0 HA A:CYS300 4.1 120.5 1.0 CA A:ILE302 4.1 121.9 1.0 N A:ILE305 4.1 77.2 1.0 HA A:SER301 4.2 115.5 1.0 P H:DC3 4.2 64.4 1.0 OP2 H:DC3 4.3 69.0 1.0 N A:GLY304 4.3 83.3 1.0 CA A:SER301 4.4 96.3 1.0 N A:SER301 4.4 95.5 1.0 O A:HOH879 4.5 75.9 1.0 CA A:CYS300 4.5 100.4 1.0 C A:PRO303 4.5 95.2 1.0 CA A:ILE305 4.6 78.0 1.0 HA A:ILE302 4.7 146.2 1.0 CB A:ILE305 4.7 81.6 1.0 O A:ALA299 4.8 95.3 1.0 HB3 A:CYS300 4.9 118.0 1.0 HA2 A:GLY306 4.9 102.0 1.0

A.Nourisson, A.Haouz, P.Legrand, S.Missoury, M.Delarue. Dna Polymerase Lambda I493R, Ttp:at CA2+ Ground State Ternary Complex To Be Published.