Sodium in PDB 9ewc: Dna Polymerase Lambda I493R 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda I493R 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex:
2.7.7.7;

The structure of Dna Polymerase Lambda I493R 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 9ewc 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)	60.26 / 3.67
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	149.904, 149.904, 272.154, 90, 90, 120
R / Rfree (%)	24 / 29.3

The structure of Dna Polymerase Lambda I493R 528-530 Ney, 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 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex (pdb code 9ewc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Lambda I493R 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 9ewc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda I493R 528-530 Ney, 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 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:16.7 occ:1.00 O A:SER339 2.2 20.0 1.0 OG A:SER339 3.2 25.8 1.0 C A:SER339 3.3 24.1 1.0 OP1 G:DA5 3.9 24.5 1.0 O A:ALA344 4.0 16.0 1.0 O A:ILE341 4.1 19.1 1.0 N A:ASN340 4.1 27.8 1.0 CA A:SER339 4.1 23.6 1.0 CA A:ASN340 4.2 24.6 1.0 CB A:SER339 4.2 19.6 1.0 C A:ASN340 4.4 19.2 1.0 OP2 G:DA5 4.4 24.6 1.0 P G:DA5 4.7 24.0 1.0 O A:ASN340 4.7 15.6 1.0 C A:ILE341 4.8 19.2 1.0 N A:ILE341 4.9 19.1 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda I493R 528-530 Ney, 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 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:0.8 occ:1.00 CB A:LEU479 3.5 31.5 1.0 O A:LEU479 3.8 23.4 1.0 CB A:ARG484 3.9 29.4 1.0 O A:PRO480 4.1 35.3 1.0 CD1 A:LEU479 4.2 23.1 1.0 C A:LEU479 4.2 22.7 1.0 CA A:GLY481 4.3 30.0 1.0 C A:PRO480 4.5 34.3 1.0 CG A:LEU479 4.5 28.8 1.0 CA A:LEU479 4.5 27.4 1.0 N A:GLY481 4.6 29.7 1.0 CA A:ARG484 4.8 30.7 1.0 C A:GLY481 4.8 32.4 1.0 O A:PRO482 5.0 36.9 1.0 N A:PRO480 5.0 26.8 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda I493R 528-530 Ney, 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 3 of Dna Polymerase Lambda I493R 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na602 b:0.0 occ:1.00 O C:SER339 3.0 22.3 1.0 OP1 I:DA5 3.9 18.6 1.0 O C:ASN340 4.1 25.7 1.0 C C:SER339 4.1 22.5 1.0 O C:ILE341 4.2 22.8 1.0 CA C:ASN340 4.2 24.7 1.0 C C:ASN340 4.3 25.3 1.0 OG C:SER339 4.5 37.2 1.0 N C:ASN340 4.6 24.2 1.0 C C:ILE341 4.7 19.5 1.0 P I:DA5 4.9 12.2 1.0 CA C:TRP342 5.0 22.3 1.0

A.Nourisson, A.Haouz, S.Missoury, M.Delarue. Dna Polymerase Lambda I493R 528-530 Ney, Ttp:at CA2+ Ground State Ternary Complex To Be Published.