Sodium in PDB 9ewg: Dna Polymerase Lambda I493K, Ttp:at CA2+ Ground State Ternary Complex

All present enzymatic activity of Dna Polymerase Lambda I493K, Ttp:at CA2+ Ground State Ternary Complex:
2.7.7.7;

The structure of Dna Polymerase Lambda I493K, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 9ewg 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)	70.70 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.042, 62.504, 141.4, 90, 90, 90
R / Rfree (%)	20.5 / 25.2

The structure of Dna Polymerase Lambda I493K, Ttp:at CA2+ Ground State Ternary Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda I493K, Ttp:at CA2+ Ground State Ternary Complex (pdb code 9ewg). 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 I493K, Ttp:at CA2+ Ground State Ternary Complex, PDB code: 9ewg:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda I493K, 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 I493K, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:79.2 occ:1.00 OD2 A:ASP490 2.3 57.2 1.0 O3P P:TMP101 2.5 124.2 1.0 O A:HOH763 2.5 45.4 1.0 OD1 A:ASP427 2.9 74.4 1.0 H3' P:DC6 3.0 75.3 1.0 CG A:ASP490 3.3 49.7 1.0 H5'' P:DC6 3.3 54.9 1.0 CG A:ASP427 3.4 58.1 1.0 OD2 A:ASP427 3.4 60.3 1.0 HB2 A:ASP429 3.5 49.4 1.0 P P:TMP101 3.6 133.3 1.0 H5'2 P:TMP101 3.6 141.1 1.0 O3' P:DC6 3.7 71.5 1.0 C3' P:DC6 3.7 62.6 1.0 HH22 A:ARG488 3.8 44.6 1.0 O1P P:TMP101 3.8 114.1 1.0 O5' P:TMP101 3.9 121.9 1.0 HB2 A:ASP490 3.9 37.9 1.0 OD2 A:ASP429 3.9 51.4 1.0 C5' P:DC6 4.0 45.7 1.0 OD1 A:ASP490 4.1 44.3 1.0 C5' P:TMP101 4.1 117.5 1.0 H5'1 P:TMP101 4.1 141.1 1.0 HH21 A:ARG488 4.2 44.6 1.0 NH2 A:ARG488 4.2 37.1 1.0 CB A:ASP490 4.2 31.5 1.0 C4' P:DC6 4.3 48.0 1.0 O5' P:DC6 4.3 39.8 1.0 HO3' P:DC6 4.3 85.9 1.0 CB A:ASP429 4.4 41.1 1.0 H4' P:DC6 4.4 57.8 1.0 O A:HOH813 4.4 87.1 1.0 HB2 A:ASP427 4.5 54.0 1.0 CB A:ASP427 4.5 44.9 1.0 CG A:ASP429 4.6 53.0 1.0 HB3 A:ASP490 4.6 37.9 1.0 HD22 A:LEU474 4.7 47.1 1.0 OP1 P:DC6 4.7 32.8 1.0 HB3 A:ASP427 4.8 54.0 1.0 H5' P:DC6 4.9 54.9 1.0 O2P P:TMP101 4.9 123.4 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda I493K, 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 I493K, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:74.5 occ:1.00 O A:HOH775 1.9 71.0 1.0 O A:ILE302 2.1 76.5 1.0 HA A:PRO303 2.6 100.3 1.0 C A:ILE302 2.7 91.5 1.0 OP1 D:DC3 3.0 66.4 1.0 O A:ILE305 3.1 80.7 1.0 H A:ILE305 3.2 80.8 1.0 N A:PRO303 3.2 94.1 1.0 CA A:PRO303 3.3 83.5 1.0 N A:ILE302 3.6 104.8 1.0 C A:SER301 3.6 100.7 1.0 O A:CYS300 3.6 93.1 1.0 O A:SER301 3.7 100.9 1.0 CA A:ILE302 3.8 103.3 1.0 H A:GLY304 3.9 98.9 1.0 H A:ILE302 3.9 125.9 1.0 C A:PRO303 4.0 96.7 1.0 HA A:SER301 4.0 121.8 1.0 N A:ILE305 4.0 67.2 1.0 C A:ILE305 4.1 67.4 1.0 N A:GLY304 4.1 82.3 1.0 P D:DC3 4.2 66.4 1.0 HB A:ILE305 4.2 87.3 1.0 HA A:ILE302 4.3 124.1 1.0 CA A:SER301 4.3 101.4 1.0 C A:CYS300 4.3 98.7 1.0 OP2 D:DC3 4.4 55.8 1.0 HB3 A:PRO303 4.4 100.4 1.0 CB A:PRO303 4.5 83.6 1.0 CD A:PRO303 4.5 91.6 1.0 CA A:ILE305 4.6 70.6 1.0 HD3 A:PRO303 4.6 110.1 1.0 N A:SER301 4.6 105.5 1.0 HG22 A:ILE302 4.8 96.1 1.0 HA2 A:GLY306 4.8 88.7 1.0 O A:PRO303 4.9 82.0 1.0 CB A:ILE305 4.9 72.7 1.0 CB A:ILE302 4.9 89.0 1.0 HB A:ILE302 5.0 107.0 1.0 O A:ALA299 5.0 95.5 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda I493K, 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 I493K, Ttp:at CA2+ Ground State Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:21.4 occ:1.00 O A:HOH806 2.2 31.2 1.0 O A:ILE341 2.3 25.5 1.0 O A:ALA344 2.3 20.7 1.0 O A:SER339 2.3 22.4 1.0 OP1 P:DA5 2.4 25.7 1.0 O P:HOH208 2.6 34.2 1.0 H A:ALA344 3.2 26.7 1.0 HA A:TRP342 3.3 28.3 1.0 C A:ILE341 3.3 25.5 1.0 C A:SER339 3.3 22.4 1.0 C A:ALA344 3.5 23.6 1.0 P P:DA5 3.6 25.2 1.0 H A:GLY343 3.6 31.5 1.0 HA A:SER339 3.7 27.2 1.0 N A:ALA344 3.8 22.1 1.0 OP2 P:DA5 3.8 25.1 1.0 HA A:ASN340 3.9 26.3 1.0 N A:ILE341 4.0 18.2 1.0 HA2 A:GLY345 4.0 25.8 1.0 CA A:TRP342 4.0 23.5 1.0 N A:TRP342 4.0 27.4 1.0 CA A:SER339 4.0 22.6 1.0 HB3 A:ALA344 4.1 27.5 1.0 HB2 A:SER339 4.1 28.8 1.0 N A:GLY343 4.1 26.1 1.0 H A:ILE341 4.1 21.9 1.0 C A:ASN340 4.1 21.5 1.0 CA A:ALA344 4.2 24.4 1.0 O P:HOH221 4.2 47.3 1.0 N A:ASN340 4.2 23.9 1.0 O A:HOH800 4.2 38.4 1.0 CA A:ILE341 4.3 22.6 1.0 CA A:ASN340 4.3 21.8 1.0 C A:TRP342 4.4 21.0 1.0 O3' P:DT4 4.5 26.0 1.0 N A:GLY345 4.5 24.2 1.0 CB A:SER339 4.6 23.9 1.0 CB A:ALA344 4.7 22.8 1.0 O A:ASN340 4.7 26.5 1.0 CA A:GLY345 4.7 21.4 1.0 HB A:ILE341 4.7 28.0 1.0 O5' P:DA5 4.8 26.6 1.0 C A:GLY343 4.8 27.2 1.0 H A:TRP342 4.8 32.9 1.0 O A:PHE338 5.0 21.8 1.0

A.Nourisson, A.Haouz, S.Missoury, M.Delarue. Dna Polymerase Lambda I493K, Ttp:at CA2+ Ground State Ternary Complex To Be Published.