Sodium in PDB 8vnu: Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S, PDB code: 8vnu was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.574, 113.574, 87.695, 90, 90, 120
R / Rfree (%)	18.3 / 21.9

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Thallium	(Tl)	2 atoms

The binding sites of Sodium atom in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S (pdb code 8vnu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S, PDB code: 8vnu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:80.0 occ:0.80 TL C:TL501 0.1 80.0 0.2 O B:HOH502 2.4 30.8 1.0 O B:HOH544 2.6 32.8 1.0 OD1 B:ASN319 2.7 34.8 1.0 O B:HOH598 2.7 45.7 1.0 OP1 C:DG414 2.8 38.1 1.0 O3' C:DA413 3.1 42.3 1.0 P C:DG414 3.5 48.5 1.0 O B:HIS298 3.7 34.4 1.0 N B:HIS298 3.7 31.4 1.0 O B:ASN319 3.8 31.6 1.0 CG B:ASN319 3.8 34.6 1.0 OG B:SER297 4.1 34.6 1.0 ND1 B:HIS301 4.2 29.2 1.0 OD1 B:ASN323 4.2 31.8 1.0 CB B:HIS298 4.3 29.3 1.0 C3' C:DA413 4.3 31.8 1.0 CA B:HIS298 4.4 33.7 1.0 C B:HIS298 4.4 36.5 1.0 CE1 B:HIS301 4.4 32.1 1.0 O C:HOH622 4.4 44.9 1.0 C B:ASN319 4.4 31.8 1.0 C4' C:DA413 4.5 33.3 1.0 ND2 B:ASN319 4.5 30.4 1.0 C B:SER297 4.5 35.1 1.0 O5' C:DG414 4.6 41.1 1.0 CA B:SER297 4.6 35.2 1.0 O B:HOH587 4.6 32.7 1.0 OP2 C:DG414 4.6 39.3 1.0 CA B:ASN319 4.9 31.9 1.0 CB B:SER297 4.9 28.7 1.0 CB B:ASN319 4.9 30.9 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 70 Mm Tl+ For 1800S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:73.7 occ:0.80 TL D:TL601 0.1 73.7 0.2 O A:HOH754 2.2 32.5 1.0 O A:HOH711 2.4 36.8 1.0 OD1 A:ASN119 2.4 34.5 1.0 O A:HOH799 2.7 46.0 1.0 O3' D:DA513 2.8 34.7 1.0 OP1 D:DG514 2.8 31.8 1.0 P D:DG514 3.5 45.4 1.0 O A:ASN119 3.5 29.9 1.0 CG A:ASN119 3.6 32.7 1.0 N A:HIS98 3.8 30.8 1.0 O A:HIS98 4.0 35.1 1.0 C3' D:DA513 4.1 34.5 1.0 C A:ASN119 4.1 31.1 1.0 OG A:SER97 4.2 34.9 1.0 C4' D:DA513 4.3 37.4 1.0 OD1 A:ASN123 4.3 34.2 1.0 ND2 A:ASN119 4.3 29.8 1.0 O5' D:DG514 4.4 35.7 1.0 ND1 A:HIS101 4.4 32.8 1.0 CA A:SER97 4.5 29.9 1.0 CB A:HIS98 4.6 33.0 1.0 CA A:HIS98 4.6 35.3 1.0 CE1 A:HIS101 4.6 35.1 1.0 C A:SER97 4.6 29.5 1.0 C A:HIS98 4.6 35.8 1.0 CA A:ASN119 4.7 32.2 1.0 OP2 D:DG514 4.7 41.7 1.0 CB A:ASN119 4.7 26.3 1.0 C2' D:DA513 4.7 33.5 1.0 O A:HOH786 4.8 35.2 1.0 O D:HOH721 4.8 45.7 1.0 C5' D:DA513 4.8 36.5 1.0 N A:LYS120 4.9 29.5 1.0 CB A:SER97 4.9 28.1 1.0

C.Chang, Y.Gao. Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.