Sodium in PDB 8vn9: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S, PDB code: 8vn9 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)	42.99 / 1.69
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.65, 113.65, 88.31, 90, 90, 120
R / Rfree (%)	18 / 19.2

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S (pdb code 8vn9). 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 I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S, PDB code: 8vn9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:16.7 occ:0.35 MG C:MG501 0.0 16.7 0.7 O C:HOH642 2.1 20.6 1.0 O3' C:DA413 2.1 19.2 0.3 OD1 B:ASN319 2.1 17.9 1.0 OP3 C:DG414 2.1 16.9 0.7 OP1 C:DG414 2.2 17.0 0.3 O B:HOH549 2.2 20.6 1.0 O B:HOH512 2.2 18.3 1.0 O3' C:DA413 2.2 19.2 0.7 P C:DG414 2.6 19.8 0.3 CG B:ASN319 3.3 17.2 1.0 P C:DG414 3.4 17.5 0.7 C3' C:DA413 3.4 18.4 0.3 C3' C:DA413 3.5 18.3 0.7 O5' C:DG414 3.6 19.3 0.3 O B:ASN319 3.8 17.7 1.0 OP1 C:DG414 3.8 20.4 0.7 OP2 C:DG414 3.8 20.4 0.3 ND2 B:ASN319 3.8 17.6 1.0 O5' C:DG414 3.9 17.2 0.7 C4' C:DA413 3.9 18.9 0.3 C4' C:DA413 4.0 18.9 0.7 N B:HIS298 4.0 17.9 1.0 O C:HOH640 4.1 24.8 1.0 C2' C:DA413 4.1 17.8 0.3 OG B:SER297 4.2 19.1 1.0 C2' C:DA413 4.2 17.9 0.7 C B:ASN319 4.2 19.5 1.0 O B:HIS298 4.3 17.2 1.0 CB B:ASN319 4.5 17.1 1.0 OD1 B:ASN323 4.5 16.9 1.0 CA B:SER297 4.6 17.9 1.0 CA B:ASN319 4.6 17.1 1.0 OP2 C:DG414 4.6 23.5 0.7 C5' C:DA413 4.6 18.7 0.3 C5' C:DA413 4.7 18.6 0.7 ND1 B:HIS301 4.7 19.4 1.0 C B:SER297 4.8 18.4 1.0 CB B:HIS298 4.8 17.1 1.0 CA B:HIS298 4.8 15.3 1.0 CB B:SER297 4.9 17.3 1.0 CE1 B:HIS301 4.9 23.9 1.0 N B:LYS320 4.9 13.8 1.0 C B:HIS298 5.0 15.9 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 80S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:17.8 occ:0.50 MG D:MG601 0.0 17.7 0.5 OP3 D:DG514 2.1 16.7 0.5 OD1 A:ASN119 2.2 16.9 1.0 O D:HOH749 2.2 21.3 1.0 O3' D:DA513 2.2 17.9 0.5 O A:HOH729 2.2 22.3 1.0 O A:HOH730 2.2 18.3 1.0 O3' D:DA513 2.3 17.9 0.5 OP1 D:DG514 2.4 16.9 0.5 P D:DG514 2.8 17.0 0.5 CG A:ASN119 3.3 18.7 1.0 P D:DG514 3.4 17.3 0.5 C3' D:DA513 3.5 19.6 0.5 C3' D:DA513 3.5 19.6 0.5 O5' D:DG514 3.7 16.4 0.5 O A:ASN119 3.8 17.2 1.0 C4' D:DA513 3.9 18.7 0.5 ND2 A:ASN119 3.9 18.2 1.0 O5' D:DG514 3.9 17.2 0.5 C4' D:DA513 3.9 18.8 0.5 OP2 D:DG514 3.9 20.9 0.5 N A:HIS98 4.0 15.3 1.0 OP2 D:DG514 4.1 21.1 0.5 C2' D:DA513 4.1 17.1 0.5 C2' D:DA513 4.1 17.1 0.5 OG A:SER97 4.2 20.1 1.0 C A:ASN119 4.2 17.5 1.0 O D:HOH751 4.3 30.3 1.0 O A:HIS98 4.3 18.3 1.0 OD1 A:ASN123 4.5 19.1 1.0 CB A:ASN119 4.5 14.2 1.0 CA A:SER97 4.6 15.8 1.0 C5' D:DA513 4.6 18.4 0.5 OP1 D:DG514 4.6 25.2 0.5 CA A:ASN119 4.6 15.4 1.0 C5' D:DA513 4.7 18.5 0.5 ND1 A:HIS101 4.7 20.1 1.0 C A:SER97 4.7 13.8 1.0 CB A:HIS98 4.8 17.8 1.0 CA A:HIS98 4.8 17.3 1.0 CB A:SER97 4.9 17.5 1.0 N A:LYS120 4.9 15.8 1.0 CE1 A:HIS101 5.0 19.4 1.0 C A:HIS98 5.0 18.1 1.0 O A:HOH790 5.0 24.7 1.0

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