Sodium in PDB 8vn8: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 40S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 40S, PDB code: 8vn8 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)	47.79 / 1.60
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 (%)	17.8 / 19.4

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 40S also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	4 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 40S (pdb code 8vn8). 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 40S, PDB code: 8vn8:
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 40S


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 40S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:17.1 occ:0.55 MG C:MG501 0.1 17.0 0.5 OP3 C:DG414 2.1 17.8 0.5 O B:HOH521 2.2 17.6 1.0 O B:HOH600 2.2 21.0 1.0 OD1 B:ASN319 2.2 18.9 1.0 O3' C:DA413 2.2 18.1 0.6 O3' C:DA413 2.3 18.1 0.5 O B:HOH544 2.3 23.0 1.0 OP1 C:DG414 2.4 17.4 0.6 P C:DG414 2.9 18.9 0.6 CG B:ASN319 3.3 16.8 1.0 P C:DG414 3.4 18.7 0.5 C3' C:DA413 3.5 17.6 0.6 C3' C:DA413 3.5 17.6 0.5 O B:ASN319 3.8 17.0 1.0 OP1 C:DG414 3.8 20.5 0.5 O5' C:DG414 3.8 18.8 0.6 C4' C:DA413 3.9 17.9 0.6 C4' C:DA413 3.9 17.9 0.5 O5' C:DG414 3.9 17.9 0.5 ND2 B:ASN319 4.0 16.5 1.0 N B:HIS298 4.0 16.1 1.0 OP2 C:DG414 4.0 20.7 0.6 C2' C:DA413 4.2 17.5 0.6 O C:HOH642 4.2 25.4 1.0 C2' C:DA413 4.2 17.4 0.5 C B:ASN319 4.2 17.5 1.0 OG B:SER297 4.2 18.7 1.0 O B:HIS298 4.3 17.8 1.0 OD1 B:ASN323 4.4 17.4 1.0 CB B:ASN319 4.5 17.2 1.0 ND1 B:HIS301 4.6 18.6 1.0 C5' C:DA413 4.6 17.5 0.5 C5' C:DA413 4.6 17.5 0.6 OP2 C:DG414 4.6 23.8 0.5 CA B:SER297 4.6 17.9 1.0 CA B:ASN319 4.6 17.0 1.0 CB B:HIS298 4.8 16.2 1.0 C B:SER297 4.8 16.7 1.0 CE1 B:HIS301 4.8 20.4 1.0 CA B:HIS298 4.8 15.2 1.0 N B:LYS320 4.9 13.9 1.0 CB B:SER297 4.9 15.6 1.0 C B:HIS298 5.0 15.8 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 40S


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 40S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:17.4 occ:0.70 MG D:MG601 0.0 17.3 0.3 OD1 A:ASN119 2.2 16.9 1.0 O A:HOH712 2.2 16.9 1.0 O A:HOH750 2.2 23.0 1.0 O A:HOH808 2.3 21.1 1.0 OP3 D:DG514 2.3 16.0 0.3 O3' D:DA513 2.3 17.1 0.7 O3' D:DA513 2.4 17.0 0.3 OP1 D:DG514 2.6 16.6 0.7 P D:DG514 3.0 15.4 0.7 CG A:ASN119 3.4 16.8 1.0 C3' D:DA513 3.5 18.6 0.7 P D:DG514 3.6 15.8 0.3 C3' D:DA513 3.6 18.5 0.3 O A:ASN119 3.7 16.4 1.0 O5' D:DG514 3.9 15.4 0.7 C4' D:DA513 3.9 18.2 0.7 N A:HIS98 3.9 16.2 1.0 C4' D:DA513 4.0 18.2 0.3 ND2 A:ASN119 4.0 17.5 1.0 O5' D:DG514 4.0 16.8 0.3 OP2 D:DG514 4.0 19.4 0.3 C A:ASN119 4.2 16.3 1.0 OP2 D:DG514 4.2 19.4 0.7 C2' D:DA513 4.2 16.2 0.7 C2' D:DA513 4.2 16.2 0.3 OG A:SER97 4.2 19.1 1.0 O A:HIS98 4.3 18.5 1.0 O D:HOH747 4.3 31.9 1.0 OD1 A:ASN123 4.4 19.0 1.0 CB A:ASN119 4.5 14.8 1.0 CA A:SER97 4.5 15.5 1.0 C5' D:DA513 4.6 17.1 0.7 CA A:ASN119 4.6 16.4 1.0 ND1 A:HIS101 4.7 20.6 1.0 C5' D:DA513 4.7 17.2 0.3 C A:SER97 4.7 14.4 1.0 CB A:HIS98 4.7 15.9 1.0 CA A:HIS98 4.7 15.6 1.0 OP1 D:DG514 4.8 22.2 0.3 CE1 A:HIS101 4.8 18.9 1.0 N A:LYS120 4.9 14.0 1.0 C A:HIS98 4.9 14.9 1.0 CB A:SER97 4.9 16.1 1.0 O A:HOH777 5.0 25.0 1.0

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