Sodium in PDB 8vn0: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 80S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 80S, PDB code: 8vn0 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)	47.84 / 1.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.88, 113.88, 88.22, 90, 90, 120
R / Rfree (%)	18 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 80S (pdb code 8vn0). 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 80S, PDB code: 8vn0:
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 PH6.0 (K+ Mes) 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 80S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:12.9 occ:0.80 MG C:MG501 0.0 13.0 0.2 OP3 C:DG414 2.1 12.7 0.2 OD1 B:ASN319 2.2 14.0 1.0 O B:HOH528 2.3 14.0 1.0 O B:HOH602 2.3 20.7 1.0 O B:HOH543 2.4 16.5 1.0 O3' C:DA413 2.4 11.1 0.8 O3' C:DA413 2.4 11.4 0.2 OP1 C:DG414 2.5 15.2 0.8 P C:DG414 3.0 14.1 0.8 CG B:ASN319 3.3 12.6 1.0 P C:DG414 3.3 16.2 0.2 C3' C:DA413 3.6 12.3 0.8 C3' C:DA413 3.7 12.3 0.2 O B:ASN319 3.7 12.5 1.0 OP1 C:DG414 3.8 14.2 0.2 O5' C:DG414 3.9 13.8 0.8 N B:HIS298 3.9 11.5 1.0 O5' C:DG414 3.9 15.1 0.2 ND2 B:ASN319 4.0 12.4 1.0 C4' C:DA413 4.0 12.5 0.8 C4' C:DA413 4.0 12.6 0.2 C B:ASN319 4.2 13.0 1.0 OG B:SER297 4.2 14.5 1.0 O C:HOH645 4.2 26.4 1.0 OP2 C:DG414 4.2 14.7 0.8 O B:HIS298 4.3 13.6 1.0 C2' C:DA413 4.3 12.6 0.8 C2' C:DA413 4.3 12.7 0.2 CA B:SER297 4.5 11.8 1.0 CB B:ASN319 4.5 10.4 1.0 OD1 B:ASN323 4.5 12.0 1.0 OP2 C:DG414 4.6 17.1 0.2 CA B:ASN319 4.6 12.1 1.0 CB B:HIS298 4.7 12.0 1.0 C B:SER297 4.7 12.8 1.0 C5' C:DA413 4.7 12.2 0.8 CA B:HIS298 4.7 12.9 1.0 C5' C:DA413 4.7 12.3 0.2 ND1 B:HIS301 4.7 14.9 1.0 C B:HIS298 4.9 12.9 1.0 CE1 B:HIS301 4.9 17.2 1.0 CB B:SER297 4.9 13.7 1.0 N B:LYS320 4.9 10.2 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) 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 PH6.0 (K+ Mes) with 500 Um MG2+ For 80S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:12.6 occ:0.80 MG D:MG601 0.0 12.8 0.2 OP3 D:DG514 2.2 12.8 0.2 O A:HOH724 2.3 12.5 1.0 OD1 A:ASN119 2.3 11.6 1.0 O3' D:DA513 2.3 12.9 0.8 O A:HOH810 2.3 17.7 1.0 O3' D:DA513 2.4 12.9 0.2 O A:HOH757 2.4 16.4 1.0 OP1 D:DG514 2.6 12.0 0.8 P D:DG514 3.0 13.0 0.8 CG A:ASN119 3.4 9.5 1.0 P D:DG514 3.5 14.7 0.2 C3' D:DA513 3.6 14.3 0.8 C3' D:DA513 3.6 14.2 0.2 O A:ASN119 3.8 11.2 1.0 OP2 D:DG514 3.8 14.4 0.2 C4' D:DA513 3.9 12.5 0.8 O5' D:DG514 3.9 12.1 0.8 N A:HIS98 3.9 11.0 1.0 C4' D:DA513 3.9 12.6 0.2 O5' D:DG514 4.0 14.0 0.2 ND2 A:ASN119 4.1 11.5 1.0 C A:ASN119 4.2 12.6 1.0 OP2 D:DG514 4.2 14.3 0.8 C2' D:DA513 4.3 12.2 0.8 C2' D:DA513 4.3 12.3 0.2 OG A:SER97 4.3 12.6 1.0 O A:HIS98 4.3 12.5 1.0 OD1 A:ASN123 4.4 13.1 1.0 O D:HOH742 4.4 30.8 1.0 CA A:SER97 4.5 10.2 1.0 C5' D:DA513 4.6 12.1 0.8 C5' D:DA513 4.6 12.3 0.2 CB A:ASN119 4.6 7.6 1.0 C A:SER97 4.7 10.2 1.0 CB A:HIS98 4.7 12.5 1.0 CA A:ASN119 4.7 11.4 1.0 ND1 A:HIS101 4.7 16.3 1.0 CA A:HIS98 4.7 14.1 1.0 OP1 D:DG514 4.7 16.6 0.2 CE1 A:HIS101 4.9 15.3 1.0 C A:HIS98 4.9 10.0 1.0 N A:LYS120 4.9 10.5 1.0 O A:HOH781 4.9 19.1 1.0 CB A:SER97 4.9 9.7 1.0

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