Sodium in PDB 8vmt: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 160S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 160S, PDB code: 8vmt 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)	49.18 / 1.48
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.58, 113.58, 87.99, 90, 90, 120
R / Rfree (%)	17.9 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 160S 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 160S (pdb code 8vmt). 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 160S, PDB code: 8vmt:
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 PH7.0 (K+ Mes) with 500 Um MG2+ For 160S


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 PH7.0 (K+ Mes) with 500 Um MG2+ For 160S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:15.1 occ:0.50 MG C:MG501 0.0 15.1 0.5 OD1 B:ASN319 2.2 17.1 1.0 O C:HOH638 2.2 21.5 1.0 OP3 C:DG414 2.2 15.4 0.5 O B:HOH530 2.2 16.3 1.0 O B:HOH544 2.2 20.8 1.0 O3' C:DA413 2.3 17.0 0.5 O3' C:DA413 2.4 17.0 0.5 OP1 C:DG414 2.4 16.6 0.5 P C:DG414 2.9 14.2 0.5 CG B:ASN319 3.3 14.2 1.0 P C:DG414 3.4 17.4 0.5 C3' C:DA413 3.6 17.1 0.5 C3' C:DA413 3.6 17.0 0.5 OP1 C:DG414 3.7 16.2 0.5 O B:ASN319 3.8 15.0 1.0 O5' C:DG414 3.8 15.5 0.5 C4' C:DA413 3.9 15.1 0.5 ND2 B:ASN319 3.9 15.0 1.0 O5' C:DG414 3.9 15.4 0.5 N B:HIS298 4.0 13.8 1.0 C4' C:DA413 4.0 15.2 0.5 O C:HOH625 4.1 25.3 1.0 C B:ASN319 4.2 15.8 1.0 OP2 C:DG414 4.2 17.2 0.5 OG B:SER297 4.2 18.1 1.0 C2' C:DA413 4.2 15.7 0.5 C2' C:DA413 4.3 15.6 0.5 O B:HIS298 4.3 16.7 1.0 CB B:ASN319 4.5 14.6 1.0 OD1 B:ASN323 4.5 15.7 1.0 OP2 C:DG414 4.5 20.2 0.5 CA B:SER297 4.6 15.7 1.0 C5' C:DA413 4.6 15.1 0.5 CA B:ASN319 4.6 14.2 1.0 C5' C:DA413 4.7 15.1 0.5 ND1 B:HIS301 4.7 18.3 1.0 C B:SER297 4.7 14.9 1.0 CB B:HIS298 4.8 15.0 1.0 CA B:HIS298 4.8 14.9 1.0 N B:LYS320 4.9 13.4 1.0 CE1 B:HIS301 4.9 18.6 1.0 CB B:SER297 4.9 16.6 1.0 C B:HIS298 4.9 15.9 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 160S


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 PH7.0 (K+ Mes) with 500 Um MG2+ For 160S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:15.7 occ:0.60 MG D:MG601 0.0 15.8 0.4 OP3 D:DG514 2.2 15.0 0.4 O A:HOH724 2.2 15.9 1.0 OD1 A:ASN119 2.2 15.4 1.0 O A:HOH744 2.2 21.1 1.0 O A:HOH811 2.3 20.4 1.0 O3' D:DA513 2.4 17.1 0.6 O3' D:DA513 2.4 17.0 0.4 OP1 D:DG514 2.5 15.2 0.6 P D:DG514 3.0 14.8 0.6 CG A:ASN119 3.4 13.7 1.0 P D:DG514 3.4 16.0 0.4 C3' D:DA513 3.6 17.9 0.6 C3' D:DA513 3.6 17.8 0.4 OP2 D:DG514 3.7 16.7 0.4 O A:ASN119 3.7 13.6 1.0 O5' D:DG514 3.9 13.7 0.6 C4' D:DA513 3.9 16.8 0.6 C4' D:DA513 3.9 16.8 0.4 O5' D:DG514 4.0 13.9 0.4 N A:HIS98 4.0 13.5 1.0 ND2 A:ASN119 4.0 15.0 1.0 C A:ASN119 4.2 14.0 1.0 C2' D:DA513 4.2 16.0 0.6 OG A:SER97 4.2 16.8 1.0 O D:HOH714 4.3 28.7 1.0 OP2 D:DG514 4.3 16.3 0.6 C2' D:DA513 4.3 16.0 0.4 O A:HIS98 4.3 17.5 1.0 OD1 A:ASN123 4.4 16.5 1.0 CA A:SER97 4.5 14.2 1.0 CB A:ASN119 4.5 12.8 1.0 C5' D:DA513 4.6 16.5 0.6 OP1 D:DG514 4.6 18.9 0.4 C5' D:DA513 4.6 16.5 0.4 CA A:ASN119 4.6 13.6 1.0 C A:SER97 4.7 13.0 1.0 ND1 A:HIS101 4.7 18.1 1.0 CB A:HIS98 4.7 15.8 1.0 CA A:HIS98 4.8 14.1 1.0 N A:LYS120 4.9 13.0 1.0 CB A:SER97 4.9 15.2 1.0 O A:HOH776 4.9 21.8 1.0 CE1 A:HIS101 4.9 17.9 1.0 C A:HIS98 4.9 15.6 1.0

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