Sodium in PDB 8vmo: Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+, PDB code: 8vmo 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)	49.40 / 1.68
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.083, 114.083, 88.123, 90, 90, 120
R / Rfree (%)	16.9 / 18.9

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+ also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+ (pdb code 8vmo). 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:Ground State at PH7.0 (K+ Mes) with Na+, PDB code: 8vmo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+


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:Ground State at PH7.0 (K+ Mes) with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:20.7 occ:1.00 OD1 B:ASN319 2.3 20.8 1.0 O B:HOH614 2.3 27.0 1.0 O B:HOH541 2.3 20.7 1.0 O B:HOH535 2.4 23.1 1.0 OP1 C:DG414 2.4 21.4 1.0 O3' C:DA413 2.5 19.3 1.0 P C:DG414 3.1 22.4 1.0 CG B:ASN319 3.4 19.8 1.0 C3' C:DA413 3.7 19.5 1.0 O B:ASN319 3.7 19.1 1.0 N B:HIS298 3.9 20.4 1.0 O5' C:DG414 4.0 23.3 1.0 C4' C:DA413 4.0 19.3 1.0 ND2 B:ASN319 4.1 19.9 1.0 C B:ASN319 4.2 20.4 1.0 OG B:SER297 4.2 21.5 1.0 OP2 C:DG414 4.3 21.8 1.0 O B:HIS298 4.3 19.6 1.0 C2' C:DA413 4.4 19.4 1.0 CA B:SER297 4.5 20.5 1.0 OD1 B:ASN323 4.5 19.6 1.0 CB B:ASN319 4.6 19.6 1.0 CB B:HIS298 4.6 20.2 1.0 C B:SER297 4.6 20.5 1.0 CA B:HIS298 4.7 20.2 1.0 C5' C:DA413 4.7 19.6 1.0 CA B:ASN319 4.7 19.5 1.0 ND1 B:HIS301 4.8 20.3 1.0 C B:HIS298 4.8 20.9 1.0 CB B:SER297 4.9 21.1 1.0 N B:LYS320 4.9 17.8 1.0 CE1 B:HIS301 4.9 21.1 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Ground State at PH7.0 (K+ Mes) with Na+


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:Ground State at PH7.0 (K+ Mes) with Na+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:16.6 occ:0.80 OD1 A:ASN119 2.3 19.6 1.0 O A:HOH726 2.3 20.7 1.0 O A:HOH808 2.4 24.4 1.0 O A:HOH747 2.5 23.4 1.0 O3' D:DA513 2.5 19.7 1.0 OP1 D:DG514 2.5 18.4 1.0 P D:DG514 3.1 20.3 1.0 CG A:ASN119 3.5 18.9 1.0 C3' D:DA513 3.7 19.4 1.0 O A:ASN119 3.8 18.2 1.0 N A:HIS98 3.9 17.9 1.0 C4' D:DA513 4.0 19.5 1.0 O5' D:DG514 4.0 19.1 1.0 ND2 A:ASN119 4.1 19.1 1.0 C A:ASN119 4.2 20.3 1.0 OG A:SER97 4.3 19.6 1.0 O A:HIS98 4.3 20.5 1.0 OP2 D:DG514 4.3 20.4 1.0 C2' D:DA513 4.4 18.5 1.0 OD1 A:ASN123 4.5 21.3 1.0 CA A:SER97 4.5 16.2 1.0 C5' D:DA513 4.6 21.1 1.0 C A:SER97 4.6 16.6 1.0 CB A:ASN119 4.6 17.4 1.0 CB A:HIS98 4.7 20.3 1.0 CA A:HIS98 4.7 20.1 1.0 CA A:ASN119 4.7 18.9 1.0 O D:HOH710 4.7 34.8 1.0 ND1 A:HIS101 4.8 21.4 1.0 N A:LYS120 4.9 17.1 1.0 CB A:SER97 4.9 17.2 1.0 C A:HIS98 4.9 18.8 1.0 CE1 A:HIS101 5.0 21.5 1.0 O A:HOH784 5.0 27.2 1.0

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