Sodium in PDB 8vnp: Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate

The structure of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate, PDB code: 8vnp 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)	34.28 / 1.79
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.695, 113.695, 87.994, 90, 90, 120
R / Rfree (%)	17.1 / 19

The structure of Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate (pdb code 8vnp). 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 at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate, PDB code: 8vnp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate


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 at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:12.8 occ:1.00 OD1 B:ASN319 2.3 13.0 1.0 O B:HOH598 2.3 17.9 1.0 O B:HOH537 2.4 14.6 1.0 O B:HOH510 2.4 14.1 1.0 OP1 C:DG414 2.5 15.1 1.0 O3' C:DA413 2.5 13.0 1.0 P C:DG414 3.1 14.3 1.0 CG B:ASN319 3.4 13.5 1.0 O B:ASN319 3.7 10.6 1.0 C3' C:DA413 3.8 12.5 1.0 N B:HIS298 3.8 12.8 1.0 O5' C:DG414 4.0 15.5 1.0 ND2 B:ASN319 4.1 13.1 1.0 C4' C:DA413 4.1 13.1 1.0 OG B:SER297 4.1 16.7 1.0 O C:HOH642 4.2 18.2 0.5 O B:HIS298 4.2 13.3 1.0 C B:ASN319 4.2 11.7 1.0 OP2 C:DG414 4.3 13.2 1.0 C2' C:DA413 4.4 10.7 1.0 CA B:SER297 4.5 12.9 1.0 OD1 B:ASN323 4.6 11.8 1.0 C B:SER297 4.6 13.9 1.0 CB B:HIS298 4.6 13.6 1.0 CA B:HIS298 4.6 14.0 1.0 CB B:ASN319 4.6 12.1 1.0 CA B:ASN319 4.7 11.6 1.0 C5' C:DA413 4.7 11.4 1.0 ND1 B:HIS301 4.8 12.2 1.0 C B:HIS298 4.8 14.7 1.0 CB B:SER297 4.8 13.0 1.0 CE1 B:HIS301 4.9 13.0 1.0 N B:LYS320 4.9 10.5 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate


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 at PH6.0 (K+ Mes) with 0.2 M Sodium Malonate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:12.7 occ:1.00 OD1 A:ASN119 2.3 12.3 1.0 O A:HOH720 2.3 12.8 1.0 O A:HOH808 2.3 16.2 1.0 O3' D:DA513 2.4 12.0 1.0 OP1 D:DG514 2.5 12.2 1.0 O A:HOH712 2.5 13.8 1.0 P D:DG514 3.1 12.9 1.0 CG A:ASN119 3.5 10.4 1.0 C3' D:DA513 3.7 12.4 1.0 O A:ASN119 3.8 12.0 1.0 N A:HIS98 3.9 10.9 1.0 C4' D:DA513 3.9 12.2 1.0 O5' D:DG514 3.9 12.9 1.0 ND2 A:ASN119 4.1 12.1 1.0 OG A:SER97 4.2 13.3 1.0 C A:ASN119 4.3 12.0 1.0 O A:HIS98 4.3 13.3 1.0 OP2 D:DG514 4.3 11.4 1.0 C2' D:DA513 4.3 13.2 1.0 CA A:SER97 4.5 11.1 1.0 OD1 A:ASN123 4.5 12.7 1.0 O D:HOH725 4.5 17.7 0.5 C5' D:DA513 4.5 12.1 1.0 C A:SER97 4.6 10.0 1.0 CB A:HIS98 4.7 13.8 1.0 CA A:HIS98 4.7 13.9 1.0 CB A:ASN119 4.7 9.3 1.0 CA A:ASN119 4.7 11.6 1.0 ND1 A:HIS101 4.8 13.5 1.0 C A:HIS98 4.8 13.4 1.0 CB A:SER97 4.8 9.2 1.0 O A:HOH784 5.0 20.5 1.0 N A:LYS120 5.0 10.4 1.0 CE1 A:HIS101 5.0 13.9 1.0

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