Sodium in PDB 8vmy: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S, PDB code: 8vmy 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 / 1.53
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 / 18.9

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 20S also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	4 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 20S (pdb code 8vmy). 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 20S, PDB code: 8vmy:
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 20S


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 20S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:13.2 occ:1.00 OD1 B:ASN319 2.3 14.5 1.0 O B:HOH597 2.3 19.1 1.0 O B:HOH540 2.3 13.2 1.0 O B:HOH544 2.4 16.0 1.0 O3' C:DA413 2.5 11.2 1.0 OP1 C:DG414 2.6 14.7 1.0 P C:DG414 3.1 14.3 1.0 CG B:ASN319 3.4 13.0 1.0 C3' C:DA413 3.7 12.4 1.0 O B:ASN319 3.8 12.4 1.0 N B:HIS298 3.9 11.4 1.0 O5' C:DG414 4.0 13.9 1.0 C4' C:DA413 4.0 12.8 1.0 ND2 B:ASN319 4.1 13.0 1.0 O C:HOH643 4.2 27.2 1.0 O B:HIS298 4.2 14.1 1.0 OG B:SER297 4.2 15.6 1.0 C B:ASN319 4.2 13.6 1.0 OP2 C:DG414 4.3 16.0 1.0 C2' C:DA413 4.4 13.1 1.0 OD1 B:ASN323 4.5 12.5 1.0 CA B:SER297 4.5 13.2 1.0 CB B:HIS298 4.6 13.0 1.0 C B:SER297 4.6 12.8 1.0 CA B:HIS298 4.6 12.1 1.0 CB B:ASN319 4.6 11.8 1.0 C5' C:DA413 4.7 11.9 1.0 CA B:ASN319 4.7 12.2 1.0 ND1 B:HIS301 4.7 14.0 1.0 C B:HIS298 4.8 13.4 1.0 CE1 B:HIS301 4.9 14.7 1.0 CB B:SER297 4.9 15.7 1.0 N B:LYS320 5.0 11.6 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 20S


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 20S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:12.8 occ:0.95 MG D:MG601 0.0 13.0 0.1 OP3 D:DG514 2.2 12.6 0.1 OD1 A:ASN119 2.3 12.7 1.0 O A:HOH723 2.3 13.6 1.0 O A:HOH763 2.4 14.9 1.0 O A:HOH810 2.4 17.5 1.0 O3' D:DA513 2.4 12.1 0.9 O3' D:DA513 2.4 12.3 0.1 OP1 D:DG514 2.6 11.5 0.9 P D:DG514 3.1 12.8 0.9 CG A:ASN119 3.4 11.2 1.0 P D:DG514 3.6 11.9 0.1 C3' D:DA513 3.6 13.2 0.1 C3' D:DA513 3.6 13.1 0.9 O A:ASN119 3.7 11.9 1.0 N A:HIS98 3.9 11.4 1.0 O5' D:DG514 3.9 12.7 0.9 C4' D:DA513 3.9 13.4 0.1 C4' D:DA513 4.0 13.4 0.9 OP2 D:DG514 4.0 14.1 0.1 ND2 A:ASN119 4.1 11.9 1.0 O5' D:DG514 4.2 12.9 0.1 C A:ASN119 4.2 13.8 1.0 O A:HIS98 4.3 13.1 1.0 OG A:SER97 4.3 13.7 1.0 C2' D:DA513 4.3 12.5 0.1 OP2 D:DG514 4.3 14.2 0.9 C2' D:DA513 4.3 12.4 0.9 CA A:SER97 4.5 11.2 1.0 OD1 A:ASN123 4.5 13.6 1.0 CB A:ASN119 4.6 10.5 1.0 C A:SER97 4.6 11.1 1.0 CB A:HIS98 4.6 14.1 1.0 C5' D:DA513 4.6 12.5 0.1 C5' D:DA513 4.6 12.4 0.9 CA A:HIS98 4.7 13.3 1.0 CA A:ASN119 4.7 12.4 1.0 O D:HOH748 4.7 28.5 1.0 OP1 D:DG514 4.7 13.4 0.1 ND1 A:HIS101 4.8 15.2 1.0 C A:HIS98 4.8 11.7 1.0 N A:LYS120 4.9 10.3 1.0 CB A:SER97 4.9 11.7 1.0 CE1 A:HIS101 5.0 15.5 1.0 O A:HOH771 5.0 19.0 1.0

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