Sodium in PDB 8vmz: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S, PDB code: 8vmz 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 / 1.57
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 (%)	18.1 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 40S also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
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 40S (pdb code 8vmz). 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 40S, PDB code: 8vmz:
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 40S


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 40S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:13.0 occ:0.90 MG C:MG501 0.0 12.9 0.1 OD1 B:ASN319 2.2 14.5 1.0 OP3 C:DG414 2.2 13.7 0.1 O B:HOH598 2.3 19.6 1.0 O B:HOH544 2.3 12.8 1.0 O3' C:DA413 2.4 11.8 0.9 O B:HOH540 2.4 16.5 1.0 O3' C:DA413 2.5 12.0 0.1 OP1 C:DG414 2.5 14.5 0.9 P C:DG414 3.0 13.5 0.9 CG B:ASN319 3.4 12.7 1.0 P C:DG414 3.5 14.3 0.1 C3' C:DA413 3.7 13.7 0.9 C3' C:DA413 3.7 13.6 0.1 O B:ASN319 3.8 12.4 1.0 OP1 C:DG414 3.9 15.0 0.1 N B:HIS298 3.9 11.3 1.0 O5' C:DG414 3.9 13.3 0.9 ND2 B:ASN319 4.0 13.2 1.0 C4' C:DA413 4.0 13.1 0.9 C4' C:DA413 4.1 13.2 0.1 O5' C:DG414 4.1 14.2 0.1 O C:HOH647 4.2 26.2 1.0 OG B:SER297 4.2 15.4 1.0 OP2 C:DG414 4.2 15.5 0.9 C B:ASN319 4.2 13.3 1.0 O B:HIS298 4.2 13.5 1.0 C2' C:DA413 4.3 12.6 0.9 C2' C:DA413 4.4 12.7 0.1 CA B:SER297 4.5 12.6 1.0 OD1 B:ASN323 4.6 12.1 1.0 CB B:ASN319 4.6 11.0 1.0 CB B:HIS298 4.6 12.3 1.0 C B:SER297 4.7 12.8 1.0 C5' C:DA413 4.7 13.0 0.9 CA B:ASN319 4.7 13.0 1.0 CA B:HIS298 4.7 12.0 1.0 C5' C:DA413 4.7 13.1 0.1 OP2 C:DG414 4.7 17.0 0.1 ND1 B:HIS301 4.8 14.3 1.0 C B:HIS298 4.8 12.7 1.0 CE1 B:HIS301 4.9 15.6 1.0 CB B:SER297 4.9 13.7 1.0 N B:LYS320 4.9 11.7 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 40S


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 40S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:13.2 occ:0.90 MG D:MG601 0.1 13.1 0.1 OD1 A:ASN119 2.3 12.8 1.0 O A:HOH714 2.3 13.4 1.0 OP3 D:DG514 2.3 12.7 0.1 O3' D:DA513 2.4 13.0 0.9 O3' D:DA513 2.4 13.3 0.1 O A:HOH808 2.4 19.1 1.0 O A:HOH737 2.4 16.0 1.0 OP1 D:DG514 2.6 12.0 0.9 P D:DG514 3.0 13.2 0.9 CG A:ASN119 3.4 10.6 1.0 C3' D:DA513 3.6 14.0 0.9 P D:DG514 3.6 13.1 0.1 C3' D:DA513 3.6 14.1 0.1 O A:ASN119 3.8 11.1 1.0 N A:HIS98 3.9 10.8 1.0 O5' D:DG514 3.9 11.9 0.9 C4' D:DA513 3.9 13.9 0.9 C4' D:DA513 4.0 13.9 0.1 OP2 D:DG514 4.0 15.0 0.1 ND2 A:ASN119 4.1 12.1 1.0 O5' D:DG514 4.2 13.5 0.1 C A:ASN119 4.2 13.1 1.0 OP2 D:DG514 4.3 15.4 0.9 OG A:SER97 4.3 14.1 1.0 O A:HIS98 4.3 13.0 1.0 C2' D:DA513 4.3 12.5 0.9 C2' D:DA513 4.3 12.6 0.1 OD1 A:ASN123 4.5 13.4 1.0 CA A:SER97 4.5 10.9 1.0 C5' D:DA513 4.6 13.2 0.9 CB A:ASN119 4.6 9.3 1.0 C5' D:DA513 4.6 13.3 0.1 CB A:HIS98 4.6 12.8 1.0 C A:SER97 4.6 10.2 1.0 O D:HOH738 4.7 29.7 1.0 CA A:ASN119 4.7 11.8 1.0 CA A:HIS98 4.7 12.3 1.0 ND1 A:HIS101 4.8 16.4 1.0 OP1 D:DG514 4.9 14.6 0.1 C A:HIS98 4.9 11.8 1.0 N A:LYS120 4.9 10.8 1.0 CB A:SER97 4.9 11.8 1.0 O A:HOH763 4.9 19.3 1.0 CE1 A:HIS101 5.0 15.2 1.0

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