Sodium in PDB 8vms: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 80S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 80S, PDB code: 8vms 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)	42.93 / 1.42
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 / 18.9

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 80S 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 80S (pdb code 8vms). 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 80S, PDB code: 8vms:
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 80S


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 80S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:15.8 occ:0.75 MG C:MG501 0.1 15.4 0.2 O B:HOH601 2.3 22.2 1.0 O B:HOH522 2.3 15.5 1.0 OP3 C:DG414 2.3 15.9 0.2 OD1 B:ASN319 2.3 16.6 1.0 OP1 C:DG414 2.4 15.9 0.8 O B:HOH549 2.4 20.9 1.0 O3' C:DA413 2.4 15.5 0.2 O3' C:DA413 2.4 15.2 0.8 P C:DG414 3.0 14.2 0.8 CG B:ASN319 3.4 14.7 1.0 P C:DG414 3.6 17.4 0.2 C3' C:DA413 3.7 14.9 0.8 C3' C:DA413 3.7 15.0 0.2 O B:ASN319 3.8 15.1 1.0 N B:HIS298 3.9 14.5 1.0 OP1 C:DG414 3.9 15.8 0.2 O5' C:DG414 3.9 15.1 0.8 C4' C:DA413 4.0 14.8 0.8 ND2 B:ASN319 4.0 15.1 1.0 O C:HOH631 4.1 26.8 1.0 C4' C:DA413 4.1 14.9 0.2 O5' C:DG414 4.1 15.6 0.2 O B:HIS298 4.2 16.2 1.0 OG B:SER297 4.2 18.3 1.0 OP2 C:DG414 4.2 16.5 0.8 C B:ASN319 4.3 15.5 1.0 C2' C:DA413 4.3 15.3 0.8 C2' C:DA413 4.4 15.3 0.2 OD1 B:ASN323 4.5 15.4 1.0 CA B:SER297 4.5 15.5 1.0 CB B:HIS298 4.6 16.5 1.0 C B:SER297 4.6 15.1 1.0 CB B:ASN319 4.6 14.9 1.0 CA B:HIS298 4.6 14.0 1.0 C5' C:DA413 4.6 14.5 0.8 OP2 C:DG414 4.7 17.5 0.2 C5' C:DA413 4.7 14.6 0.2 CA B:ASN319 4.7 15.6 1.0 ND1 B:HIS301 4.7 17.3 1.0 C B:HIS298 4.8 14.5 1.0 CE1 B:HIS301 4.9 18.8 1.0 CB B:SER297 4.9 17.3 1.0 N B:LYS320 5.0 14.2 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 80S


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 80S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:15.8 occ:0.80 MG D:MG601 0.0 15.8 0.2 OD1 A:ASN119 2.2 16.0 1.0 O A:HOH713 2.2 15.9 1.0 O A:HOH735 2.3 19.2 1.0 OP3 D:DG514 2.4 15.9 0.2 O A:HOH806 2.4 22.2 1.0 O3' D:DA513 2.4 15.4 0.8 O3' D:DA513 2.4 15.6 0.2 OP1 D:DG514 2.5 15.9 0.8 P D:DG514 3.1 13.9 0.8 CG A:ASN119 3.4 13.5 1.0 P D:DG514 3.6 16.4 0.2 C3' D:DA513 3.6 15.2 0.8 C3' D:DA513 3.7 15.3 0.2 O A:ASN119 3.7 14.1 1.0 N A:HIS98 3.9 13.5 1.0 O5' D:DG514 3.9 14.5 0.8 C4' D:DA513 3.9 15.1 0.8 C4' D:DA513 4.0 15.2 0.2 OP2 D:DG514 4.0 16.5 0.2 ND2 A:ASN119 4.0 15.2 1.0 O5' D:DG514 4.1 15.2 0.2 C A:ASN119 4.2 15.2 1.0 OG A:SER97 4.2 16.2 1.0 O A:HIS98 4.3 16.2 1.0 C2' D:DA513 4.3 15.4 0.8 OP2 D:DG514 4.3 16.9 0.8 C2' D:DA513 4.3 15.3 0.2 OD1 A:ASN123 4.4 15.7 1.0 CA A:SER97 4.5 14.0 1.0 O D:HOH713 4.5 32.0 1.0 CB A:ASN119 4.6 13.3 1.0 C5' D:DA513 4.6 14.8 0.8 C A:SER97 4.6 14.3 1.0 CB A:HIS98 4.6 16.3 1.0 CA A:ASN119 4.6 13.6 1.0 C5' D:DA513 4.6 14.9 0.2 CA A:HIS98 4.7 14.4 1.0 OP1 D:DG514 4.7 15.6 0.2 ND1 A:HIS101 4.8 17.7 1.0 C A:HIS98 4.8 14.7 1.0 CB A:SER97 4.9 14.4 1.0 N A:LYS120 4.9 13.8 1.0 CE1 A:HIS101 4.9 17.7 1.0 O A:HOH771 5.0 22.4 1.0

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