Sodium in PDB 8vmr: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 40S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 40S, PDB code: 8vmr 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 / 1.50
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 (%)	18.3 / 19.4

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 40S also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Magnesium	(Mg)	1 atom

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 40S (pdb code 8vmr). 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 40S, PDB code: 8vmr:
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 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 40S within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:15.3 occ:0.80 MG C:MG501 0.0 15.3 0.2 OD1 B:ASN319 2.2 16.3 1.0 O B:HOH597 2.3 19.9 1.0 O B:HOH528 2.3 15.6 1.0 O B:HOH557 2.4 19.0 1.0 O3' C:DA413 2.4 15.4 0.8 OP3 C:DG414 2.4 16.7 0.2 OP1 C:DG414 2.5 16.5 0.8 O3' C:DA413 2.5 15.5 0.2 P C:DG414 3.0 14.6 0.8 CG B:ASN319 3.4 15.9 1.0 C3' C:DA413 3.7 16.2 0.8 O B:ASN319 3.7 14.7 1.0 C3' C:DA413 3.7 16.2 0.2 P C:DG414 3.7 20.8 0.2 N B:HIS298 3.9 14.5 1.0 O5' C:DG414 3.9 15.4 0.8 C4' C:DA413 3.9 15.6 0.8 C4' C:DA413 4.0 15.7 0.2 ND2 B:ASN319 4.0 15.6 1.0 O C:HOH642 4.1 27.6 1.0 O5' C:DG414 4.1 16.4 0.2 OG B:SER297 4.2 18.6 1.0 C B:ASN319 4.2 16.8 1.0 OP1 C:DG414 4.2 17.6 0.2 O B:HIS298 4.2 16.1 1.0 OP2 C:DG414 4.2 18.0 0.8 C2' C:DA413 4.3 15.8 0.8 C2' C:DA413 4.3 15.8 0.2 CA B:SER297 4.5 15.0 1.0 OD1 B:ASN323 4.5 15.5 1.0 CB B:ASN319 4.5 14.7 1.0 CA B:ASN319 4.6 16.1 1.0 C5' C:DA413 4.6 15.6 0.8 C5' C:DA413 4.6 15.6 0.2 CB B:HIS298 4.6 15.2 1.0 C B:SER297 4.6 15.4 1.0 CA B:HIS298 4.7 14.3 1.0 ND1 B:HIS301 4.8 16.7 1.0 C B:HIS298 4.8 15.8 1.0 CB B:SER297 4.9 17.2 1.0 N B:LYS320 4.9 14.2 1.0 CE1 B:HIS301 4.9 16.5 1.0 OP2 C:DG414 5.0 18.4 0.2

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 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 PH7.0 (K+ Mes) with 500 Um MG2+ For 40S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:15.5 occ:1.00 OD1 A:ASN119 2.3 15.7 1.0 O A:HOH712 2.3 16.1 1.0 O A:HOH813 2.3 20.4 1.0 O A:HOH726 2.4 19.2 1.0 O3' D:DA513 2.4 17.1 1.0 OP1 D:DG514 2.5 15.5 1.0 P D:DG514 3.1 16.9 1.0 CG A:ASN119 3.4 14.8 1.0 C3' D:DA513 3.7 16.3 1.0 O A:ASN119 3.7 14.4 1.0 N A:HIS98 3.9 13.4 1.0 C4' D:DA513 4.0 15.7 1.0 O5' D:DG514 4.0 15.0 1.0 ND2 A:ASN119 4.1 15.3 1.0 OG A:SER97 4.2 16.6 1.0 C A:ASN119 4.2 15.2 1.0 O A:HIS98 4.2 17.1 1.0 C2' D:DA513 4.3 15.2 1.0 OP2 D:DG514 4.3 17.6 1.0 O D:HOH749 4.4 32.0 1.0 CA A:SER97 4.5 13.9 1.0 OD1 A:ASN123 4.5 16.1 1.0 C5' D:DA513 4.6 14.5 1.0 CB A:ASN119 4.6 13.3 1.0 C A:SER97 4.6 14.4 1.0 CB A:HIS98 4.6 15.0 1.0 CA A:ASN119 4.6 15.1 1.0 CA A:HIS98 4.7 14.1 1.0 ND1 A:HIS101 4.8 16.3 1.0 C A:HIS98 4.8 15.8 1.0 CB A:SER97 4.8 15.6 1.0 N A:LYS120 4.9 13.5 1.0 CE1 A:HIS101 4.9 16.1 1.0 O A:HOH768 5.0 21.5 1.0

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