Sodium in PDB 8vn7: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S, PDB code: 8vn7 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)	42.99 / 1.67
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.65, 113.65, 88.31, 90, 90, 120
R / Rfree (%)	17.7 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) with 500 Um MG2+ For 20S 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 PH8.0 (Tris) with 500 Um MG2+ For 20S (pdb code 8vn7). 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 PH8.0 (Tris) with 500 Um MG2+ For 20S, PDB code: 8vn7:
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 PH8.0 (Tris) 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 PH8.0 (Tris) with 500 Um MG2+ For 20S within 5.0Å range: probe atom residue distance (Å) B Occ c:Na502 b:16.4 occ:0.65 MG c:MG501 0.0 16.3 0.3 O B:HOH606 2.2 22.5 1.0 OD1 B:ASN319 2.2 17.2 1.0 O B:HOH504 2.3 21.2 1.0 O B:HOH528 2.3 16.5 1.0 O3' C:DA413 2.4 17.2 0.7 OP2 c:DG414 2.4 17.1 0.7 O3' C:DA413 2.5 17.2 0.3 P c:DG414 2.9 17.9 0.7 CG B:ASN319 3.3 16.8 1.0 P c:DG414 3.4 16.1 0.3 C3' C:DA413 3.6 17.6 0.7 C3' C:DA413 3.7 17.6 0.3 O B:ASN319 3.8 15.3 1.0 O5' c:DG414 3.8 17.0 0.7 OP1 c:DG414 3.8 18.5 0.3 N B:HIS298 3.9 17.5 1.0 O5' c:DG414 4.0 17.3 0.3 ND2 B:ASN319 4.0 16.5 1.0 C4' C:DA413 4.0 17.8 0.7 OG B:SER297 4.0 19.3 1.0 C4' C:DA413 4.1 17.8 0.3 OP1 c:DG414 4.2 19.1 0.7 O B:HIS298 4.2 16.9 1.0 O c:HOH614 4.2 26.5 1.0 C B:ASN319 4.2 18.4 1.0 C2' C:DA413 4.3 16.5 0.7 C2' C:DA413 4.3 16.6 0.3 CA B:SER297 4.5 17.1 1.0 OD1 B:ASN323 4.5 15.9 1.0 CB B:ASN319 4.6 16.5 1.0 OP2 c:DG414 4.6 22.1 0.3 C B:SER297 4.7 17.4 1.0 CA B:ASN319 4.7 14.5 1.0 C5' C:DA413 4.7 16.8 0.7 CA B:HIS298 4.7 16.7 1.0 ND1 B:HIS301 4.7 16.8 1.0 CB B:HIS298 4.7 16.7 1.0 C5' C:DA413 4.7 16.9 0.3 CB B:SER297 4.8 16.7 1.0 C B:HIS298 4.8 15.4 1.0 CE1 B:HIS301 4.9 20.6 1.0 N B:LYS320 5.0 13.3 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH8.0 (Tris) 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 PH8.0 (Tris) with 500 Um MG2+ For 20S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:16.7 occ:0.75 MG A:MG603 0.0 16.6 0.2 OD1 A:ASN119 2.2 17.0 1.0 O A:HOH722 2.3 16.9 1.0 O A:HOH813 2.3 20.9 1.0 O A:HOH710 2.3 21.9 1.0 O3' D:DA513 2.4 16.9 0.8 O3' D:DA513 2.4 16.9 0.2 OP1 d:DG514 2.5 16.6 0.8 P d:DG514 3.0 15.3 0.8 CG A:ASN119 3.4 15.7 1.0 P d:DG514 3.6 15.9 0.2 C3' D:DA513 3.6 17.8 0.8 C3' D:DA513 3.7 17.7 0.2 O A:ASN119 3.7 15.1 1.0 O5' d:DG514 3.9 15.1 0.8 N A:HIS98 3.9 14.9 1.0 C4' D:DA513 3.9 16.2 0.8 OP2 d:DG514 3.9 18.4 0.2 ND2 A:ASN119 4.0 15.7 1.0 C4' D:DA513 4.0 16.3 0.2 O5' d:DG514 4.1 16.2 0.2 OG A:SER97 4.2 18.5 1.0 C A:ASN119 4.2 14.7 1.0 O A:HIS98 4.2 16.4 1.0 OP2 d:DG514 4.3 17.6 0.8 C2' D:DA513 4.3 15.8 0.8 C2' D:DA513 4.3 15.9 0.2 OD1 A:ASN123 4.5 16.4 1.0 O d:HOH606 4.5 33.5 1.0 CA A:SER97 4.5 13.9 1.0 CB A:ASN119 4.6 13.2 1.0 C5' D:DA513 4.6 17.9 0.8 C A:SER97 4.6 12.6 1.0 CA A:ASN119 4.6 14.5 1.0 C5' D:DA513 4.7 17.9 0.2 CB A:HIS98 4.7 17.3 1.0 CA A:HIS98 4.7 17.4 1.0 OP1 d:DG514 4.7 19.4 0.2 ND1 A:HIS101 4.7 17.1 1.0 CB A:SER97 4.8 15.4 1.0 C A:HIS98 4.9 15.4 1.0 CE1 A:HIS101 4.9 15.5 1.0 N A:LYS120 4.9 13.1 1.0

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