Sodium in PDB 8vn4: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1200S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1200S, PDB code: 8vn4 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 / 1.75
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 (%)	18.3 / 20.2

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MG2+ For 1200S 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 1200S (pdb code 8vn4). 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 1200S, PDB code: 8vn4:
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 1200S


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 1200S within 5.0Å range: probe atom residue distance (Å) B Occ c:Na502 b:13.5 occ:0.05 MG c:MG501 0.0 13.3 0.9 O c:HOH617 2.1 15.0 1.0 OD1 B:ASN319 2.1 12.4 1.0 O c:HOH606 2.1 17.1 0.2 OP2 c:DG414 2.1 16.8 0.1 O B:HOH583 2.1 15.0 1.0 O B:HOH529 2.2 14.9 1.0 O3' C:DA413 2.2 16.3 0.1 O3' C:DA413 2.3 16.6 0.9 P c:DG414 2.6 15.7 0.1 CG B:ASN319 3.2 16.2 1.0 P c:DG414 3.2 17.7 0.8 C3' C:DA413 3.6 14.4 0.1 OP1 c:DG414 3.6 16.6 0.8 O5' c:DG414 3.6 15.8 0.1 C3' C:DA413 3.6 14.3 0.9 O5' c:DG414 3.8 15.0 0.8 ND2 B:ASN319 3.8 14.8 1.0 OP1 c:DG414 3.9 16.8 0.1 O B:ASN319 3.9 14.8 1.0 C4' C:DA413 4.1 13.4 0.1 N B:HIS298 4.1 15.0 1.0 C4' C:DA413 4.2 13.1 0.9 O c:HOH614 4.2 24.9 1.0 OG B:SER297 4.2 14.7 1.0 C2' C:DA413 4.2 13.9 0.1 C B:ASN319 4.3 13.6 1.0 C2' C:DA413 4.3 13.8 0.9 O B:HIS298 4.4 13.6 1.0 CB B:ASN319 4.5 13.3 1.0 OP2 c:DG414 4.5 18.9 0.8 OD1 B:ASN323 4.5 11.8 1.0 CA B:SER297 4.6 15.8 1.0 CA B:ASN319 4.6 11.5 1.0 ND1 B:HIS301 4.7 14.8 1.0 C5' C:DA413 4.8 15.8 0.1 CB B:HIS298 4.8 12.5 1.0 C B:SER297 4.8 15.1 1.0 C5' C:DA413 4.8 15.9 0.9 CA B:HIS298 4.9 12.5 1.0 CB B:SER297 4.9 13.7 1.0 CE1 B:HIS301 4.9 21.0 1.0 N B:LYS320 5.0 10.3 1.0 C5' c:DG414 5.0 16.4 0.1

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 1200S


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 1200S within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:12.7 occ:0.05 MG D:MG601 0.0 12.5 0.9 O3' D:DA513 2.1 16.2 0.1 O A:HOH718 2.1 14.2 1.0 O D:HOH734 2.2 15.0 1.0 O3' D:DA513 2.2 16.2 0.9 OD1 A:ASN119 2.2 12.2 1.0 O A:HOH770 2.2 16.4 1.0 O d:HOH604 2.2 17.9 0.3 OP1 d:DG514 2.3 17.5 0.1 P d:DG514 2.7 15.1 0.1 CG A:ASN119 3.3 13.4 1.0 P d:DG514 3.3 14.9 0.7 C3' D:DA513 3.4 16.9 0.9 C3' D:DA513 3.4 16.6 0.1 O5' d:DG514 3.7 14.4 0.1 OP2 d:DG514 3.7 17.5 0.7 O A:ASN119 3.8 13.5 1.0 O5' d:DG514 3.8 12.7 0.7 OP2 d:DG514 3.9 16.9 0.1 C4' D:DA513 3.9 16.4 0.9 C4' D:DA513 3.9 16.2 0.1 ND2 A:ASN119 3.9 12.8 1.0 C2' D:DA513 4.1 14.8 0.9 C2' D:DA513 4.1 14.7 0.1 N A:HIS98 4.1 11.7 1.0 C A:ASN119 4.2 13.6 1.0 O d:HOH614 4.3 24.3 1.0 OG A:SER97 4.3 13.8 1.0 OD1 A:ASN123 4.4 13.8 1.0 CB A:ASN119 4.5 7.1 1.0 O A:HIS98 4.5 14.8 1.0 CA A:SER97 4.6 14.1 1.0 OP1 d:DG514 4.6 17.6 0.7 C5' D:DA513 4.6 14.7 0.1 C5' D:DA513 4.6 14.4 0.9 CA A:ASN119 4.7 9.6 1.0 ND1 A:HIS101 4.7 16.6 1.0 C A:SER97 4.8 9.2 1.0 O A:HOH791 4.8 23.5 1.0 N A:LYS120 4.9 10.6 1.0 CB A:HIS98 4.9 10.8 1.0 CB A:SER97 4.9 12.3 1.0 CA A:HIS98 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.