Sodium in PDB 8vnr: Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs, PDB code: 8vnr 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)	47.93 / 1.98
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.09, 114.09, 88.412, 90, 90, 120
R / Rfree (%)	18.8 / 21.6

The structure of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs (pdb code 8vnr). 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 H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs, PDB code: 8vnr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:35.9 occ:1.00 OD1 B:ASN319 2.3 28.8 1.0 O B:HOH579 2.4 35.3 1.0 OP1 C:DG414 2.4 34.7 1.0 O B:HOH519 2.4 31.9 1.0 O B:HOH549 2.5 34.5 1.0 O3' C:DA413 2.5 33.4 1.0 P C:DG414 3.0 36.2 1.0 CG B:ASN319 3.4 31.6 1.0 C3' C:DA413 3.7 30.0 1.0 O B:ASN319 3.8 30.1 1.0 O5' C:DG414 3.9 33.8 1.0 N B:ALA298 4.0 34.0 1.0 C4' C:DA413 4.0 31.5 1.0 ND2 B:ASN319 4.1 33.3 1.0 OP2 C:DG414 4.2 32.9 1.0 C B:ASN319 4.2 32.3 1.0 OG B:SER297 4.3 31.1 1.0 O B:ALA298 4.3 31.6 1.0 C2' C:DA413 4.4 33.0 1.0 OD1 B:ASN323 4.5 30.1 1.0 CA B:SER297 4.6 31.1 1.0 CB B:ASN319 4.6 30.7 1.0 C5' C:DA413 4.7 32.0 1.0 CA B:ASN319 4.7 30.5 1.0 C B:SER297 4.7 34.7 1.0 CA B:ALA298 4.8 31.1 1.0 CB B:ALA298 4.8 29.6 1.0 ND1 B:HIS301 4.9 31.2 1.0 C B:ALA298 4.9 33.1 1.0 N B:LYS320 4.9 28.4 1.0 CB B:SER297 5.0 31.6 1.0

Sodium binding site 2 out of 2 in the Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homing Endonuclease H98A I-Ppoi-Dna Complex at PH6.0 (K+ Mes) with 1 Mm MN2+ For 600S and Then 100 Mm Imidazole For 15 Hrs within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:34.6 occ:1.00 OD1 A:ASN119 2.3 29.3 1.0 O A:HOH727 2.3 32.3 1.0 O A:HOH738 2.4 36.2 1.0 O A:HOH719 2.5 34.2 1.0 OP1 D:DG514 2.5 30.6 1.0 O3' D:DA513 2.6 32.0 1.0 P D:DG514 3.2 31.7 1.0 CG A:ASN119 3.4 30.7 1.0 O A:ASN119 3.7 28.2 1.0 C3' D:DA513 3.8 32.1 1.0 N A:ALA98 3.9 29.2 1.0 O5' D:DG514 4.0 28.3 1.0 ND2 A:ASN119 4.1 29.8 1.0 C4' D:DA513 4.1 31.3 1.0 OG A:SER97 4.2 29.5 1.0 O A:ALA98 4.2 33.1 1.0 C A:ASN119 4.2 27.5 1.0 OP2 D:DG514 4.4 31.8 1.0 CA A:SER97 4.4 27.9 1.0 OD1 A:ASN123 4.5 32.4 1.0 C2' D:DA513 4.5 31.8 1.0 C A:SER97 4.6 28.2 1.0 CB A:ASN119 4.6 24.2 1.0 CA A:ASN119 4.7 28.4 1.0 CA A:ALA98 4.7 31.0 1.0 CB A:ALA98 4.7 29.1 1.0 C5' D:DA513 4.7 34.6 1.0 C A:ALA98 4.8 31.4 1.0 CB A:SER97 4.8 28.9 1.0 ND1 A:HIS101 4.9 33.0 1.0 N A:LYS120 4.9 27.3 1.0

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