Sodium in PDB 8vmv: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S, PDB code: 8vmv 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 / 1.59
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 / 19.6

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S 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 600S (pdb code 8vmv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S, PDB code: 8vmv:

Sodium binding site 1 out of 1 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH7.0 (K+ Mes) with 500 Um MG2+ For 600S


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 600S within 5.0Å range: probe atom residue distance (Å) B Occ d:Na602 b:14.1 occ:0.10 MG d:MG601 0.0 14.4 0.9 O A:HOH761 2.1 16.5 1.0 OD1 A:ASN119 2.1 14.3 1.0 O A:HOH720 2.1 13.4 1.0 OP1 d:DG514 2.1 15.0 0.1 OP3 d:DG514 2.1 15.4 0.9 O d:HOH715 2.1 17.2 1.0 O3' D:DA513 2.2 17.1 0.9 O3' D:DA513 2.3 16.4 0.1 P d:DG514 2.6 35.0 0.1 CG A:ASN119 3.2 14.4 1.0 P d:DG514 3.3 15.0 0.9 C3' D:DA513 3.5 17.9 0.9 O5' d:DG514 3.6 16.5 0.1 C3' D:DA513 3.6 17.7 0.1 OP2 d:DG514 3.6 17.4 0.9 OP2 d:DG514 3.7 16.4 0.1 ND2 A:ASN119 3.8 14.8 1.0 O5' d:DG514 3.8 13.7 0.9 O A:ASN119 3.8 13.5 1.0 C4' D:DA513 4.0 16.8 0.9 C4' D:DA513 4.0 16.7 0.1 C2' D:DA513 4.1 14.7 0.9 N A:HIS98 4.1 13.4 1.0 O d:HOH707 4.1 21.8 1.0 C2' D:DA513 4.2 15.0 0.1 C A:ASN119 4.2 13.9 1.0 OG A:SER97 4.2 16.6 1.0 O A:HIS98 4.4 16.4 1.0 OD1 A:ASN123 4.4 15.2 1.0 CB A:ASN119 4.4 12.1 1.0 OP1 d:DG514 4.5 18.3 0.9 CA A:SER97 4.6 12.6 1.0 ND1 A:HIS101 4.6 18.2 1.0 CA A:ASN119 4.6 14.3 1.0 C5' D:DA513 4.7 15.6 0.9 C5' D:DA513 4.8 16.2 0.1 C A:SER97 4.8 12.6 1.0 CE1 A:HIS101 4.8 17.2 1.0 N A:LYS120 4.9 11.8 1.0 CB A:HIS98 4.9 13.9 1.0 CA A:HIS98 4.9 13.7 1.0 CB A:SER97 4.9 14.4 1.0 O A:HOH781 4.9 20.9 1.0 C5' d:DG514 5.0 15.5 0.1

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