Sodium in PDB 1suz: The Structure of K92A Ecorv Bound to Cognate Dna and MG2+

All present enzymatic activity of The Structure of K92A Ecorv Bound to Cognate Dna and MG2+:
3.1.21.4;

The structure of The Structure of K92A Ecorv Bound to Cognate Dna and MG2+, PDB code: 1suz was solved by N.C.Horton, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.410, 48.790, 63.400, 97.10, 108.80, 107.30
R / Rfree (%)	19.7 / 24.4

The structure of The Structure of K92A Ecorv Bound to Cognate Dna and MG2+ also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the The Structure of K92A Ecorv Bound to Cognate Dna and MG2+ (pdb code 1suz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of K92A Ecorv Bound to Cognate Dna and MG2+, PDB code: 1suz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of K92A Ecorv Bound to Cognate Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of K92A Ecorv Bound to Cognate Dna and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:20.7 occ:1.00 OP2 C:DT8 2.4 15.4 1.0 O A:THR106 2.4 14.1 1.0 O C:HOH195 2.5 19.6 1.0 O A:HOH540 2.6 14.7 1.0 OG1 A:THR106 2.7 15.9 1.0 C A:THR106 3.3 15.4 1.0 C2' C:DA7 3.5 20.0 1.0 C3' C:DA7 3.5 20.1 1.0 P C:DT8 3.7 19.5 1.0 O A:HOH439 3.7 18.8 1.0 CB A:THR106 3.8 15.1 1.0 CB A:ALA92 3.9 15.0 1.0 CA A:THR106 4.0 14.8 1.0 O3' C:DA7 4.1 18.1 1.0 N A:THR106 4.2 15.6 1.0 O5' C:DT8 4.2 16.7 1.0 N A:LEU107 4.3 14.4 1.0 CA A:ALA92 4.3 12.8 1.0 O A:ILE91 4.5 13.4 1.0 CA A:LEU107 4.5 16.7 1.0 OD1 A:ASN188 4.6 15.7 1.0 OP1 C:DA7 4.6 20.3 1.0 OP2 C:DA7 4.6 21.1 1.0 N A:GLY108 4.7 16.3 1.0 O5' C:DA7 4.8 20.0 1.0 P C:DA7 4.9 19.2 1.0 OP1 C:DT8 4.9 17.0 1.0 C4' C:DA7 4.9 20.4 1.0 C A:LEU107 5.0 16.6 1.0 C1' C:DA7 5.0 20.0 1.0

Sodium binding site 2 out of 2 in the The Structure of K92A Ecorv Bound to Cognate Dna and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of K92A Ecorv Bound to Cognate Dna and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:20.7 occ:1.00 OP2 D:DT8 2.4 17.9 1.0 O B:THR106 2.5 15.0 1.0 O B:HOH497 2.5 16.6 1.0 O B:HOH427 2.6 14.2 1.0 OG1 B:THR106 2.7 17.2 1.0 C B:THR106 3.3 15.9 1.0 C2' D:DA7 3.5 18.7 1.0 C3' D:DA7 3.6 18.4 1.0 CB B:THR106 3.7 16.4 1.0 P D:DT8 3.7 19.4 1.0 O B:HOH434 3.7 24.0 1.0 CB B:ALA92 3.9 14.7 1.0 CA B:THR106 4.0 15.8 1.0 O3' D:DA7 4.1 19.4 1.0 N B:LEU107 4.2 15.1 1.0 N B:THR106 4.2 17.7 1.0 O5' D:DT8 4.3 19.1 1.0 CA B:ALA92 4.3 15.4 1.0 CA B:LEU107 4.4 14.2 1.0 OD1 B:ASN188 4.4 15.8 1.0 N B:GLY108 4.6 13.4 1.0 O B:ILE91 4.6 17.6 1.0 OP2 D:DA7 4.6 19.3 1.0 OP1 D:DA7 4.7 14.7 1.0 O5' D:DA7 4.7 17.2 1.0 P D:DA7 4.9 19.0 1.0 OP1 D:DT8 4.9 21.2 1.0 C B:LEU107 4.9 15.0 1.0 C4' D:DA7 5.0 16.7 1.0

N.C.Horton, J.J.Perona. Dna Cleavage By Ecorv Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites. Biochemistry V. 43 6841 2004.
ISSN: ISSN 0006-2960
PubMed: 15170321
DOI: 10.1021/BI0499056