Sodium in PDB 7mxt: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr), PDB code: 7mxt was solved by Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.50 / 3.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.857, 72.857, 181.382, 90, 90, 90
R / Rfree (%)	21.1 / 26

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr) also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr) (pdb code 7mxt). 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 Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr), PDB code: 7mxt:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Na403 b:104.4 occ:1.00 OP2 A:DT4 2.4 136.9 1.0 O A:HOH102 2.4 125.8 1.0 O Z:SER222 2.4 117.7 1.0 OG Z:SER229 2.4 128.9 1.0 O Z:HOH557 2.4 82.1 1.0 O Z:ILE233 2.5 114.8 1.0 OP1 A:DT4 3.1 131.6 1.0 P A:DT4 3.1 134.1 1.0 CB Z:SER229 3.1 121.2 1.0 C Z:SER222 3.5 102.9 1.0 C Z:ILE233 3.5 109.5 1.0 CA Z:GLY234 3.7 89.3 1.0 O Z:HOH544 3.9 81.9 1.0 N Z:GLY234 4.0 107.2 1.0 O5' A:DT4 4.1 139.8 1.0 CA Z:SER222 4.3 100.7 1.0 N Z:GLY223 4.4 90.1 1.0 O3' A:DC3 4.4 131.6 1.0 CA Z:GLY223 4.6 76.9 1.0 CA Z:SER229 4.6 113.7 1.0 C3' A:DC3 4.7 129.1 1.0 CA Z:ILE233 4.8 106.2 1.0 C Z:GLY234 4.8 91.6 1.0 O Z:LEU221 4.8 90.0 1.0 O Z:HOH558 4.9 86.2 1.0 O Z:LEU230 4.9 118.7 1.0 N Z:ILE233 5.0 119.5 1.0 O Z:HOH551 5.0 106.8 1.0

Y.Shi, H.W.Hellinga, L.S.Beese. Structures of Reaction Intermediates Reveal Transient MG2+-Binding Events That Dynamically Coordinate Human Exonuclease I Activities To Be Published.