Magnesium in PDB 5v08: Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi), PDB code: 5v08 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)	39.46 / 2.81
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.259, 74.259, 179.385, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 26.2

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) (pdb code 5v08). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi), PDB code: 5v08:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg401 b:0.9 occ:1.00 OP1 B:DC2 2.1 0.0 1.0 OD2 Z:ASP152 2.1 90.0 1.0 O Z:HOH508 2.1 96.4 1.0 O Z:HOH509 2.1 95.4 1.0 O Z:HOH501 2.1 0.9 1.0 OD2 Z:ASP171 2.1 99.5 1.0 P B:DC2 3.2 0.6 1.0 CG Z:ASP152 3.3 90.7 1.0 CG Z:ASP171 3.4 97.6 1.0 O5' B:DC2 3.4 0.0 1.0 MG B:MG101 3.6 96.2 1.0 O Z:HOH502 3.8 94.0 1.0 OD1 Z:ASP152 3.9 94.2 1.0 OP2 B:DC2 4.0 0.7 1.0 O Z:HOH532 4.1 85.1 1.0 OD1 Z:ASP171 4.1 0.0 1.0 C5' B:DC2 4.1 0.9 1.0 CB Z:ASP171 4.4 86.1 1.0 CB Z:ASP152 4.4 85.4 1.0 OD1 Z:ASP225 4.4 91.1 1.0 O3' B:DT1 4.4 78.5 1.0 OE1 Z:GLU150 4.4 82.9 1.0 O Z:HOH524 4.4 93.5 1.0 CD1 Z:LEU174 4.5 68.0 1.0 O Z:HOH511 4.7 81.5 1.0 O Z:HOH514 4.8 93.2 1.0 CB Z:ALA173 5.0 79.9 1.0 CE2 Z:PHE177 5.0 79.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:96.2 occ:1.00 OP1 B:DC2 2.0 0.0 1.0 O Z:HOH511 2.1 81.5 1.0 O Z:HOH502 2.1 94.0 1.0 O Z:HOH517 2.1 75.2 1.0 OD1 Z:ASP152 2.2 94.2 1.0 O3' B:DT1 2.5 78.5 1.0 P B:DC2 2.8 0.6 1.0 CG Z:ASP152 2.9 90.7 1.0 OD2 Z:ASP152 3.0 90.0 1.0 MG Z:MG401 3.6 0.9 1.0 C3' B:DT1 3.8 0.4 1.0 O5' B:DC2 3.8 0.0 1.0 OP2 B:DC2 3.9 0.7 1.0 OD1 Z:ASP78 4.0 75.4 1.0 OE1 Z:GLU150 4.0 82.9 1.0 O Z:HOH508 4.1 96.4 1.0 OD2 Z:ASP78 4.1 65.1 1.0 OD2 Z:ASP30 4.1 73.7 1.0 C4' B:DT1 4.2 0.7 1.0 CB Z:ASP152 4.4 85.4 1.0 N Z:ASP152 4.5 71.5 1.0 CG Z:ASP78 4.5 68.4 1.0 O Z:HOH521 4.5 95.5 1.0 C5' B:DT1 4.6 0.0 1.0 OD1 Z:ASP30 4.7 74.4 1.0 C2' B:DT1 4.7 0.3 1.0 OD2 Z:ASP171 4.7 99.5 1.0 CG Z:ASP30 4.8 74.2 1.0 NZ Z:LYS85 4.9 92.9 1.0 N Z:ALA151 4.9 65.0 1.0 CA Z:ASP152 4.9 75.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Exonuclease 1 EXO1 (D173A) in Complex with 5' Recessed-End Dna (Rvi) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:98.8 occ:1.00 O Z:HOH515 2.1 0.3 1.0 OP1 B:DT1 2.4 0.1 1.0 P B:DT1 3.4 0.7 1.0 OP3 B:DT1 3.5 0.3 1.0 OE1 Z:GLU89 3.6 0.7 1.0 O B:HOH204 4.0 96.5 1.0 OP2 B:DT1 4.1 0.7 1.0 O Z:HOH507 4.1 0.0 1.0 CD Z:GLU89 4.5 0.4 1.0 CE2 Z:TYR32 4.7 90.0 1.0 OE2 Z:GLU89 4.7 0.8 1.0 O5' B:DT1 4.7 0.9 1.0 O Z:HOH521 4.8 95.5 1.0 O Z:ILE125 4.8 95.4 1.0

Y.Shi, H.W.Hellinga, L.S.Beese. Interplay of Catalysis, Fidelity, Threading, and Processivity in the Exo- and Endonucleolytic Reactions of Human Exonuclease I. Proc. Natl. Acad. Sci. V. 114 6010 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28533382
DOI: 10.1073/PNAS.1704845114