Magnesium in PDB 5v0d: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II), PDB code: 5v0d 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)	33.98 / 2.63
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.976, 72.976, 180.612, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.7

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II) 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 (Wt) in Complex with 5' Flap Dna (F2II) (pdb code 5v0d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II), PDB code: 5v0d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II)


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 (Wt) in Complex with 5' Flap Dna (F2II) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg401 b:67.7 occ:1.00 OD2 Z:ASP171 2.1 62.4 1.0 OP3 B:DG1 2.1 76.0 1.0 OD1 Z:ASP152 2.1 60.6 1.0 OD1 Z:ASP173 2.1 62.5 1.0 O Z:HOH513 2.1 69.7 1.0 OP2 B:DG1 2.1 75.1 1.0 P B:DG1 2.6 75.1 1.0 CG Z:ASP173 3.0 64.2 1.0 CG Z:ASP171 3.1 62.8 1.0 CB Z:ASP173 3.2 64.3 1.0 CG Z:ASP152 3.3 60.0 1.0 OD1 Z:ASP171 3.6 64.3 1.0 OP1 B:DG1 3.6 77.9 1.0 MG Z:MG402 3.7 69.8 1.0 O5' B:DG1 3.8 78.2 1.0 O Z:HOH537 3.9 62.4 1.0 OD2 Z:ASP225 3.9 68.4 1.0 OD2 Z:ASP152 3.9 58.5 1.0 O B:HOH102 3.9 64.3 1.0 N Z:GLY2 4.1 71.2 1.0 OD2 Z:ASP173 4.2 66.0 1.0 OE1 Z:GLU150 4.2 63.7 1.0 C5' B:DG1 4.3 82.4 1.0 CB Z:ASP171 4.4 61.5 1.0 CB Z:ASP152 4.4 61.7 1.0 O Z:HOH526 4.6 64.6 1.0 CA Z:ASP173 4.7 66.1 1.0 O3' E:DA2 4.7 85.3 1.0 CA Z:GLY2 4.8 74.5 1.0 NZ Z:LYS85 4.8 75.0 1.0 O Z:HOH527 5.0 64.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (F2II)


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 (Wt) in Complex with 5' Flap Dna (F2II) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg402 b:69.8 occ:1.00 O Z:HOH526 2.1 64.6 1.0 O B:HOH102 2.1 64.3 1.0 OD2 Z:ASP152 2.1 58.5 1.0 OP2 B:DG1 2.1 75.1 1.0 O Z:HOH525 2.1 67.7 1.0 O3' E:DA2 2.2 85.3 1.0 CG Z:ASP152 3.0 60.0 1.0 OD1 Z:ASP152 3.1 60.6 1.0 P B:DG1 3.5 75.1 1.0 C3' E:DA2 3.6 97.0 1.0 MG Z:MG401 3.7 67.7 1.0 OD2 Z:ASP171 4.0 62.4 1.0 O Z:HOH511 4.0 76.7 1.0 O5' B:DG1 4.1 78.2 1.0 OP1 B:DG1 4.1 77.9 1.0 OD1 Z:ASP78 4.2 59.4 1.0 OD2 Z:ASP30 4.2 62.8 1.0 C4' E:DA2 4.2 0.6 1.0 C2' E:DA2 4.3 0.8 1.0 OD2 Z:ASP78 4.3 61.1 1.0 CB Z:ASP152 4.4 61.7 1.0 N Z:ASP152 4.4 60.1 1.0 OE1 Z:GLU150 4.5 63.7 1.0 OP3 B:DG1 4.5 76.0 1.0 O Z:HOH513 4.6 69.7 1.0 OD1 Z:ASP30 4.6 64.3 1.0 CG Z:ASP78 4.7 62.2 1.0 NZ Z:LYS85 4.7 75.0 1.0 CG Z:ASP30 4.9 64.0 1.0 CA Z:ASP152 4.9 60.9 1.0 CG Z:ASP171 4.9 62.8 1.0 C5' E:DA2 4.9 0.0 1.0 N Z:ALA151 4.9 61.8 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