Manganese in PDB 5v05: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii), PDB code: 5v05 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)	38.98 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.906, 73.906, 183.512, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.8

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

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii) (pdb code 5v05). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii), PDB code: 5v05:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:0.6 occ:1.00 OD2 Z:ASP152 2.2 99.3 1.0 O B:HOH101 2.2 0.2 1.0 O Z:HOH532 2.2 0.5 1.0 O Z:HOH531 2.2 89.9 1.0 O Z:HOH509 2.2 69.7 1.0 CG Z:ASP152 2.9 87.9 1.0 OD1 Z:ASP152 3.0 78.1 1.0 MN Z:MN402 3.2 0.4 1.0 OD2 Z:ASP171 3.8 76.9 1.0 OP1 B:DC2 3.8 0.4 1.0 O B:HOH107 4.2 62.0 1.0 OD2 Z:ASP30 4.2 91.2 1.0 CB Z:ASP152 4.4 82.0 1.0 OD2 Z:ASP78 4.5 94.5 1.0 N Z:ASP152 4.6 78.1 1.0 OD1 Z:ASP78 4.6 78.5 1.0 CG Z:ASP171 4.8 73.6 1.0 CA Z:ASP152 4.9 76.8 1.0 CG Z:ASP78 5.0 83.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riii) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:0.4 occ:1.00 OD1 Z:ASP173 2.2 75.2 1.0 OD2 Z:ASP171 2.2 76.9 1.0 OD1 Z:ASP152 2.2 78.1 1.0 O B:HOH107 2.2 62.0 1.0 CG Z:ASP173 3.1 74.8 1.0 MN Z:MN401 3.2 0.6 1.0 CG Z:ASP152 3.3 87.9 1.0 CB Z:ASP173 3.3 62.9 1.0 CG Z:ASP171 3.4 73.6 1.0 O Z:HOH509 3.7 69.7 1.0 OD2 Z:ASP152 3.8 99.3 1.0 OP1 B:DC2 3.9 0.4 1.0 OD1 Z:ASP171 4.0 87.9 1.0 O Z:HOH526 4.0 76.5 1.0 OD2 Z:ASP173 4.2 90.2 1.0 O B:HOH101 4.2 0.2 1.0 OD1 Z:ASP225 4.4 0.6 1.0 N Z:GLY2 4.5 90.4 1.0 CB Z:ASP171 4.5 64.8 1.0 CB Z:ASP152 4.5 82.0 1.0 O Z:HOH532 4.6 0.5 1.0 CA Z:ASP173 4.8 61.2 1.0 O B:HOH106 5.0 0.8 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