Manganese in PDB 5v0b: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Rix)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Rix), PDB code: 5v0b 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)	38.85 / 2.63
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.764, 73.764, 182.796, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.1

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Rix) 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 (Rix) (pdb code 5v0b). 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 (Rix), PDB code: 5v0b:
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 (Rix)


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 (Rix) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:0.0 occ:1.00 OD2 Z:ASP173 2.2 73.8 1.0 OD2 Z:ASP152 2.2 80.2 1.0 OD2 Z:ASP171 2.2 76.7 1.0 OP2 B:DC1 2.4 0.3 1.0 CG Z:ASP173 3.1 67.5 1.0 CG Z:ASP152 3.3 77.6 1.0 CG Z:ASP171 3.4 58.5 1.0 CB Z:ASP173 3.5 56.5 1.0 MN Z:MN402 3.6 0.3 1.0 P B:DC1 3.6 0.3 1.0 O Z:HOH507 3.7 79.4 1.0 OP3 B:DC1 3.8 0.3 1.0 OD1 Z:ASP152 3.8 86.4 1.0 O Z:HOH552 3.9 74.6 1.0 OD1 Z:ASP171 4.0 68.2 1.0 O B:HOH102 4.0 79.7 1.0 OD2 Z:ASP225 4.1 0.9 1.0 OD1 Z:ASP173 4.3 77.4 1.0 CB Z:ASP152 4.5 67.3 1.0 CB Z:ASP171 4.5 61.4 1.0 O5' B:DC1 4.6 0.2 1.0 OP1 B:DC1 4.7 1.0 1.0 CA Z:ASP173 4.9 56.0 1.0 CG Z:ASP225 5.0 96.8 1.0 CA Z:GLY2 5.0 81.7 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 (Rix)


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 (Rix) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:0.3 occ:1.00 O Z:HOH507 2.2 79.4 1.0 OD1 Z:ASP152 2.2 86.4 1.0 O Z:HOH517 2.2 64.9 1.0 O B:HOH102 2.2 79.7 1.0 CG Z:ASP152 3.1 77.6 1.0 OD2 Z:ASP152 3.3 80.2 1.0 OP2 B:DC1 3.6 0.3 1.0 MN Z:MN401 3.6 0.0 1.0 OD1 Z:ASP78 3.8 59.8 1.0 OD2 Z:ASP30 4.0 64.1 1.0 OD2 Z:ASP78 4.1 77.2 1.0 OD2 Z:ASP171 4.2 76.7 1.0 CG Z:ASP78 4.3 67.0 1.0 N Z:ASP152 4.4 54.5 1.0 CB Z:ASP152 4.5 67.3 1.0 OD1 Z:ASP30 4.5 71.4 1.0 O B:HOH103 4.6 83.0 1.0 CG Z:ASP30 4.7 67.2 1.0 N Z:ALA151 4.7 61.7 1.0 CB Z:ALA151 4.9 52.2 1.0 CA Z:ASP152 4.9 58.4 1.0 P B:DC1 4.9 0.3 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