Manganese in PDB 5v06: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv), PDB code: 5v06 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)	38.47 / 2.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.281, 74.281, 179.889, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.6

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv) 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 (Riv) (pdb code 5v06). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv), PDB code: 5v06:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv)


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 (Riv) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:90.2 occ:1.00 OP1 B:DC2 2.0 0.7 1.0 OD2 Z:ASP152 2.1 69.1 1.0 OD2 Z:ASP171 2.1 86.0 1.0 OD2 Z:ASP173 2.2 0.9 1.0 O Z:HOH502 2.2 81.1 1.0 CG Z:ASP173 3.1 0.1 1.0 P B:DC2 3.3 1.0 1.0 CB Z:ASP173 3.3 82.9 1.0 CG Z:ASP171 3.3 74.1 1.0 CG Z:ASP152 3.3 74.0 1.0 O5' B:DC2 3.6 0.7 1.0 MN B:MN101 3.7 0.3 1.0 OD1 Z:ASP171 3.8 77.2 1.0 OD1 Z:ASP152 3.9 81.7 1.0 OP2 B:DC2 4.1 0.8 1.0 O Z:HOH501 4.2 72.2 1.0 OD1 Z:ASP173 4.3 1.0 1.0 CB Z:ASP152 4.5 73.0 1.0 O3' B:DT1 4.5 0.0 1.0 CB Z:ASP171 4.5 75.6 1.0 OE1 Z:GLU150 4.5 94.2 1.0 C5' B:DC2 4.6 0.0 1.0 N Z:GLY2 4.6 0.3 1.0 O Z:HOH508 4.6 71.8 1.0 OD2 Z:ASP225 4.7 1.0 1.0 CA Z:ASP173 4.7 82.8 1.0 N Z:ASP173 5.0 74.0 1.0

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


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 (Riv) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:0.3 occ:1.00 OD1 Z:ASP152 2.2 81.7 1.0 O Z:HOH501 2.2 72.2 1.0 O Z:HOH504 2.2 86.8 1.0 O Z:HOH508 2.2 71.8 1.0 OP1 B:DC2 2.2 0.7 1.0 O3' B:DT1 2.5 0.0 1.0 P B:DC2 2.9 1.0 1.0 CG Z:ASP152 3.0 74.0 1.0 OD2 Z:ASP152 3.2 69.1 1.0 MN Z:MN401 3.7 90.2 1.0 C3' B:DT1 3.8 0.1 1.0 OD1 Z:ASP78 3.9 61.0 1.0 O5' B:DC2 4.0 0.7 1.0 OP2 B:DC2 4.0 0.8 1.0 C4' B:DT1 4.2 0.3 1.0 OD2 Z:ASP171 4.2 86.0 1.0 CB Z:ASP152 4.5 73.0 1.0 N Z:ASP152 4.5 62.4 1.0 OD2 Z:ASP78 4.5 74.6 1.0 OD2 Z:ASP30 4.5 70.1 1.0 C5' B:DT1 4.6 0.1 1.0 CG Z:ASP78 4.6 71.3 1.0 C2' B:DT1 4.6 0.5 1.0 OD1 Z:ASP30 4.7 81.2 1.0 NZ Z:LYS85 4.7 65.1 1.0 O Z:HOH502 4.7 81.1 1.0 OE1 Z:GLU150 4.8 94.2 1.0 N Z:ALA151 4.9 65.2 1.0 CA Z:ASP152 4.9 69.1 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Riv) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:0.6 occ:1.00 OP1 B:DT1 2.3 1.0 1.0 OP3 B:DT1 3.3 0.5 1.0 P B:DT1 3.3 0.0 1.0 OE2 Z:GLU89 3.6 0.9 1.0 OE1 Z:GLU89 3.8 0.6 1.0 CD Z:GLU89 4.0 0.9 1.0 OP2 B:DT1 4.1 0.1 1.0 O5' B:DT1 4.6 0.6 1.0 C5' B:DT1 4.8 0.1 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