Manganese in PDB 3qeb: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna and MN2+ (Complex III)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna and MN2+ (Complex III), PDB code: 3qeb was solved by J.Orans, E.A.Mcsweeney, R.R.Iyer, M.A.Hast, H.W.Hellinga, P.Modrich, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.03 / 3.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.406, 70.406, 182.883, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.8

The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna and MN2+ (Complex III) (pdb code 3qeb). 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 Dna and MN2+ (Complex III), PDB code: 3qeb:
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 Dna and MN2+ (Complex III)


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 Dna and MN2+ (Complex III) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn353 b:86.8 occ:1.00 OP1 B:DT1 2.3 0.2 1.0 O Z:HOH359 2.3 53.2 1.0 OD2 Z:ASP152 2.4 69.8 1.0 O Z:HOH356 2.5 0.0 1.0 OP3 B:DT1 3.2 1.0 1.0 CG Z:ASP152 3.3 64.7 1.0 P B:DT1 3.3 0.6 1.0 OD1 Z:ASP152 3.5 51.2 1.0 OD2 Z:ASP30 4.0 78.6 1.0 O5' B:DT1 4.1 0.2 1.0 MN Z:MN354 4.1 86.5 1.0 OD2 Z:ASP171 4.1 83.0 1.0 OD1 Z:ASP78 4.2 70.5 1.0 O2 B:DT1 4.4 0.5 1.0 OD1 Z:ASP30 4.6 87.3 1.0 OP2 B:DT1 4.6 0.6 1.0 CB Z:ASP152 4.7 56.3 1.0 N Z:ASP152 4.7 67.6 1.0 CG Z:ASP30 4.7 80.6 1.0 OD2 Z:ASP78 4.8 73.4 1.0 CG Z:ASP171 4.9 76.4 1.0 CG Z:ASP78 4.9 69.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with Dna and MN2+ (Complex III)


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 Dna and MN2+ (Complex III) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn354 b:86.5 occ:1.00 OP1 B:DT1 2.3 0.2 1.0 OD1 Z:ASP152 2.5 51.2 1.0 OD2 Z:ASP171 2.5 83.0 1.0 OD2 Z:ASP173 2.6 85.6 1.0 O Z:HOH355 2.6 60.2 1.0 CG Z:ASP173 3.0 75.7 1.0 P B:DT1 3.1 0.6 1.0 O5' B:DT1 3.3 0.2 1.0 CG Z:ASP171 3.4 76.4 1.0 CB Z:ASP173 3.4 63.2 1.0 OP2 B:DT1 3.5 0.6 1.0 OD1 Z:ASP171 3.6 76.4 1.0 CG Z:ASP152 3.6 64.7 1.0 OD1 Z:ASP173 3.8 79.5 1.0 OD2 Z:ASP225 3.9 64.2 1.0 MN Z:MN353 4.1 86.8 1.0 OD2 Z:ASP152 4.2 69.8 1.0 N Z:GLY2 4.3 96.5 1.0 O Z:HOH356 4.5 0.0 1.0 OP3 B:DT1 4.5 1.0 1.0 C5' B:DT1 4.5 0.2 1.0 CG Z:ASP225 4.6 69.3 1.0 OE1 Z:GLU150 4.6 69.1 1.0 CB Z:ASP171 4.7 69.2 1.0 CB Z:ASP152 4.8 56.3 1.0 O Z:HOH363 4.8 68.3 1.0 CA Z:ASP173 4.9 56.4 1.0 OD1 Z:ASP225 4.9 82.3 1.0

J.Orans, E.A.Mcsweeney, R.R.Iyer, M.A.Hast, H.W.Hellinga, P.Modrich, L.S.Beese. Structures of Human Exonuclease 1 Dna Complexes Suggest A Unified Mechanism For Nuclease Family. Cell(Cambridge,Mass.) V. 145 212 2011.
ISSN: ISSN 0092-8674
PubMed: 21496642
DOI: 10.1016/J.CELL.2011.03.005