Manganese in PDB 7mxq: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (R-1)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (R-1), PDB code: 7mxq 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)	38.58 / 3.23
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.058, 74.058, 180.807, 90, 90, 90
R / Rfree (%)	20.4 / 24.9

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (R-1) 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 (R-1) (pdb code 7mxq). 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 (R-1), PDB code: 7mxq:
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 (R-1)


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 (R-1) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:88.9 occ:1.00 OD2 Z:ASP171 2.1 129.2 1.0 O Z:HOH507 2.2 96.0 1.0 OD1 Z:ASP152 2.4 87.9 1.0 OD1 Z:ASP173 2.7 106.0 1.0 CG Z:ASP152 3.1 89.2 1.0 MN B:MN101 3.1 140.3 1.0 OP1 B:DC2 3.2 132.0 1.0 OD2 Z:ASP152 3.3 92.2 1.0 CG Z:ASP171 3.3 113.7 1.0 O Z:HOH523 3.4 55.3 1.0 CG Z:ASP173 3.5 105.0 1.0 O Z:HOH504 3.6 100.5 1.0 OD1 Z:ASP171 3.9 115.0 1.0 CB Z:ASP173 3.9 104.8 1.0 O Z:HOH508 4.2 88.5 1.0 OD2 Z:ASP225 4.2 113.7 1.0 OD2 Z:ASP173 4.4 106.0 1.0 CB Z:ASP152 4.4 84.3 1.0 CB Z:ASP171 4.4 102.3 1.0 P B:DC2 4.5 141.1 1.0 O5' B:DC2 5.0 148.9 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 (R-1)


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 (R-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:140.3 occ:1.00 O Z:HOH514 2.1 136.8 1.0 O Z:HOH504 2.2 100.5 1.0 O Z:HOH508 2.3 88.5 1.0 OD2 Z:ASP152 2.6 92.2 1.0 MN Z:MN401 3.1 88.9 1.0 OP1 B:DC2 3.2 132.0 1.0 CG Z:ASP152 3.5 89.2 1.0 OD1 Z:ASP152 3.7 87.9 1.0 OD2 Z:ASP171 3.8 129.2 1.0 OD2 Z:ASP78 4.1 100.5 1.0 OD1 Z:ASP78 4.4 99.0 1.0 OD2 Z:ASP30 4.4 98.5 1.0 P B:DC2 4.6 141.1 1.0 O Z:HOH507 4.7 96.0 1.0 CG Z:ASP78 4.7 95.2 1.0 O Z:HOH526 4.8 83.1 1.0 CG Z:ASP171 4.9 113.7 1.0 O3' B:DT1 4.9 207.9 1.0 CB Z:ASP152 4.9 84.3 1.0 N Z:ASP152 5.0 77.9 1.0

Y.Shi, H.W.Hellinga, L.S.Beese. Structures of Reaction Intermediates Reveal Transient MG2+-Binding Events That Dynamically Coordinate Human Exonuclease I Activities To Be Published.