Manganese in PDB 7mxu: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2), PDB code: 7mxu 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)	38.73 / 3.04
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.169, 73.169, 182.621, 90, 90, 90
R / Rfree (%)	23 / 26.9

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2) 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' Flap Dna (CF2) (pdb code 7mxu). 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' Flap Dna (CF2), PDB code: 7mxu:
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' Flap Dna (CF2)


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' Flap Dna (CF2) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:78.2 occ:1.00 O B:HOH101 2.1 89.2 1.0 O Z:HOH524 2.2 87.9 1.0 OP1 B:DC1 2.2 118.2 1.0 O Z:HOH527 2.2 74.6 1.0 O Z:HOH511 2.2 80.8 1.0 OD1 Z:ASP152 2.2 70.0 1.0 CG Z:ASP152 3.1 70.7 1.0 OD2 Z:ASP152 3.3 72.0 1.0 P B:DC1 3.4 119.1 1.0 OP3 B:DC1 3.6 122.0 1.0 MN Z:MN402 3.6 65.9 1.0 OD2 Z:ASP30 4.1 74.2 1.0 OD2 Z:ASP171 4.1 77.0 1.0 O5' B:DC1 4.2 123.4 1.0 OD1 Z:ASP78 4.2 75.6 1.0 OD2 Z:ASP78 4.3 77.4 1.0 N Z:ASP152 4.5 69.3 1.0 CB Z:ASP152 4.5 70.7 1.0 C5' B:DC1 4.6 129.3 1.0 OP2 B:DC1 4.6 114.6 1.0 CG Z:ASP78 4.7 77.1 1.0 OD1 Z:ASP30 4.8 75.4 1.0 N Z:ALA151 4.8 74.0 1.0 CG Z:ASP30 4.9 75.6 1.0 OE1 Z:GLU150 4.9 80.0 1.0 CA Z:ASP152 5.0 69.5 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)


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' Flap Dna (CF2) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:65.9 occ:1.00 OP1 B:DC1 2.0 118.2 1.0 OD2 Z:ASP171 2.1 77.0 1.0 OD2 Z:ASP152 2.2 72.0 1.0 OD1 Z:ASP173 2.2 78.5 1.0 OP2 B:DC1 2.5 114.6 1.0 P B:DC1 2.6 119.1 1.0 CG Z:ASP173 3.1 78.5 1.0 MN Z:MN403 3.2 94.2 1.0 CG Z:ASP171 3.3 77.7 1.0 CG Z:ASP152 3.3 70.7 1.0 CB Z:ASP173 3.4 76.1 1.0 MN Z:MN401 3.6 78.2 1.0 O5' B:DC1 3.7 123.4 1.0 O Z:HOH511 3.7 80.8 1.0 O Z:HOH529 3.7 85.5 1.0 OP3 B:DC1 3.8 122.0 1.0 OD1 Z:ASP152 3.8 70.0 1.0 OD1 Z:ASP171 3.8 79.8 1.0 OD1 Z:ASP225 4.0 89.2 1.0 OD2 Z:ASP173 4.2 81.0 1.0 OE1 Z:GLU150 4.4 80.0 1.0 CB Z:ASP171 4.5 76.6 1.0 CB Z:ASP152 4.5 70.7 1.0 N Z:GLY2 4.6 87.7 1.0 CA Z:ASP173 4.8 76.5 1.0 O B:HOH101 4.9 89.2 1.0 C5' B:DC1 4.9 129.3 1.0 O Z:HOH524 5.0 87.9 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (CF2)


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' Flap Dna (CF2) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn403 b:94.2 occ:1.00 OP2 B:DC1 2.0 114.6 1.0 N Z:GLY2 2.2 87.7 1.0 OD1 Z:ASP173 2.2 78.5 1.0 OD1 Z:ASP225 2.3 89.2 1.0 CA Z:GLY2 2.6 89.8 1.0 MN Z:MN402 3.2 65.9 1.0 P B:DC1 3.2 119.1 1.0 CG Z:ASP173 3.2 78.5 1.0 CG Z:ASP225 3.4 90.9 1.0 OD1 Z:ASP171 3.5 79.8 1.0 O5' B:DC1 3.5 123.4 1.0 OD2 Z:ASP173 3.6 81.0 1.0 OD2 Z:ASP171 3.7 77.0 1.0 OD2 Z:ASP225 3.8 92.2 1.0 CG Z:ASP171 3.9 77.7 1.0 OP1 B:DC1 4.0 118.2 1.0 C Z:GLY2 4.1 93.4 1.0 OP3 B:DC1 4.4 122.0 1.0 OP2 B:DG2 4.4 122.0 1.0 O Z:HOH528 4.5 81.8 1.0 CB Z:ASP173 4.6 76.1 1.0 CB Z:ASP225 4.7 91.9 1.0 OP1 B:DG2 4.7 125.0 1.0 C3' B:DC1 4.8 129.4 1.0 C5' B:DC1 4.8 129.3 1.0 O Z:GLY2 4.8 97.9 1.0 O Z:HOH529 4.8 85.5 1.0 N Z:ILE3 4.8 87.2 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.