Magnesium in PDB 7mxw: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1), PDB code: 7mxw 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)	30.30 / 2.84
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.955, 71.955, 179.874, 90, 90, 90
R / Rfree (%)	21.9 / 26.5

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1) (pdb code 7mxw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1), PDB code: 7mxw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg401 b:68.0 occ:1.00 OP1 B:DA1 2.1 82.5 1.0 O Z:HOH505 2.1 67.1 1.0 OD2 Z:ASP171 2.1 69.5 1.0 OD2 Z:ASP152 2.1 62.1 1.0 OD2 Z:ASP173 2.1 65.6 1.0 OP3 B:DA1 2.3 84.4 1.0 P B:DA1 2.7 83.8 1.0 CG Z:ASP173 3.1 66.0 1.0 CG Z:ASP171 3.1 69.8 1.0 CG Z:ASP152 3.2 62.6 1.0 CB Z:ASP173 3.3 66.1 1.0 MG Z:MG403 3.3 80.5 1.0 OE1 Z:GLU150 3.5 66.3 1.0 OD1 Z:ASP171 3.5 70.1 1.0 OP2 B:DA1 3.6 83.8 1.0 OD1 Z:ASP152 3.7 60.9 1.0 MG Z:MG402 3.7 73.1 1.0 O Z:HOH516 3.7 68.7 1.0 O5' B:DA1 4.0 85.2 1.0 OD2 Z:ASP225 4.1 69.3 1.0 OD1 Z:ASP173 4.2 66.5 1.0 C5' B:DA1 4.3 86.0 1.0 CB Z:ASP171 4.4 69.7 1.0 CB Z:ASP152 4.5 65.6 1.0 CD Z:GLU150 4.6 67.7 1.0 N Z:GLY2 4.6 84.0 1.0 CA Z:ASP173 4.7 66.6 1.0 O Z:HOH517 4.9 76.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg402 b:73.1 occ:1.00 OP1 B:DA1 2.1 82.5 1.0 O Z:HOH517 2.1 76.7 1.0 O Z:HOH520 2.1 69.2 1.0 O Z:HOH516 2.1 68.7 1.0 O B:HOH101 2.1 78.0 1.0 OD1 Z:ASP152 2.1 60.9 1.0 CG Z:ASP152 3.1 62.6 1.0 P B:DA1 3.3 83.8 1.0 OD2 Z:ASP152 3.4 62.1 1.0 O5' B:DA1 3.6 85.2 1.0 MG Z:MG401 3.7 68.0 1.0 OD2 Z:ASP171 3.8 69.5 1.0 OD1 Z:ASP78 3.9 69.3 1.0 CG Z:GLU150 3.9 67.2 1.0 OE1 Z:GLU150 4.0 66.3 1.0 OD2 Z:ASP78 4.0 71.9 1.0 C5' B:DA1 4.0 86.0 1.0 OP2 B:DA1 4.1 83.8 1.0 N Z:ASP152 4.2 64.4 1.0 OD2 Z:ASP30 4.3 66.8 1.0 OP3 B:DA1 4.4 84.4 1.0 CG Z:ASP78 4.4 70.8 1.0 CB Z:ASP152 4.4 65.6 1.0 CD Z:GLU150 4.5 67.7 1.0 OD1 Z:ASP30 4.6 67.0 1.0 N Z:ALA151 4.6 63.6 1.0 CA Z:ASP152 4.8 66.1 1.0 NZ Z:LYS85 4.8 78.0 1.0 CG Z:ASP171 4.8 69.8 1.0 O Z:HOH505 4.8 67.1 1.0 CB Z:ALA151 4.8 62.0 1.0 CG Z:ASP30 4.9 67.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Flap Dna (UF1) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg403 b:80.5 occ:1.00 N Z:GLY2 1.9 84.0 1.0 OD2 Z:ASP173 2.1 65.6 1.0 OD2 Z:ASP225 2.2 69.3 1.0 OP3 B:DA1 2.2 84.4 1.0 CG Z:ASP173 3.1 66.0 1.0 CG Z:ASP225 3.2 70.9 1.0 OD1 Z:ASP173 3.3 66.5 1.0 MG Z:MG401 3.3 68.0 1.0 CA Z:GLY2 3.4 84.9 1.0 P B:DA1 3.6 83.8 1.0 OD1 Z:ASP171 3.6 70.1 1.0 OD1 Z:ASP225 3.7 72.5 1.0 O Z:HOH505 3.8 67.1 1.0 OP2 B:DA1 4.0 83.8 1.0 OD2 Z:ASP171 4.2 69.5 1.0 C Z:GLY2 4.2 88.2 1.0 NH1 Z:ARG92 4.3 112.7 1.0 CG Z:ASP171 4.3 69.8 1.0 CB Z:ASP225 4.3 70.8 1.0 OP1 B:DA1 4.4 82.5 1.0 CB Z:ASP173 4.5 66.1 1.0 O Z:GLY2 4.5 93.1 1.0 O5' B:DA1 4.5 85.2 1.0 C5' B:DA1 4.7 86.0 1.0 C3' B:DA1 4.9 88.6 1.0 OP1 B:DC2 5.0 95.0 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.