Manganese in PDB 7mxr: Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (R-2)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (R-2), PDB code: 7mxr 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)	38.59 / 3.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.15, 74.15, 180.737, 90, 90, 90
R / Rfree (%)	22.1 / 27.1

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (R-2) 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-2) (pdb code 7mxr). 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 (R-2), PDB code: 7mxr:
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 (R-2)


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-2) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:83.5 occ:1.00 OP1 B:DC2 2.0 177.2 1.0 OD2 Z:ASP152 2.1 94.0 1.0 OD2 Z:ASP171 2.2 109.6 1.0 OD2 Z:ASP173 2.2 113.0 1.0 O B:HOH201 2.3 64.5 1.0 CG Z:ASP173 3.1 98.0 1.0 P B:DC2 3.2 161.5 1.0 CG Z:ASP171 3.3 91.8 1.0 CB Z:ASP173 3.3 80.2 1.0 O5' B:DC2 3.3 148.5 1.0 CG Z:ASP152 3.4 83.2 1.0 MN B:MN101 3.4 98.4 1.0 O Z:HOH508 3.7 57.5 1.0 OD1 Z:ASP171 3.9 97.3 1.0 OD1 Z:ASP152 4.0 104.0 1.0 N Z:GLY2 4.1 97.8 1.0 OP2 B:DC2 4.2 167.2 1.0 OD1 Z:ASP173 4.3 106.6 1.0 OE1 Z:GLU150 4.3 72.8 1.0 O3' B:DT1 4.3 159.1 1.0 OD2 Z:ASP225 4.4 119.9 1.0 CB Z:ASP152 4.4 65.9 1.0 C5' B:DC2 4.4 135.7 1.0 O Z:HOH501 4.5 69.8 1.0 CB Z:ASP171 4.5 76.7 1.0 CA Z:ASP173 4.7 72.5 1.0 CA Z:GLY2 4.9 100.9 1.0 O Z:HOH513 4.9 51.2 1.0 N Z:ASP173 5.0 67.7 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 (R-2)


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-2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:98.4 occ:1.00 OD1 Z:ASP152 2.2 104.0 1.0 OP1 B:DC2 2.2 177.2 1.0 O Z:HOH513 2.2 51.2 1.0 O Z:HOH512 2.2 82.5 1.0 O Z:HOH501 2.3 69.8 1.0 O3' B:DT1 2.4 159.1 1.0 OD2 Z:ASP152 2.7 94.0 1.0 CG Z:ASP152 2.8 83.2 1.0 P B:DC2 2.8 161.5 1.0 MN Z:MN401 3.4 83.5 1.0 O5' B:DC2 3.7 148.5 1.0 C3' B:DT1 3.8 172.5 1.0 OD2 Z:ASP171 3.9 109.6 1.0 OP2 B:DC2 4.1 167.2 1.0 C4' B:DT1 4.2 181.2 1.0 CB Z:ASP152 4.3 65.9 1.0 OE1 Z:GLU150 4.3 72.8 1.0 OD2 Z:ASP78 4.5 70.2 1.0 C2' B:DT1 4.5 178.4 1.0 N Z:ASP152 4.5 71.5 1.0 OD2 Z:ASP30 4.5 86.6 1.0 NZ Z:LYS85 4.5 99.4 1.0 O B:HOH201 4.6 64.5 1.0 OD1 Z:ASP78 4.7 76.0 1.0 C5' B:DT1 4.8 185.8 1.0 CG Z:ASP171 4.8 91.8 1.0 CA Z:ASP152 4.9 64.0 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 (R-2)


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 (R-2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:120.0 occ:1.00 OP3 B:DT1 2.6 179.8 1.0 O Z:HOH526 2.6 78.7 1.0 OE2 Z:GLU89 2.8 138.0 1.0 CD Z:GLU89 3.8 140.2 1.0 P B:DT1 3.9 184.0 1.0 OP1 B:DT1 4.2 186.2 1.0 OE1 Z:GLU89 4.3 137.0 1.0 OP2 B:DT1 4.4 180.8 1.0 CG Z:GLU89 5.0 146.3 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.