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

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur), PDB code: 7mxv 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)	38.65 / 2.21
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.586, 74.586, 180.736, 90, 90, 90
R / Rfree (%)	22.1 / 24.4

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur) 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 (Ur) (pdb code 7mxv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur), PDB code: 7mxv:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur)


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 (Ur) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:48.0 occ:1.00 O B:HOH103 2.2 54.0 1.0 OP1 B:DT1 2.2 100.5 1.0 O Z:HOH506 2.2 42.6 1.0 O Z:HOH525 2.2 43.8 1.0 O Z:HOH522 2.2 41.7 1.0 OD1 Z:ASP152 2.2 58.0 1.0 CG Z:ASP152 3.1 51.8 1.0 OD2 Z:ASP152 3.3 48.4 1.0 P B:DT1 3.4 99.6 1.0 MN Z:MN402 3.6 49.3 1.0 OP3 B:DT1 3.6 104.2 1.0 O5' B:DT1 3.9 101.2 1.0 OD2 Z:ASP171 4.0 54.2 1.0 OD1 Z:ASP78 4.1 61.2 1.0 OD2 Z:ASP30 4.2 61.7 1.0 OD2 Z:ASP78 4.2 64.1 1.0 C5' B:DT1 4.3 98.0 1.0 OE1 Z:GLU150 4.3 62.6 1.0 NZ Z:LYS85 4.5 73.5 1.0 N Z:ASP152 4.5 36.0 1.0 CB Z:ASP152 4.5 45.4 1.0 CG Z:ASP78 4.6 60.8 1.0 O Z:HOH505 4.6 53.2 1.0 OD1 Z:ASP30 4.6 48.4 1.0 OP2 B:DT1 4.7 100.0 1.0 CG Z:ASP30 4.9 56.8 1.0 N Z:ALA151 5.0 41.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur)


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 (Ur) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:49.3 occ:1.00 OD2 Z:ASP152 2.1 48.4 1.0 OD2 Z:ASP171 2.1 54.2 1.0 OD2 Z:ASP173 2.2 62.2 1.0 OP1 B:DT1 2.2 100.5 1.0 O Z:HOH505 2.2 53.2 1.0 MN Z:MN404 3.1 84.5 1.0 P B:DT1 3.1 99.6 1.0 CG Z:ASP173 3.1 61.8 1.0 OP2 B:DT1 3.1 100.0 1.0 CG Z:ASP171 3.2 47.9 1.0 CG Z:ASP152 3.3 51.8 1.0 CB Z:ASP173 3.3 53.5 1.0 MN Z:MN401 3.6 48.0 1.0 OD1 Z:ASP171 3.7 51.7 1.0 OD1 Z:ASP152 3.8 58.0 1.0 O Z:HOH506 3.9 42.6 1.0 OD1 Z:ASP225 3.9 58.6 1.0 OP3 B:DT1 3.9 104.2 1.0 O Z:HOH523 4.0 55.9 1.0 OE1 Z:GLU150 4.1 62.6 1.0 OD1 Z:ASP173 4.3 61.3 1.0 O5' B:DT1 4.3 101.2 1.0 CB Z:ASP171 4.5 44.1 1.0 CB Z:ASP152 4.5 45.4 1.0 C5' B:DT1 4.5 98.0 1.0 N Z:GLY2 4.8 81.9 1.0 CA Z:ASP173 4.8 43.8 1.0 NZ Z:LYS85 4.8 73.5 1.0 O Z:HOH525 4.8 43.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur)


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 (Ur) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn403 b:74.9 occ:1.00 O Z:HOH539 2.2 56.2 1.0 O Z:HOH540 2.2 71.7 1.0 SG Z:CYS80 2.4 66.5 1.0 CD1 Z:ILE325 3.6 53.7 1.0 CB Z:CYS80 3.7 65.5 1.0 CZ Z:PHE335 4.2 69.3 1.0 CE1 Z:PHE335 4.4 67.4 1.0 O Z:PRO148 4.4 47.1 1.0 CG1 Z:VAL317 4.6 63.0 1.0 OH Z:TYR149 4.8 54.1 1.0 CG2 Z:VAL317 4.8 56.2 1.0 CZ Z:TYR149 4.9 53.0 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Ur) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn404 b:84.5 occ:1.00 OD1 Z:ASP225 2.2 58.6 1.0 OD2 Z:ASP173 2.2 62.2 1.0 N Z:GLY2 2.2 81.9 1.0 OP2 B:DT1 2.2 100.0 1.0 MN Z:MN402 3.1 49.3 1.0 CA Z:GLY2 3.1 82.5 1.0 CG Z:ASP225 3.1 52.5 1.0 CG Z:ASP173 3.2 61.8 1.0 OD2 Z:ASP225 3.4 62.9 1.0 P B:DT1 3.5 99.6 1.0 O Z:HOH505 3.7 53.2 1.0 OD1 Z:ASP173 3.7 61.3 1.0 OD1 Z:ASP171 3.9 51.7 1.0 OP1 B:DT1 3.9 100.5 1.0 O Z:HOH503 4.0 52.1 1.0 OD2 Z:ASP171 4.0 54.2 1.0 C Z:GLY2 4.2 85.1 1.0 CG Z:ASP171 4.3 47.9 1.0 O Z:GLY2 4.4 87.0 1.0 OP3 B:DT1 4.4 104.2 1.0 NH1 Z:ARG92 4.4 78.5 1.0 CB Z:ASP225 4.4 59.6 1.0 O5' B:DT1 4.5 101.2 1.0 CB Z:ASP173 4.5 53.5 1.0 C5' B:DT1 4.7 98.0 1.0 O Z:HOH523 4.7 55.9 1.0 OP1 B:DC2 4.8 98.7 1.0 C3' B:DT1 4.8 97.4 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.