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

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr), PDB code: 7mxt 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)	38.50 / 3.05
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.857, 72.857, 181.382, 90, 90, 90
R / Rfree (%)	21.1 / 26

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


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 (Cmr) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:73.5 occ:1.00 O Z:HOH515 2.1 90.8 1.0 OD2 Z:ASP171 2.1 95.9 1.0 OD2 Z:ASP152 2.2 85.9 1.0 OD1 Z:ASP173 2.2 107.9 1.0 OP2 B:DC1 2.2 117.9 0.5 OP3 B:DC1 2.3 118.6 0.5 OP1 B:DC1 2.4 117.0 0.5 MN Z:MN402 2.8 62.6 0.5 P B:DC1 2.9 103.7 0.5 CG Z:ASP173 3.0 103.7 1.0 CG Z:ASP152 3.3 74.3 1.0 CG Z:ASP171 3.3 79.8 1.0 CB Z:ASP173 3.3 94.4 1.0 MN B:MN101 3.5 69.6 1.0 P B:DC1 3.7 111.4 0.5 OD1 Z:ASP152 3.7 88.5 1.0 O B:HOH202 3.8 93.2 1.0 OD1 Z:ASP171 3.8 85.3 1.0 OP2 B:DC1 3.9 105.0 0.5 O Z:HOH533 3.9 88.7 1.0 OD1 Z:ASP225 4.0 116.5 1.0 OD2 Z:ASP173 4.1 112.9 1.0 OP3 B:DC1 4.2 121.8 0.5 O5' B:DC1 4.2 107.6 0.5 OE1 Z:GLU150 4.2 81.8 1.0 CB Z:ASP171 4.5 79.2 1.0 N Z:GLY2 4.5 99.9 1.0 CB Z:ASP152 4.5 64.7 1.0 O Z:HOH524 4.5 93.5 1.0 C5' B:DC1 4.5 102.5 0.5 O5' B:DC1 4.5 105.6 0.5 OP1 B:DC1 4.6 112.3 0.5 O B:HOH203 4.8 75.2 1.0 CA Z:ASP173 4.8 77.2 1.0 O B:HOH201 4.9 49.9 0.5

Manganese binding site 2 out of 3 in the Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cmr)


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 (Cmr) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:62.6 occ:0.50 OP1 B:DC1 2.1 117.0 0.5 OP3 B:DC1 2.1 121.8 0.5 OD1 Z:ASP173 2.1 107.9 1.0 OD1 Z:ASP225 2.2 116.5 1.0 OP2 B:DC1 2.2 117.9 0.5 O B:HOH201 2.2 49.9 0.5 N Z:GLY2 2.3 99.9 1.0 P B:DC1 2.6 111.4 0.5 MN Z:MN401 2.8 73.5 1.0 CA Z:GLY2 3.1 110.0 1.0 OD2 Z:ASP171 3.3 95.9 1.0 CG Z:ASP225 3.3 110.7 1.0 CG Z:ASP173 3.3 103.7 1.0 P B:DC1 3.4 103.7 0.5 O Z:HOH515 3.4 90.8 1.0 O5' B:DC1 3.5 105.6 0.5 C5' B:DC1 3.6 100.6 0.5 OD1 Z:ASP171 3.8 85.3 1.0 OP3 B:DC1 3.8 118.6 0.5 OD2 Z:ASP225 3.9 117.1 1.0 CG Z:ASP171 3.9 79.8 1.0 OP1 B:DC1 3.9 112.3 0.5 OD2 Z:ASP173 3.9 112.9 1.0 O5' B:DC1 4.0 107.6 0.5 C3' B:DC1 4.4 101.3 0.5 C5' B:DC1 4.5 102.5 0.5 C Z:GLY2 4.5 126.5 1.0 CB Z:ASP173 4.5 94.4 1.0 CB Z:ASP225 4.5 104.2 1.0 OP2 B:DC1 4.6 105.0 0.5 OP1 B:DG2 4.7 102.0 0.5 OP2 B:DG2 4.8 108.8 0.5 O Z:HOH533 4.8 88.7 1.0 O Z:HOH502 4.9 70.0 1.0 OD2 Z:ASP152 4.9 85.9 1.0 C4' B:DC1 5.0 98.8 0.5 C2' B:DC1 5.0 90.9 0.5

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


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 (Cmr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:69.6 occ:1.00 OP3 B:DC1 2.0 118.6 0.5 OD1 Z:ASP152 2.2 88.5 1.0 O Z:HOH520 2.2 62.7 1.0 O Z:HOH524 2.2 93.5 1.0 O B:HOH202 2.2 93.2 1.0 O B:HOH203 2.2 75.2 1.0 OP2 B:DC1 2.8 105.0 0.5 P B:DC1 3.0 103.7 0.5 CG Z:ASP152 3.0 74.3 1.0 OD2 Z:ASP152 3.3 85.9 1.0 MN Z:MN401 3.5 73.5 1.0 OP2 B:DC1 3.7 117.9 0.5 OD1 Z:ASP78 3.8 87.1 1.0 OP1 B:DC1 4.0 117.0 0.5 OD2 Z:ASP171 4.0 95.9 1.0 O5' B:DC1 4.0 107.6 0.5 O Z:HOH515 4.3 90.8 1.0 OD2 Z:ASP78 4.3 103.4 1.0 C5' B:DC1 4.4 102.5 0.5 N Z:ASP152 4.4 75.8 1.0 CB Z:ASP152 4.5 64.7 1.0 OD2 Z:ASP30 4.5 98.3 1.0 OE1 Z:GLU150 4.5 81.8 1.0 CG Z:ASP78 4.5 91.4 1.0 OP1 B:DC1 4.7 112.3 0.5 P B:DC1 4.7 111.4 0.5 OD1 Z:ASP30 4.7 101.3 1.0 N Z:ALA151 4.7 76.9 1.0 CB Z:ALA151 4.9 69.8 1.0 NZ Z:LYS85 4.9 108.0 1.0 CA Z:ASP152 4.9 67.9 1.0 CG Z:ASP30 5.0 92.0 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.