Manganese in PDB 7mxx: Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4), PDB code: 7mxx 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)	32.45 / 2.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.885, 70.885, 182.462, 90, 90, 90
R / Rfree (%)	25.8 / 29.8

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4) (pdb code 7mxx). 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 (R92A) in Complex with 5' Flap Dna (UF4), PDB code: 7mxx:
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 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:69.6 occ:1.00 OP1 B:DT1 2.0 169.2 1.0 OP2 B:DT1 2.1 170.0 1.0 OD1 Z:ASP173 2.2 75.8 1.0 OD1 Z:ASP152 2.2 66.2 1.0 OD2 Z:ASP171 2.2 77.2 1.0 P B:DT1 2.3 170.6 1.0 CG Z:ASP173 3.1 75.6 1.0 CG Z:ASP171 3.2 76.3 1.0 CG Z:ASP152 3.3 66.3 1.0 MN Z:MN403 3.3 98.3 1.0 OP3 B:DT1 3.3 170.7 1.0 CB Z:ASP173 3.4 74.7 1.0 MN Z:MN402 3.6 64.6 1.0 O5' B:DT1 3.6 174.2 1.0 OD1 Z:ASP171 3.6 76.9 1.0 OD2 Z:ASP152 3.8 66.0 1.0 C5' B:DT1 4.0 174.9 1.0 OE1 Z:GLU150 4.1 70.9 1.0 O B:HOH101 4.1 88.7 1.0 OD1 Z:ASP225 4.1 83.0 1.0 OD2 Z:ASP173 4.3 76.2 1.0 CB Z:ASP152 4.5 66.7 1.0 CB Z:ASP171 4.5 74.5 1.0 CD Z:GLU150 4.5 70.9 1.0 CG Z:ASP225 4.6 81.7 1.0 N Z:GLY2 4.7 90.2 1.0 O B:HOH104 4.8 82.8 1.0 O B:HOH103 4.8 96.8 1.0 CA Z:ASP173 4.8 73.7 1.0 OD2 Z:ASP225 4.8 80.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:64.6 occ:1.00 OD2 Z:ASP152 2.1 66.0 1.0 O B:HOH101 2.2 88.7 1.0 O B:HOH103 2.2 96.8 1.0 O B:HOH104 2.2 82.8 1.0 O Z:HOH517 2.3 71.8 1.0 OP1 B:DT1 2.3 169.2 1.0 CG Z:ASP152 3.0 66.3 1.0 OD1 Z:ASP152 3.2 66.2 1.0 OP3 B:DT1 3.5 170.7 1.0 P B:DT1 3.5 170.6 1.0 MN Z:MN401 3.6 69.6 1.0 OD2 Z:ASP171 4.0 77.2 1.0 CG Z:GLU150 4.0 70.1 1.0 OD1 Z:ASP78 4.0 63.8 1.0 OD2 Z:ASP78 4.2 67.5 1.0 N Z:ASP152 4.4 66.8 1.0 CB Z:ASP152 4.4 66.7 1.0 OE1 Z:GLU150 4.5 70.9 1.0 O5' B:DT1 4.5 174.2 1.0 CG Z:ASP78 4.5 66.7 1.0 OP2 B:DT1 4.6 170.0 1.0 CD Z:GLU150 4.6 70.9 1.0 OD2 Z:ASP30 4.7 72.1 1.0 OD1 Z:ASP30 4.8 71.1 1.0 N Z:ALA151 4.8 66.9 1.0 CA Z:ASP152 4.9 66.2 1.0 CG Z:ASP171 4.9 76.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn403 b:98.3 occ:1.00 OP2 B:DT1 2.0 170.0 1.0 OD2 Z:ASP225 2.1 80.2 1.0 OP2 B:DC2 2.2 177.1 1.0 OD1 Z:ASP173 2.2 75.8 1.0 OD1 Z:ASP225 2.2 83.0 1.0 N Z:GLY2 2.2 90.2 1.0 CG Z:ASP225 2.4 81.7 1.0 CG Z:ASP173 3.1 75.6 1.0 P B:DT1 3.2 170.6 1.0 MN Z:MN401 3.3 69.6 1.0 OD2 Z:ASP173 3.4 76.2 1.0 O5' B:DT1 3.4 174.2 1.0 P B:DC2 3.5 180.6 1.0 C5' B:DT1 3.5 174.9 1.0 CA Z:GLY2 3.6 89.7 1.0 OD1 Z:ASP171 3.8 76.9 1.0 CB Z:ASP225 3.9 82.0 1.0 OP1 B:DC2 4.0 181.1 1.0 OP1 B:DT1 4.1 169.2 1.0 O3' B:DT1 4.2 181.4 1.0 OD2 Z:ASP171 4.3 77.2 1.0 OP3 B:DT1 4.3 170.7 1.0 C3' B:DT1 4.4 181.2 1.0 C Z:GLY2 4.4 92.1 1.0 C4' B:DT1 4.4 178.8 1.0 CG Z:ASP171 4.5 76.3 1.0 CB Z:ASP173 4.5 74.7 1.0 O Z:GLY2 4.6 95.2 1.0 O5' B:DC2 4.6 184.6 1.0 N Z:ASP225 4.7 79.1 1.0 CA Z:ASP225 4.8 79.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Human Exonuclease 1 EXO1 (R92A) in Complex with 5' Flap Dna (UF4)


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 (R92A) in Complex with 5' Flap Dna (UF4) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn404 b:80.2 occ:1.00 SG Z:CYS80 2.3 70.0 1.0 CB Z:CYS80 3.2 71.4 1.0 CD1 Z:ILE325 3.9 74.5 1.0 O Z:PRO148 4.1 65.9 1.0 OH Z:TYR149 4.4 74.0 1.0 CZ Z:TYR149 4.5 72.2 1.0 CG1 Z:VAL317 4.6 79.8 1.0 CE1 Z:TYR149 4.6 71.8 1.0 CA Z:CYS80 4.7 73.2 1.0 CZ Z:PHE335 4.7 74.9 1.0 CE1 Z:PHE335 4.8 76.9 1.0 N Z:CYS80 5.0 69.7 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.