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

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (Wt) in Complex with 5' Recessed-End Dna (Cr), PDB code: 7mxs 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)	38.58 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.553, 73.553, 181.237, 90, 90, 90
R / Rfree (%)	21.3 / 24.7

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


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 (Cr) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn401 b:56.5 occ:1.00 OD2 Z:ASP171 2.1 60.3 1.0 OD2 Z:ASP152 2.1 45.8 1.0 OD1 Z:ASP173 2.2 68.1 1.0 OP3 B:DC1 2.2 96.5 1.0 O Z:HOH517 2.3 79.0 1.0 OP1 B:DC1 2.4 95.7 1.0 P B:DC1 2.8 88.1 1.0 MN Z:MN402 2.9 91.1 1.0 CG Z:ASP173 3.0 71.9 1.0 CG Z:ASP152 3.2 60.4 1.0 CG Z:ASP171 3.3 62.6 1.0 CB Z:ASP173 3.3 70.6 1.0 O5' B:DC1 3.6 90.4 1.0 OD1 Z:ASP152 3.7 58.8 1.0 MN B:MN101 3.7 77.4 1.0 OD1 Z:ASP171 3.8 59.1 1.0 O B:HOH202 3.9 70.5 1.0 OD1 Z:ASP225 3.9 98.2 1.0 O Z:HOH544 4.0 70.2 1.0 OP2 B:DC1 4.1 92.6 1.0 OD2 Z:ASP173 4.1 81.5 1.0 OE1 Z:GLU150 4.2 68.0 1.0 CB Z:ASP171 4.4 43.9 1.0 CB Z:ASP152 4.5 60.7 1.0 N Z:GLY2 4.6 131.9 1.0 O Z:HOH503 4.7 110.2 1.0 CA Z:ASP173 4.8 65.9 1.0 O Z:HOH514 5.0 99.7 1.0 NZ Z:LYS85 5.0 78.4 1.0 C5' B:DC1 5.0 92.6 1.0 O B:HOH203 5.0 68.2 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 (Cr)


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 (Cr) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn402 b:91.1 occ:1.00 N Z:GLY2 2.0 131.9 1.0 OP1 B:DC1 2.1 95.7 1.0 OD1 Z:ASP225 2.1 98.2 1.0 O Z:HOH514 2.2 99.7 1.0 OD1 Z:ASP173 2.2 68.1 1.0 MN Z:MN401 2.9 56.5 1.0 CA Z:GLY2 3.1 122.0 1.0 CG Z:ASP225 3.2 85.0 1.0 CG Z:ASP173 3.3 71.9 1.0 P B:DC1 3.3 88.1 1.0 OD2 Z:ASP171 3.5 60.3 1.0 OD2 Z:ASP225 3.5 87.6 1.0 O Z:HOH517 3.6 79.0 1.0 O5' B:DC1 3.6 90.4 1.0 OD2 Z:ASP173 3.8 81.5 1.0 OD1 Z:ASP171 3.9 59.1 1.0 OP3 B:DC1 4.0 96.5 1.0 CG Z:ASP171 4.1 62.6 1.0 O Z:HOH502 4.2 117.4 1.0 C Z:GLY2 4.3 115.1 1.0 O Z:GLY2 4.5 116.3 1.0 CB Z:ASP225 4.5 70.4 1.0 OP2 B:DC1 4.5 92.6 1.0 OP2 B:DG2 4.6 97.5 1.0 CB Z:ASP173 4.6 70.6 1.0 O Z:HOH528 4.6 59.0 1.0 C3' B:DC1 4.8 100.8 1.0 O Z:HOH544 4.8 70.2 1.0 C5' B:DC1 4.9 92.6 1.0 NH2 Z:ARG92 5.0 105.3 1.0 OP1 B:DG2 5.0 93.1 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 (Cr)


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 (Cr) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mn404 b:123.2 occ:1.00 O Z:ARG243 2.6 95.4 1.0 O Z:ALA245 3.1 100.3 1.0 C Z:ARG243 3.5 94.3 1.0 O Z:LEU242 3.6 96.7 1.0 OD2 Z:ASP208 3.8 111.4 1.0 C Z:ALA245 3.8 105.3 1.0 OD1 Z:ASP208 4.1 113.6 1.0 CA Z:ARG243 4.1 91.7 1.0 CG Z:ASP208 4.3 110.6 1.0 N Z:ALA245 4.3 99.7 1.0 N Z:ASN246 4.4 120.3 1.0 CA Z:ASN246 4.5 130.6 1.0 N Z:LEU244 4.6 90.3 1.0 C Z:LEU242 4.6 91.4 1.0 NZ Z:LYS214 4.6 81.9 1.0 CA Z:ALA245 4.7 101.8 1.0 C Z:LEU244 4.7 94.4 1.0 N Z:ARG243 4.9 95.5 1.0 CB Z:ASN246 4.9 140.2 1.0 CA Z:LEU244 5.0 89.5 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 (Cr)


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 (Cr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:77.4 occ:1.00 OP3 B:DC1 2.0 96.5 1.0 O B:HOH203 2.1 68.2 1.0 O Z:HOH503 2.2 110.2 1.0 O Z:HOH505 2.2 58.0 1.0 OD1 Z:ASP152 2.2 58.8 1.0 O B:HOH202 2.2 70.5 1.0 CG Z:ASP152 3.2 60.4 1.0 P B:DC1 3.3 88.1 1.0 OP2 B:DC1 3.4 92.6 1.0 OD2 Z:ASP152 3.5 45.8 1.0 MN Z:MN401 3.7 56.5 1.0 OD1 Z:ASP78 3.8 67.6 1.0 OD2 Z:ASP78 3.9 74.4 1.0 O5' B:DC1 4.1 90.4 1.0 OD2 Z:ASP171 4.2 60.3 1.0 CG Z:ASP78 4.2 67.8 1.0 OD2 Z:ASP30 4.2 82.2 1.0 OP1 B:DC1 4.3 95.7 1.0 N Z:ASP152 4.3 55.7 1.0 OD1 Z:ASP30 4.5 82.3 1.0 CB Z:ASP152 4.6 60.7 1.0 N Z:ALA151 4.6 62.7 1.0 C5' B:DC1 4.6 92.6 1.0 NZ Z:LYS85 4.6 78.4 1.0 OE1 Z:GLU150 4.6 68.0 1.0 CB Z:ALA151 4.7 56.3 1.0 CG Z:ASP30 4.8 76.5 1.0 O Z:HOH517 4.8 79.0 1.0 CA Z:ASP152 4.9 59.2 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.