Magnesium in PDB 3fdg: The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19

The structure of The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19, PDB code: 3fdg was solved by R.Zhang, C.Hatzos, L.Freeman, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.33 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.246, 50.683, 81.594, 82.42, 73.61, 68.18
R / Rfree (%)	17.5 / 22.3

The binding sites of Magnesium atom in the The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19 (pdb code 3fdg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19, PDB code: 3fdg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg356 b:22.8 occ:1.00 OE2 A:GLU137 2.0 18.7 1.0 NE2 A:HIS210 2.2 14.2 1.0 O A:HOH582 2.2 48.0 1.0 O A:HOH416 2.2 19.2 1.0 NE2 A:HIS231 2.3 13.5 1.0 O A:HOH492 2.4 21.6 1.0 CD A:GLU137 3.1 19.2 1.0 CE1 A:HIS210 3.1 16.7 1.0 CD2 A:HIS210 3.2 17.1 1.0 CD2 A:HIS231 3.2 11.9 1.0 CE1 A:HIS231 3.3 16.5 1.0 OE1 A:GLU137 3.6 17.9 1.0 MG A:MG357 3.7 20.6 1.0 O A:HOH562 3.8 33.1 1.0 NH2 A:ARG242 3.9 14.2 1.0 NE2 A:HIS11 3.9 15.2 1.0 O A:HOH463 4.0 19.0 1.0 OD1 A:ASP304 4.1 17.5 1.0 NE1 A:TRP164 4.1 22.5 1.0 CD1 A:TRP164 4.2 22.4 1.0 OD2 A:ASP304 4.2 20.2 1.0 ND1 A:HIS210 4.3 13.9 1.0 CG A:HIS210 4.3 12.9 1.0 CG A:GLU137 4.4 12.3 1.0 CE1 A:HIS11 4.4 18.0 1.0 ND1 A:HIS231 4.4 15.9 1.0 CG A:HIS231 4.4 14.0 1.0 O A:HOH430 4.5 20.4 1.0 CD2 A:HIS11 4.5 15.9 1.0 CG A:ASP304 4.5 18.4 1.0 CZ A:ARG242 4.8 15.8 1.0 NE A:ARG242 4.9 14.9 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg357 b:20.6 occ:1.00 OE1 A:GLU137 2.0 17.9 1.0 O A:HOH463 2.1 19.0 1.0 OD2 A:ASP13 2.1 16.5 1.0 O A:HOH582 2.1 48.0 1.0 OD1 A:ASP13 2.1 18.4 1.0 NE2 A:HIS11 2.1 15.2 1.0 CG A:ASP13 2.4 18.1 1.0 CD A:GLU137 2.9 19.2 1.0 CE1 A:HIS11 3.0 18.0 1.0 CD2 A:HIS11 3.2 15.9 1.0 OE2 A:GLU137 3.2 18.7 1.0 MG A:MG356 3.7 22.8 1.0 O A:HOH562 3.8 33.1 1.0 OD1 A:ASP304 3.9 17.5 1.0 CB A:ASP13 4.0 15.7 1.0 O A:HOH492 4.1 21.6 1.0 ND1 A:HIS11 4.2 17.4 1.0 CB A:ALA54 4.3 14.2 1.0 CG A:HIS11 4.3 15.3 1.0 CG A:GLU137 4.3 12.3 1.0 NE2 A:HIS231 4.5 13.5 1.0 CB A:TYR56 4.6 20.1 1.0 CG A:TYR56 4.7 19.7 1.0 CB A:GLU137 4.8 13.8 1.0 O A:HOH474 4.8 18.5 1.0 CA A:ASP13 4.8 15.7 1.0 CD2 A:TYR56 5.0 21.3 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg356 b:21.9 occ:1.00 OE1 B:GLU137 2.0 16.9 1.0 OD2 B:ASP13 2.0 19.1 1.0 O B:HOH464 2.1 17.1 1.0 NE2 B:HIS11 2.2 13.0 1.0 OD1 B:ASP13 2.2 22.8 1.0 CG B:ASP13 2.4 19.2 1.0 CD B:GLU137 3.0 18.8 1.0 CE1 B:HIS11 3.0 12.8 1.0 OE2 B:GLU137 3.2 19.6 1.0 CD2 B:HIS11 3.3 13.2 1.0 MG B:MG357 3.6 25.8 1.0 OD1 B:ASP304 3.9 19.6 1.0 CB B:ASP13 4.0 16.0 1.0 O B:HOH422 4.0 26.8 1.0 ND1 B:HIS11 4.2 12.9 1.0 CB B:ALA54 4.3 15.3 1.0 CG B:HIS11 4.3 14.8 1.0 CG B:GLU137 4.3 15.1 1.0 NE2 B:HIS231 4.5 12.1 1.0 CB B:TYR56 4.6 21.6 1.0 CB B:GLU137 4.7 16.0 1.0 CG B:TYR56 4.8 22.1 1.0 CA B:ASP13 4.8 15.9 1.0 O B:HOH377 4.8 18.8 1.0 N B:ASP13 5.0 13.9 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg357 b:25.8 occ:1.00 OE2 B:GLU137 2.1 19.6 1.0 NE2 B:HIS210 2.2 16.8 1.0 NE2 B:HIS231 2.3 12.1 1.0 O B:HOH383 2.3 20.4 1.0 O B:HOH422 2.4 26.8 1.0 CE1 B:HIS210 3.1 16.3 1.0 CD2 B:HIS210 3.2 15.4 1.0 CD B:GLU137 3.2 18.8 1.0 CD2 B:HIS231 3.2 12.8 1.0 CE1 B:HIS231 3.2 14.2 1.0 MG B:MG356 3.6 21.9 1.0 OE1 B:GLU137 3.6 16.9 1.0 NE2 B:HIS11 3.8 13.0 1.0 NH2 B:ARG242 3.9 17.5 1.0 O B:HOH464 4.1 17.1 1.0 OD1 B:ASP304 4.1 19.6 1.0 OD2 B:ASP304 4.1 22.0 1.0 ND1 B:HIS210 4.3 15.2 1.0 NE1 B:TRP164 4.3 23.3 1.0 CE1 B:HIS11 4.3 12.8 1.0 CD1 B:TRP164 4.3 22.3 1.0 CG B:HIS210 4.3 15.2 1.0 ND1 B:HIS231 4.4 15.4 1.0 CG B:HIS231 4.4 16.6 1.0 CD2 B:HIS11 4.4 13.2 1.0 CG B:GLU137 4.4 15.1 1.0 CG B:ASP304 4.5 20.7 1.0 O B:HOH457 4.6 21.9 1.0 CZ B:ARG242 4.8 20.3 1.0 OD2 B:ASP13 4.9 19.1 1.0 NE B:ARG242 5.0 16.7 1.0

R.Zhang, C.Hatzos, L.Freeman, A.Joachimiak. The Crystal Structure of the Dipeptidase Ac, Metallo Peptidase. Merops Family M19 To Be Published.