Magnesium in PDB 8pno: The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx

All present enzymatic activity of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx:
3.1.3.10;

The structure of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx, PDB code: 8pno was solved by P.Baumann, D.Zappala, Y.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.04 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.259, 79.325, 80.297, 90, 108.52, 90
R / Rfree (%)	21.2 / 25.7

The structure of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Calcium	(Ca)	2 atoms

The binding sites of Magnesium atom in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx (pdb code 8pno). 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 MGF3(H2O) Transition State Analog Complex of E. Coli Yihx, PDB code: 8pno:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:31.3 occ:1.00 MG1 A:KQB302 0.0 31.3 1.0 F3 A:KQB302 1.8 30.9 1.0 O1 A:KQB302 1.8 35.2 1.0 F2 A:KQB302 1.8 34.6 1.0 F1 A:KQB302 1.8 34.3 1.0 OD1 A:ASP6 2.0 34.8 1.0 O A:HOH429 2.0 28.3 1.0 CG A:ASP6 2.9 36.0 1.0 OD2 A:ASP6 3.3 32.4 1.0 MG A:MG306 3.4 35.8 1.0 O A:HOH405 3.7 29.5 1.0 NZ A:LYS141 3.7 34.8 1.0 N A:GLY8 3.9 34.8 1.0 O2 A:EDO305 4.0 39.7 1.0 N A:LEU7 4.1 37.3 1.0 OG A:SER107 4.1 28.6 1.0 O A:ASN108 4.2 31.0 1.0 N A:ASN108 4.3 32.0 1.0 O1 A:GOL308 4.3 51.0 1.0 CB A:ASP6 4.3 35.3 1.0 C1 A:GOL308 4.4 56.9 1.0 CE A:LYS141 4.4 32.6 1.0 O A:GLY8 4.5 36.8 1.0 CA A:GLY8 4.5 36.1 1.0 O A:HOH445 4.5 33.5 1.0 CA A:SER107 4.5 29.2 1.0 CA A:ASP6 4.8 38.2 1.0 C A:LEU7 4.8 34.1 1.0 CB A:SER107 4.8 28.8 1.0 CB A:ASN108 4.8 30.4 1.0 CA A:LEU7 4.8 36.2 1.0 O A:LEU106 4.9 27.2 1.0 OD2 A:ASP165 4.9 36.4 1.0 C A:ASP6 4.9 37.4 1.0 CB A:LEU7 4.9 41.3 1.0 CA A:ASN108 5.0 30.5 1.0 C A:SER107 5.0 33.0 1.0 C A:GLY8 5.0 36.9 1.0 C2 A:EDO305 5.0 47.0 1.0

Magnesium binding site 2 out of 4 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg306 b:35.8 occ:1.00 F1 A:KQB302 2.0 34.3 1.0 O A:HOH445 2.0 33.5 1.0 OD1 A:ASP166 2.0 38.1 1.0 OD2 A:ASP6 2.0 32.4 1.0 O A:HOH405 2.0 29.5 1.0 O A:GLY8 2.0 36.8 1.0 CG A:ASP6 3.1 36.0 1.0 C A:GLY8 3.1 36.9 1.0 CG A:ASP166 3.1 40.4 1.0 O1 A:KQB302 3.2 35.2 1.0 MG1 A:KQB302 3.4 31.3 1.0 OD1 A:ASP6 3.5 34.8 1.0 OD2 A:ASP166 3.5 39.1 1.0 CA A:GLY8 3.7 36.1 1.0 N A:GLY8 4.0 34.8 1.0 OD1 A:ASP165 4.0 31.3 1.0 O A:HOH452 4.2 48.8 1.0 N A:ASN9 4.2 36.9 1.0 F3 A:KQB302 4.3 30.9 1.0 CB A:ASP6 4.4 35.3 1.0 CB A:ASP166 4.4 42.0 1.0 O A:HOH429 4.5 28.3 1.0 N A:ASP166 4.6 42.9 1.0 CG2 A:VAL10 4.6 34.7 1.0 CB A:ASN9 4.6 41.3 1.0 CA A:ASN9 4.7 38.6 1.0 CG A:ASP165 4.8 37.5 1.0 C A:ASN9 4.9 34.6 1.0 C A:LEU7 4.9 34.1 1.0

Magnesium binding site 3 out of 4 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:28.9 occ:1.00 MG1 B:KQB302 0.0 28.9 1.0 F3 B:KQB302 1.8 27.6 1.0 O1 B:KQB302 1.8 35.7 1.0 F2 B:KQB302 1.8 34.9 1.0 F1 B:KQB302 1.8 34.8 1.0 OD1 B:ASP6 2.0 34.8 1.0 O B:HOH438 2.0 24.7 1.0 CG B:ASP6 3.0 35.7 1.0 OD2 B:ASP6 3.4 31.7 1.0 MG B:MG305 3.4 36.2 1.0 O B:HOH407 3.6 35.1 1.0 NZ B:LYS141 3.7 36.3 1.0 N B:GLY8 4.0 33.8 1.0 C3 B:PEG304 4.1 60.7 1.0 N B:LEU7 4.1 34.9 1.0 O2 B:EDO303 4.1 45.6 1.0 OG B:SER107 4.2 26.3 1.0 O B:ASN108 4.2 30.3 1.0 CB B:ASP6 4.3 35.0 1.0 N B:ASN108 4.3 33.6 1.0 CE B:LYS141 4.4 35.4 1.0 O B:GLY8 4.5 38.0 1.0 O B:HOH427 4.5 26.8 1.0 CA B:SER107 4.5 32.1 1.0 C2 B:EDO303 4.6 50.6 1.0 CA B:GLY8 4.6 33.5 1.0 O4 B:PEG304 4.6 67.6 1.0 OD2 B:ASP165 4.7 43.2 1.0 CA B:ASP6 4.8 35.1 1.0 CB B:SER107 4.8 30.6 1.0 O B:LEU106 4.8 26.9 1.0 CB B:ASN108 4.9 31.6 1.0 C B:LEU7 4.9 31.7 1.0 CA B:LEU7 4.9 33.5 1.0 C B:ASP6 4.9 36.6 1.0 C4 B:PEG304 4.9 62.2 1.0 C B:SER107 5.0 33.4 1.0 CA B:ASN108 5.0 30.1 1.0

Magnesium binding site 4 out of 4 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:36.2 occ:1.00 F1 B:KQB302 2.0 34.8 1.0 OD1 B:ASP166 2.0 39.3 1.0 O B:HOH427 2.0 26.8 1.0 OD2 B:ASP6 2.0 31.7 1.0 O B:HOH407 2.0 35.1 1.0 O B:GLY8 2.0 38.0 1.0 CG B:ASP6 3.0 35.7 1.0 CG B:ASP166 3.1 40.3 1.0 C B:GLY8 3.2 36.4 1.0 OD1 B:ASP6 3.4 34.8 1.0 MG1 B:KQB302 3.4 28.9 1.0 O1 B:KQB302 3.4 35.7 1.0 OD2 B:ASP166 3.5 39.5 1.0 OD1 B:ASP165 3.8 33.8 1.0 CA B:GLY8 3.9 33.5 1.0 N B:GLY8 4.1 33.8 1.0 N B:ASN9 4.3 34.2 1.0 CB B:ASP166 4.4 41.7 1.0 F3 B:KQB302 4.4 27.6 1.0 CB B:ASP6 4.4 35.0 1.0 N B:ASP166 4.4 39.6 1.0 CG2 B:VAL10 4.5 35.7 1.0 CG B:ASP165 4.6 39.8 1.0 CB B:ASN9 4.6 38.8 1.0 O B:HOH438 4.6 24.7 1.0 O4 B:PEG304 4.7 67.6 1.0 C B:ASN9 4.7 37.9 1.0 CA B:ASN9 4.7 36.9 1.0 OD2 B:ASP165 4.9 43.2 1.0 CA B:ASP166 4.9 40.1 1.0 C B:LEU7 4.9 31.7 1.0 O B:ASN9 5.0 38.5 1.0

P.Baumann, D.Zappala, Y.Jin. The MGF3(H2O)- Transition State Analog Complex of E. Coli Yihx To Be Published.