Magnesium in PDB 3mhy: A New Pii Protein Structure

The structure of A New Pii Protein Structure, PDB code: 3mhy was solved by F.K.Winkler, D.Truan, X.D.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.980, 87.950, 116.880, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.8

The binding sites of Magnesium atom in the A New Pii Protein Structure (pdb code 3mhy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A New Pii Protein Structure, PDB code: 3mhy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the A New Pii Protein Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A New Pii Protein Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg115 b:17.1 occ:1.00 OE1 A:GLN39 2.0 19.7 1.0 O2G A:ATP113 2.0 17.1 1.0 O2 A:AKG114 2.1 16.5 1.0 O1A A:ATP113 2.1 14.9 1.0 O1B A:ATP113 2.1 16.4 1.0 O5 A:AKG114 2.1 17.8 1.0 C1 A:AKG114 2.8 18.6 1.0 C2 A:AKG114 2.8 19.9 1.0 PB A:ATP113 3.2 15.9 1.0 CD A:GLN39 3.2 19.9 1.0 PG A:ATP113 3.2 16.7 1.0 PA A:ATP113 3.3 15.1 1.0 O3B A:ATP113 3.5 16.1 1.0 O3A A:ATP113 3.5 15.0 1.0 O1G A:ATP113 3.8 18.9 1.0 N A:GLY87 3.8 17.7 1.0 N A:ARG38 3.9 18.2 1.0 NE2 A:GLN39 3.9 22.1 1.0 O A:HOH134 4.0 19.5 1.0 O1 A:AKG114 4.0 19.9 1.0 N A:GLN39 4.1 24.0 1.0 O2A A:ATP113 4.1 14.4 1.0 CA A:GLY37 4.2 18.4 1.0 CA A:GLY87 4.2 17.4 1.0 C3 A:AKG114 4.3 25.6 1.0 CG A:GLN39 4.3 25.5 1.0 C A:GLY37 4.3 18.9 1.0 CB A:GLN39 4.4 27.4 1.0 CB A:ILE86 4.4 27.1 1.0 O3G A:ATP113 4.5 18.9 1.0 O5' A:ATP113 4.5 14.9 1.0 O2B A:ATP113 4.5 16.6 1.0 N A:GLY37 4.6 16.5 1.0 C A:ILE86 4.6 19.3 1.0 CA A:ARG38 4.8 21.7 1.0 CA A:ILE86 4.8 20.1 1.0 CB A:ARG38 4.9 25.6 1.0 CA A:GLN39 4.9 25.1 1.0 C4 A:AKG114 4.9 26.2 1.0 C A:ARG38 5.0 24.0 1.0

Magnesium binding site 2 out of 4 in the A New Pii Protein Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A New Pii Protein Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg116 b:24.8 occ:0.50 O A:HOH120 2.1 21.1 0.5 O A:HOH119 2.1 34.9 0.5 O A:HOH117 2.1 34.7 0.5 O C:HOH116 2.2 34.1 0.5 O C:HOH117 2.2 34.1 0.5 O C:HOH248 3.5 34.5 1.0 O B:HOH212 4.1 36.5 1.0 OD2 A:ASP95 4.2 25.7 1.0 O A:HOH225 4.5 38.3 1.0 OD2 C:ASP95 4.7 26.2 1.0 CB A:ASP95 4.9 12.8 1.0 CG A:ASP95 5.0 20.5 1.0 O B:HOH119 5.0 28.6 1.0

Magnesium binding site 3 out of 4 in the A New Pii Protein Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A New Pii Protein Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg115 b:12.7 occ:1.00 O2G B:ATP113 2.0 12.3 1.0 O2 B:AKG114 2.0 13.8 1.0 O2B B:ATP113 2.0 12.0 1.0 OE1 B:GLN39 2.1 14.7 1.0 O2A B:ATP113 2.1 12.3 1.0 O5 B:AKG114 2.2 14.0 1.0 C1 B:AKG114 2.8 14.1 1.0 C2 B:AKG114 2.8 14.8 1.0 PB B:ATP113 3.1 11.8 1.0 PG B:ATP113 3.2 12.3 1.0 CD B:GLN39 3.3 13.2 1.0 PA B:ATP113 3.3 11.8 1.0 O3B B:ATP113 3.5 12.1 1.0 O3A B:ATP113 3.5 11.3 1.0 N B:GLY87 3.7 14.4 1.0 O3G B:ATP113 3.8 14.1 1.0 NE2 B:GLN39 3.9 15.6 1.0 O B:HOH130 4.0 15.9 1.0 O1 B:AKG114 4.0 13.6 1.0 N B:ARG38 4.0 12.0 1.0 CA B:GLY87 4.1 14.8 1.0 CA B:GLY37 4.1 11.4 1.0 O1A B:ATP113 4.2 12.3 1.0 N B:GLN39 4.2 15.0 1.0 C3 B:AKG114 4.3 21.2 1.0 C B:GLY37 4.3 10.7 1.0 CB B:ILE86 4.4 22.3 1.0 CG B:GLN39 4.4 16.8 1.0 CB B:GLN39 4.4 15.4 1.0 O5' B:ATP113 4.4 9.7 1.0 O1G B:ATP113 4.5 14.1 1.0 O1B B:ATP113 4.5 13.3 1.0 N B:GLY37 4.5 12.3 1.0 C B:ILE86 4.6 15.0 1.0 CG B:ARG38 4.6 15.2 1.0 CA B:ILE86 4.8 17.4 1.0 C4 B:AKG114 4.9 22.4 1.0 CA B:GLN39 4.9 13.1 1.0 O4 B:AKG114 5.0 19.9 1.0 CA B:ARG38 5.0 13.2 1.0

Magnesium binding site 4 out of 4 in the A New Pii Protein Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A New Pii Protein Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg115 b:15.0 occ:1.00 O1G C:ATP113 2.0 14.0 1.0 OE1 C:GLN39 2.0 16.2 1.0 O2 C:AKG114 2.0 16.6 1.0 O1B C:ATP113 2.1 13.6 1.0 O1A C:ATP113 2.1 12.9 1.0 O5 C:AKG114 2.1 16.6 1.0 C1 C:AKG114 2.8 17.2 1.0 C2 C:AKG114 2.8 18.4 1.0 PB C:ATP113 3.2 13.8 1.0 PG C:ATP113 3.2 16.0 1.0 CD C:GLN39 3.2 18.6 1.0 PA C:ATP113 3.3 12.7 1.0 O3B C:ATP113 3.5 14.4 1.0 O3A C:ATP113 3.6 14.3 1.0 N C:GLY87 3.7 16.4 1.0 O3G C:ATP113 3.8 15.6 1.0 NE2 C:GLN39 3.9 21.4 1.0 O1 C:AKG114 4.0 18.2 1.0 N C:ARG38 4.0 15.9 1.0 O C:HOH129 4.1 16.2 1.0 CA C:GLY37 4.1 14.2 1.0 CA C:GLY87 4.1 18.6 1.0 O2A C:ATP113 4.2 14.7 1.0 N C:GLN39 4.2 18.0 1.0 C3 C:AKG114 4.3 24.7 1.0 C C:GLY37 4.3 16.5 1.0 CG C:GLN39 4.4 19.5 1.0 CB C:GLN39 4.4 20.4 1.0 O2G C:ATP113 4.5 17.4 1.0 O5' C:ATP113 4.5 11.5 1.0 CB C:ILE86 4.5 27.1 1.0 N C:GLY37 4.5 15.1 1.0 O2B C:ATP113 4.5 13.7 1.0 CG C:ARG38 4.6 19.4 1.0 C C:ILE86 4.6 20.4 1.0 CA C:ILE86 4.8 23.9 1.0 C4 C:AKG114 4.9 26.6 1.0 CA C:GLN39 4.9 19.8 1.0 CA C:ARG38 5.0 16.4 1.0 O3 C:AKG114 5.0 19.9 1.0

D.Truan, L.F.Huergo, L.S.Chubatsu, M.Merrick, X.D.Li, F.K.Winkler. A New P(II) Protein Structure Identifies the 2-Oxoglutarate Binding Site. J.Mol.Biol. V. 400 531 2010.
ISSN: ISSN 0022-2836
PubMed: 20493877
DOI: 10.1016/J.JMB.2010.05.036