Magnesium in PDB 2rd5: Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana

All present enzymatic activity of Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana:
2.7.2.8;

The structure of Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana, PDB code: 2rd5 was solved by Y.Mizuno, G.B.G.Moorhead, K.K.S.Ng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.51
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	171.133, 171.133, 171.133, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.9

The binding sites of Magnesium atom in the Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana (pdb code 2rd5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana, PDB code: 2rd5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:66.0 occ:1.00 O1B B:ADP2000 2.1 42.5 1.0 O2A B:ADP2000 2.1 54.4 1.0 PA B:ADP2000 3.3 45.5 1.0 OD2 B:ASP196 3.4 74.3 1.0 PB B:ADP2000 3.5 49.6 1.0 NZ B:LYS255 3.6 62.0 1.0 O B:GLY251 3.6 64.5 1.0 O5' B:ADP2000 3.8 55.5 1.0 O3A B:ADP2000 3.9 50.2 1.0 CA B:GLY251 4.0 57.7 1.0 CE B:LYS255 4.1 58.5 1.0 C B:GLY251 4.2 61.7 1.0 ND2 B:ASN194 4.2 54.7 1.0 CG B:ASP196 4.2 63.1 1.0 O3B B:ADP2000 4.4 51.0 1.0 OD1 B:ASN194 4.4 63.4 1.0 OD1 B:ASP196 4.4 70.6 1.0 O2B B:ADP2000 4.5 51.8 1.0 NZ B:LYS41 4.5 63.4 1.0 O1A B:ADP2000 4.6 63.6 1.0 O B:HOH2005 4.6 43.1 1.0 CG B:ASN194 4.8 62.9 1.0 OE1 B:NLG2001 4.8 49.3 1.0 O B:HOH2024 5.0 52.7 1.0 O B:GLY96 5.0 64.8 1.0

Magnesium binding site 2 out of 3 in the Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:60.2 occ:1.00 O3G C:ATP1000 2.1 54.5 1.0 O2B C:ATP1000 2.1 50.7 1.0 O2A C:ATP1000 2.1 64.8 1.0 O C:GLY48 2.3 61.0 1.0 O1A C:ATP1000 2.6 73.1 1.0 PA C:ATP1000 2.7 57.4 1.0 PB C:ATP1000 3.1 49.3 1.0 C C:GLY48 3.2 60.5 1.0 PG C:ATP1000 3.3 50.8 1.0 O3A C:ATP1000 3.3 53.0 1.0 O3B C:ATP1000 3.5 49.3 1.0 CA C:GLY48 3.6 57.4 1.0 O C:HOH1005 3.8 51.1 1.0 N C:GLY99 3.9 60.6 1.0 CA C:GLY99 4.0 58.8 1.0 O2G C:ATP1000 4.2 56.5 1.0 O5' C:ATP1000 4.2 68.1 1.0 CG2 C:ILE98 4.3 60.8 1.0 N C:GLY48 4.3 57.8 1.0 O1G C:ATP1000 4.4 48.8 1.0 N C:ALA49 4.4 61.3 1.0 O1B C:ATP1000 4.5 50.8 1.0 OE1 C:GLU55 4.5 60.0 1.0 C5' C:ATP1000 4.9 51.6 1.0 C C:ILE98 4.9 60.9 1.0 CA C:ALA49 5.0 61.9 1.0

Magnesium binding site 3 out of 3 in the Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:64.8 occ:1.00 O3G D:ATP1000 2.1 63.8 1.0 O2B D:ATP1000 2.1 61.2 1.0 O2A D:ATP1000 2.1 65.6 1.0 O D:GLY48 2.3 61.5 1.0 PA D:ATP1000 2.7 60.9 1.0 O1A D:ATP1000 2.7 78.5 1.0 PB D:ATP1000 3.1 60.8 1.0 C D:GLY48 3.3 61.7 1.0 O3A D:ATP1000 3.3 66.9 1.0 PG D:ATP1000 3.3 60.6 1.0 O3B D:ATP1000 3.6 55.2 1.0 CA D:GLY48 3.6 60.2 1.0 N D:GLY99 3.9 62.2 1.0 O D:HOH1012 3.9 52.8 1.0 CA D:GLY99 3.9 60.4 1.0 O2G D:ATP1000 4.1 64.8 1.0 O5' D:ATP1000 4.2 74.4 1.0 CG2 D:ILE98 4.2 64.4 1.0 N D:GLY48 4.3 61.9 1.0 OE1 D:GLU55 4.4 58.9 1.0 O1G D:ATP1000 4.5 56.1 1.0 N D:ALA49 4.5 61.6 1.0 O1B D:ATP1000 4.5 66.5 1.0 C D:ILE98 4.9 62.4 1.0 C5' D:ATP1000 4.9 64.0 1.0

Y.Mizuno, G.B.Moorhead, K.K.Ng. Structural Basis For the Regulation of N-Acetylglutamate Kinase By Pii in Arabidopsis Thaliana. J.Biol.Chem. V. 282 35733 2007.
ISSN: ISSN 0021-9258
PubMed: 17913711
DOI: 10.1074/JBC.M707127200