Magnesium in PDB 4oop: Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp

All present enzymatic activity of Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp:
3.6.1.23;

The structure of Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp, PDB code: 4oop was solved by N.Inoguchi, M.Bajaj, H.Moriyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.97 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.089, 70.680, 75.064, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.9

The binding sites of Magnesium atom in the Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp (pdb code 4oop). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp, PDB code: 4oop:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:15.9 occ:1.00 O2A B:DUP203 2.0 17.8 1.0 O A:HOH393 2.0 17.6 1.0 O A:HOH323 2.1 16.6 1.0 O2B B:DUP203 2.1 16.4 1.0 O1G B:DUP203 2.1 15.7 1.0 O B:HOH405 2.1 18.5 1.0 PB B:DUP203 3.1 18.6 1.0 PG B:DUP203 3.2 17.8 1.0 PA B:DUP203 3.3 17.0 1.0 O3B B:DUP203 3.4 17.5 1.0 N3A B:DUP203 3.7 18.6 1.0 O3G B:DUP203 3.7 20.9 1.0 NH2 B:ARG156 3.9 23.3 1.0 O A:HOH331 4.0 20.2 1.0 OD1 A:ASP52 4.2 16.4 1.0 NE A:ARG88 4.2 15.9 1.0 O B:HOH349 4.3 22.8 1.0 O1A B:DUP203 4.3 18.8 1.0 OE1 A:GLN134 4.3 16.7 1.0 OG1 B:THR164 4.3 21.1 1.0 NH2 A:ARG88 4.4 21.0 1.0 C5' B:DUP203 4.4 15.1 1.0 O5' B:DUP203 4.4 14.6 1.0 OD2 A:ASP52 4.4 20.5 1.0 O2G B:DUP203 4.4 20.5 1.0 O1B B:DUP203 4.5 16.6 1.0 O C:HOH337 4.6 24.7 1.0 CG A:ASP52 4.7 17.7 1.0 CZ A:ARG88 4.8 17.3 1.0 CZ B:ARG156 4.8 20.1 1.0 OD2 C:ASP105 4.9 16.6 1.0 CD A:GLN134 4.9 14.0 1.0 NH1 B:ARG156 5.0 19.5 1.0 NE2 A:GLN134 5.0 16.4 1.0

Magnesium binding site 2 out of 3 in the Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:20.3 occ:1.00 O A:HOH447 1.9 22.0 1.0 O1G A:DUP201 2.0 25.6 1.0 O B:HOH463 2.0 21.0 1.0 O2A A:DUP201 2.1 20.5 1.0 O2B A:DUP201 2.1 22.4 1.0 O B:HOH366 2.1 26.5 1.0 PB A:DUP201 3.1 22.0 1.0 PG A:DUP201 3.2 25.9 1.0 PA A:DUP201 3.3 18.8 1.0 O3B A:DUP201 3.5 24.3 1.0 N3A A:DUP201 3.6 19.7 1.0 O2G A:DUP201 4.1 31.3 1.0 O B:HOH361 4.1 26.1 1.0 OD1 B:ASP52 4.1 18.7 1.0 NE B:ARG88 4.2 22.8 1.0 O A:HOH415 4.2 36.1 1.0 O1A A:DUP201 4.3 18.6 1.0 O3G A:DUP201 4.3 30.9 1.0 OE1 B:GLN134 4.3 19.4 1.0 O A:HOH383 4.4 31.8 1.0 OD2 B:ASP52 4.4 30.3 1.0 NH2 B:ARG88 4.4 22.3 1.0 O5' A:DUP201 4.4 16.6 1.0 O A:HOH449 4.4 23.4 1.0 O1B A:DUP201 4.5 19.6 1.0 C5' A:DUP201 4.5 17.1 1.0 CG B:ASP52 4.7 20.1 1.0 CZ B:ARG88 4.8 26.9 1.0 O B:HOH341 4.9 25.2 1.0 CD B:GLN134 4.9 15.2 1.0 NE2 B:GLN134 4.9 14.0 1.0

Magnesium binding site 3 out of 3 in the Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Arabidopsis Thaliana Dutpase with with Magnesium and Alpha,Beta-Imido- Dutp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:24.4 occ:1.00 O B:HOH408 2.0 25.3 1.0 O B:HOH464 2.0 24.8 1.0 O2A B:DUP202 2.1 20.9 1.0 O2B B:DUP202 2.1 25.0 1.0 O1G B:DUP202 2.1 34.5 1.0 O C:HOH339 2.1 25.7 1.0 PB B:DUP202 3.1 26.0 1.0 PG B:DUP202 3.3 28.5 1.0 PA B:DUP202 3.3 24.0 1.0 O3B B:DUP202 3.6 31.0 1.0 N3A B:DUP202 3.6 25.9 1.0 O3G B:DUP202 3.9 28.3 1.0 O C:HOH378 4.1 25.5 1.0 O B:HOH413 4.2 37.4 1.0 OD1 C:ASP52 4.2 21.9 1.0 O A:HOH426 4.2 31.6 1.0 NE C:ARG88 4.2 24.1 1.0 O1A B:DUP202 4.3 22.6 1.0 O B:HOH382 4.3 28.0 1.0 NH2 C:ARG88 4.3 24.3 1.0 OE1 C:GLN134 4.4 21.4 1.0 OD2 C:ASP52 4.4 31.4 1.0 O5' B:DUP202 4.5 19.5 1.0 O1B B:DUP202 4.5 20.6 1.0 O2G B:DUP202 4.5 37.1 1.0 C5' B:DUP202 4.5 23.3 1.0 CG C:ASP52 4.8 23.9 1.0 CZ C:ARG88 4.8 23.0 1.0 NE2 C:GLN134 4.9 17.0 1.0 CD C:GLN134 4.9 17.2 1.0 O B:HOH343 4.9 22.4 1.0

N.Inoguchi, M.Bajaj, H.Moriyama. Structural Analysis of Apo and Holo Dutpase From Arabidopsis Thaliana To Be Published.