Magnesium in PDB 3o98: Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp

All present enzymatic activity of Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp:
3.5.1.78; 6.3.1.8;

The structure of Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp, PDB code: 3o98 was solved by C.H.Pai, C.H.Lin, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.380, 76.200, 84.220, 70.81, 74.37, 78.64
R / Rfree (%)	22 / 26.2

The binding sites of Magnesium atom in the Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp (pdb code 3o98). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp, PDB code: 3o98:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4000 b:37.6 occ:1.00 OE2 A:GLU330 1.9 35.1 1.0 O A:HOH4001 2.0 34.8 1.0 OD1 A:ASN332 2.0 34.6 1.0 O2B A:ADP3001 2.0 34.2 1.0 OE1 A:GLU330 2.0 37.1 1.0 O A:HOH4002 2.1 34.3 1.0 CD A:GLU330 2.2 37.5 1.0 CG A:ASN332 3.0 35.7 1.0 O A:HOH5001 3.1 33.2 1.0 PB A:ADP3001 3.2 31.8 1.0 MG A:MG5000 3.3 32.9 1.0 ND2 A:ASN332 3.4 36.1 1.0 O3B A:ADP3001 3.5 32.9 1.0 CG A:GLU330 3.6 36.1 1.0 NZ A:LYS498 3.9 26.9 1.0 O3A A:ADP3001 3.9 32.5 1.0 OD2 A:ASP318 4.3 35.8 1.0 CA A:ARG538 4.3 40.8 1.0 CB A:ASN332 4.4 36.9 1.0 CB A:ARG538 4.4 42.2 1.0 O1B A:ADP3001 4.4 36.3 1.0 O2A A:ADP3001 4.5 32.4 1.0 O A:HOH8048 4.5 48.1 1.0 O A:HOH8049 4.6 2.9 1.0 CB A:GLU330 4.7 36.8 1.0 N A:CYS539 4.7 42.5 1.0 O A:GLY537 4.7 36.0 1.0 PA A:ADP3001 4.8 33.0 1.0 CA A:ASN332 5.0 37.8 1.0

Magnesium binding site 2 out of 4 in the Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5000 b:32.9 occ:1.00 OE2 A:GLU330 1.9 35.1 1.0 O A:HOH5002 1.9 33.1 1.0 O3B A:ADP3001 2.0 32.9 1.0 O2A A:ADP3001 2.0 32.4 1.0 OD2 A:ASP318 2.0 35.8 1.0 O A:HOH5001 2.1 33.2 1.0 PB A:ADP3001 3.0 31.8 1.0 CD A:GLU330 3.1 37.5 1.0 PA A:ADP3001 3.2 33.0 1.0 CG A:ASP318 3.3 36.2 1.0 MG A:MG4000 3.3 37.6 1.0 O3A A:ADP3001 3.3 32.5 1.0 O2B A:ADP3001 3.4 34.2 1.0 O A:HOH4002 3.6 34.3 1.0 CG A:GLU330 3.8 36.1 1.0 OD1 A:ASP318 4.0 36.4 1.0 OE1 A:GLU330 4.1 37.1 1.0 ND2 A:ASN332 4.2 36.1 1.0 O5' A:ADP3001 4.2 34.4 1.0 CB A:ASP318 4.3 35.1 1.0 C5' A:ADP3001 4.3 32.6 1.0 O3' A:ADP3001 4.3 33.5 1.0 O1A A:ADP3001 4.3 30.9 1.0 NH2 A:ARG316 4.3 44.4 1.0 O1B A:ADP3001 4.4 36.3 1.0 OD1 A:ASN332 4.6 34.6 1.0 C3' A:ADP3001 4.8 33.4 1.0 CG A:ASN332 4.8 35.7 1.0

Magnesium binding site 3 out of 4 in the Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg6000 b:39.2 occ:1.00 OE2 B:GLU330 1.9 35.6 1.0 O B:HOH6001 2.0 37.0 1.0 OD1 B:ASN332 2.0 38.8 1.0 O2B B:ADP3002 2.0 36.7 1.0 OE1 B:GLU330 2.1 35.8 1.0 O B:HOH6002 2.1 35.1 1.0 CD B:GLU330 2.2 36.0 1.0 CG B:ASN332 3.0 40.1 1.0 O B:HOH7001 3.1 32.9 1.0 PB B:ADP3002 3.2 33.3 1.0 MG B:MG7000 3.3 34.7 1.0 ND2 B:ASN332 3.4 43.1 1.0 O3B B:ADP3002 3.4 35.7 1.0 CG B:GLU330 3.7 36.7 1.0 O3A B:ADP3002 4.0 34.9 1.0 NZ B:LYS498 4.2 29.8 1.0 CB B:ARG538 4.2 54.3 1.0 CA B:ARG538 4.2 52.2 1.0 OD2 B:ASP318 4.2 37.0 1.0 CB B:ASN332 4.4 39.8 1.0 O B:HOH8196 4.4 23.5 1.0 O1B B:ADP3002 4.4 36.2 1.0 O2A B:ADP3002 4.5 35.8 1.0 O B:GLY537 4.7 47.7 1.0 CB B:GLU330 4.7 36.4 1.0 NH2 B:ARG316 4.7 53.3 1.0 N B:CYS539 4.8 53.9 1.0 PA B:ADP3002 4.9 37.2 1.0 CE B:LYS498 5.0 29.4 1.0 CA B:ASN332 5.0 39.9 1.0

Magnesium binding site 4 out of 4 in the Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Glutathionylspermidine Synthetase/Amidase C59A Complex with Adp and Gsp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg7000 b:34.7 occ:1.00 OE2 B:GLU330 1.9 35.6 1.0 O B:HOH7002 2.0 34.4 1.0 O2A B:ADP3002 2.0 35.8 1.0 O3B B:ADP3002 2.0 35.7 1.0 OD2 B:ASP318 2.0 37.0 1.0 O B:HOH7001 2.0 32.9 1.0 PB B:ADP3002 3.0 33.3 1.0 CD B:GLU330 3.1 36.0 1.0 PA B:ADP3002 3.2 37.2 1.0 CG B:ASP318 3.2 39.4 1.0 MG B:MG6000 3.3 39.2 1.0 O3A B:ADP3002 3.3 34.9 1.0 O B:HOH6002 3.4 35.1 1.0 O2B B:ADP3002 3.4 36.7 1.0 CG B:GLU330 3.8 36.7 1.0 OD1 B:ASP318 4.0 39.5 1.0 OE1 B:GLU330 4.1 35.8 1.0 ND2 B:ASN332 4.2 43.1 1.0 CB B:ASP318 4.2 36.9 1.0 O1A B:ADP3002 4.2 32.5 1.0 O5' B:ADP3002 4.3 37.0 1.0 O3' B:ADP3002 4.3 42.1 1.0 O1B B:ADP3002 4.4 36.2 1.0 C5' B:ADP3002 4.4 40.1 1.0 NH2 B:ARG316 4.5 53.3 1.0 OD1 B:ASN332 4.5 38.8 1.0 O B:HOH8036 4.7 36.0 1.0 CG B:ASN332 4.8 40.1 1.0 C3' B:ADP3002 4.9 40.5 1.0 CB B:GLU330 5.0 36.4 1.0

C.-H.Pai, H.-J.Wu, C.-H.Lin, A.H.-J.Wang. Structure and Mechanism of Escherichia Coli Glutathionylspermidine Amidase Belonging to the Family of Cysteine; Histidine-Dependent Amidohydrolases/Peptidases Protein Sci. V. 20 557 2011.
ISSN: ISSN 0961-8368
PubMed: 21226054
DOI: 10.1002/PRO.589