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Magnesium in PDB 2ioa: E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor

Enzymatic activity of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor

All present enzymatic activity of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor:
3.5.1.78; 6.3.1.8;

Protein crystallography data

The structure of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor, PDB code: 2ioa was solved by C.H.Pai, B.Y.Chiang, T.P.Ko, C.C.Chou, C.M.Chong, F.J.Yen, J.K.Coward, A.H.-J.Wang, C.H.Lin, 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 (°) 60.030, 75.290, 84.660, 70.09, 74.06, 77.55
R / Rfree (%) 17.3 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor (pdb code 2ioa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor, PDB code: 2ioa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2ioa

Go back to Magnesium Binding Sites List in 2ioa
Magnesium binding site 1 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5001

b:8.0
occ:1.00
 O2B A:ADP3001 2.2 12.4 1.0
OD1 A:ASN332 2.2 9.2 1.0
O64 A:GGA6001 2.3 22.5 1.0
OE1 A:GLU330 2.5 13.3 1.0
OE2 A:GLU330 2.9 11.2 1.0
CD A:GLU330 3.0 13.7 1.0
CG A:ASN332 3.4 11.4 1.0
O A:HOH4016 3.5 15.5 1.0
P60 A:GGA6001 3.6 22.5 1.0
PB A:ADP3001 3.6 9.6 1.0
CB A:ARG538 3.7 19.3 1.0
CA A:ARG538 3.9 17.1 1.0
NZ A:LYS498 3.9 8.2 1.0
O A:HOH4296 4.0 12.7 1.0
O3B A:ADP3001 4.1 8.7 1.0
O A:GLY537 4.1 16.6 1.0
ND2 A:ASN332 4.2 11.1 1.0
C29 A:GGA6001 4.3 28.5 1.0
O62 A:GGA6001 4.3 25.0 1.0
O66 A:GGA6001 4.3 25.0 1.0
CG A:GLU330 4.4 14.1 1.0
O58 A:GGA6001 4.4 25.4 1.0
CB A:ASN332 4.5 12.0 1.0
O3A A:ADP3001 4.5 10.4 1.0
O1B A:ADP3001 4.5 9.8 1.0
MG A:MG5002 4.6 8.4 1.0
N A:CYS539 4.7 17.7 1.0
P34 A:GGA6001 4.8 25.8 1.0
N A:ARG538 4.8 17.4 1.0
C A:GLY537 4.8 15.8 1.0
C A:ARG538 4.9 16.7 1.0
CA A:ASN332 4.9 12.0 1.0

Magnesium binding site 2 out of 4 in 2ioa

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Magnesium binding site 2 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5002

b:8.4
occ:1.00
 O3B A:ADP3001 2.0 8.7 1.0
O2A A:ADP3001 2.0 1.0 1.0
OD2 A:ASP318 2.2 20.9 1.0
O66 A:GGA6001 2.2 25.0 1.0
OE2 A:GLU330 2.3 11.2 1.0
O A:HOH4190 3.0 10.6 1.0
PB A:ADP3001 3.2 9.6 1.0
PA A:ADP3001 3.2 7.6 1.0
CD A:GLU330 3.3 13.7 1.0
CG A:ASP318 3.4 17.6 1.0
O3A A:ADP3001 3.4 10.4 1.0
P60 A:GGA6001 3.5 22.5 1.0
O64 A:GGA6001 3.6 22.5 1.0
O2B A:ADP3001 3.7 12.4 1.0
C5' A:ADP3001 3.7 14.7 1.0
CG A:GLU330 3.9 14.1 1.0
O5' A:ADP3001 3.9 10.6 1.0
O3' A:ADP3001 4.0 16.6 1.0
OD1 A:ASP318 4.2 17.2 1.0
OE1 A:GLU330 4.3 13.3 1.0
O62 A:GGA6001 4.3 25.0 1.0
CB A:ASP318 4.3 14.8 1.0
C3' A:ADP3001 4.3 18.1 1.0
O1B A:ADP3001 4.4 9.8 1.0
O1A A:ADP3001 4.5 6.8 1.0
C4' A:ADP3001 4.5 18.7 1.0
O58 A:GGA6001 4.5 25.4 1.0
MG A:MG5001 4.6 8.0 1.0
ND2 A:ASN332 4.7 11.1 1.0
NE2 A:GLN582 4.8 21.5 1.0
NH2 A:ARG316 4.8 12.7 1.0
O A:HOH4241 5.0 17.4 1.0
OD1 A:ASN332 5.0 9.2 1.0

Magnesium binding site 3 out of 4 in 2ioa

Go back to Magnesium Binding Sites List in 2ioa
Magnesium binding site 3 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5003

b:10.5
occ:1.00
 O2B B:ADP3002 2.0 15.3 1.0
O64 B:GGA6002 2.1 26.7 1.0
OD1 B:ASN332 2.2 6.6 1.0
OE1 B:GLU330 2.4 19.9 1.0
OE2 B:GLU330 2.5 18.6 1.0
O B:HOH4024 2.5 27.2 1.0
CD B:GLU330 2.8 18.1 1.0
PB B:ADP3002 3.3 15.6 1.0
CG B:ASN332 3.3 9.3 1.0
P60 B:GGA6002 3.4 25.3 1.0
O3B B:ADP3002 3.7 17.9 1.0
CA B:ARG538 3.8 21.7 1.0
CB B:ARG538 3.8 22.3 1.0
O B:GLY537 3.9 22.0 1.0
ND2 B:ASN332 3.9 9.5 1.0
O66 B:GGA6002 4.1 24.6 1.0
NZ B:LYS498 4.1 22.6 1.0
O62 B:GGA6002 4.1 25.7 1.0
O58 B:GGA6002 4.2 25.6 1.0
O3A B:ADP3002 4.3 14.7 1.0
C29 B:GGA6002 4.3 29.3 1.0
MG B:MG5004 4.3 13.0 1.0
CG B:GLU330 4.3 19.1 1.0
O1B B:ADP3002 4.3 16.5 1.0
CB B:ASN332 4.6 11.0 1.0
C B:GLY537 4.6 21.7 1.0
N B:ARG538 4.6 22.2 1.0
N B:CYS539 4.6 21.9 1.0
P34 B:GGA6002 4.7 22.8 1.0
C B:ARG538 4.8 21.5 1.0

Magnesium binding site 4 out of 4 in 2ioa

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Magnesium binding site 4 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp and Phosphinate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5004

b:13.0
occ:1.00
 O66 B:GGA6002 2.0 24.6 1.0
O3B B:ADP3002 2.1 17.9 1.0
O2A B:ADP3002 2.2 6.7 1.0
OE2 B:GLU330 2.3 18.6 1.0
O B:HOH4293 2.3 28.3 1.0
OD2 B:ASP318 2.3 29.2 1.0
P60 B:GGA6002 3.2 25.3 1.0
CD B:GLU330 3.3 18.1 1.0
PB B:ADP3002 3.3 15.6 1.0
CG B:ASP318 3.4 25.9 1.0
O64 B:GGA6002 3.4 26.7 1.0
PA B:ADP3002 3.4 12.8 1.0
O3A B:ADP3002 3.7 14.7 1.0
CG B:GLU330 3.8 19.1 1.0
O2B B:ADP3002 3.9 15.3 1.0
O B:HOH4308 3.9 15.8 1.0
O3' B:ADP3002 4.1 19.8 1.0
OD1 B:ASP318 4.1 28.1 1.0
O62 B:GGA6002 4.2 25.7 1.0
NH2 B:ARG316 4.2 15.0 1.0
O58 B:GGA6002 4.3 25.6 1.0
CB B:ASP318 4.3 20.3 1.0
ND2 B:ASN332 4.3 9.5 1.0
MG B:MG5003 4.3 10.5 1.0
C5' B:ADP3002 4.3 18.9 1.0
O5' B:ADP3002 4.4 17.6 1.0
OE1 B:GLU330 4.4 19.9 1.0
O1B B:ADP3002 4.5 16.5 1.0
O1A B:ADP3002 4.6 15.5 1.0
C3' B:ADP3002 4.7 19.5 1.0
NE2 B:GLN582 4.7 35.4 1.0
OD1 B:ASN332 4.9 6.6 1.0
OE1 B:GLN582 4.9 37.0 1.0
C4' B:ADP3002 5.0 18.9 1.0

Reference:

C.H.Pai, B.Y.Chiang, T.P.Ko, C.C.Chou, C.M.Chong, F.J.Yen, S.Chen, J.K.Coward, A.H.-J.Wang, C.H.Lin. Dual Binding Sites For Translocation Catalysis By Escherichia Coli Glutathionylspermidine Synthetase Embo J. V. 25 5970 2006.
ISSN: ISSN 0261-4189
PubMed: 17124497
DOI: 10.1038/SJ.EMBOJ.7601440
Page generated: Wed Aug 14 00:13:38 2024

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