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Magnesium in PDB 2io9: E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp

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

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

Protein crystallography data

The structure of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp, PDB code: 2io9 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 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.912, 75.480, 84.006, 70.44, 74.17, 78.06
R / Rfree (%) 17 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp (pdb code 2io9). 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+ ,Gsh and Adp, PDB code: 2io9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2io9

Go back to Magnesium Binding Sites List in 2io9
Magnesium binding site 1 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp


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+ ,Gsh and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7001

b:19.4
occ:1.00
 O A:HOH7625 2.0 19.1 1.0
OE2 A:GLU330 2.0 16.4 1.0
OD1 A:ASN332 2.0 16.5 1.0
O2B A:ADP3001 2.0 17.5 1.0
O A:HOH7624 2.0 13.6 1.0
OE1 A:GLU330 2.2 16.7 1.0
CD A:GLU330 2.3 17.0 1.0
CG A:ASN332 3.0 18.2 1.0
PB A:ADP3001 3.1 15.3 1.0
O A:HOH7626 3.2 17.7 1.0
O3B A:ADP3001 3.3 14.2 1.0
ND2 A:ASN332 3.4 17.3 1.0
MG A:MG7002 3.5 17.2 1.0
CG A:GLU330 3.8 17.5 1.0
NZ A:LYS498 3.9 20.1 1.0
O3A A:ADP3001 4.0 18.0 1.0
CA A:ARG538 4.0 23.2 1.0
N1 A:GSH5001 4.2 24.5 1.0
CB A:ARG538 4.3 27.0 1.0
O1B A:ADP3001 4.3 19.2 1.0
O A:HOH7068 4.3 27.4 1.0
CB A:ASN332 4.4 16.5 1.0
O A:GLY537 4.4 21.7 1.0
O A:HOH7442 4.5 40.8 1.0
OD2 A:ASP318 4.5 19.9 1.0
O A:HOH7069 4.5 16.4 1.0
N A:CYS539 4.6 22.0 1.0
CE A:LYS498 4.6 17.1 1.0
O2A A:ADP3001 4.6 16.3 1.0
O11 A:GSH5001 4.8 30.3 1.0
CB A:GLU330 4.8 15.9 1.0
C A:ARG538 4.8 22.9 1.0
PA A:ADP3001 4.9 17.2 1.0
CA A:ASN332 4.9 17.1 1.0
CA1 A:GSH5001 4.9 29.6 1.0
C1 A:GSH5001 4.9 29.5 1.0
O A:HOH7072 5.0 17.9 1.0

Magnesium binding site 2 out of 4 in 2io9

Go back to Magnesium Binding Sites List in 2io9
Magnesium binding site 2 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp


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+ ,Gsh and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7002

b:17.2
occ:1.00
 OD2 A:ASP318 2.0 19.9 1.0
O3B A:ADP3001 2.0 14.2 1.0
OE2 A:GLU330 2.0 16.4 1.0
O2A A:ADP3001 2.1 16.3 1.0
O A:HOH7627 2.1 15.8 1.0
O A:HOH7626 2.2 17.7 1.0
PB A:ADP3001 3.1 15.3 1.0
CD A:GLU330 3.1 17.0 1.0
CG A:ASP318 3.2 17.8 1.0
PA A:ADP3001 3.3 17.2 1.0
O A:HOH7625 3.4 19.1 1.0
O3A A:ADP3001 3.4 18.0 1.0
MG A:MG7001 3.5 19.4 1.0
O2B A:ADP3001 3.6 17.5 1.0
O A:HOH7145 3.7 16.2 1.0
CG A:GLU330 3.7 17.5 1.0
ND2 A:ASN332 3.9 17.3 1.0
N1 A:GSH5001 4.0 24.5 1.0
CB A:ASP318 4.1 15.5 1.0
OD1 A:ASP318 4.1 16.5 1.0
OE1 A:GLU330 4.2 16.7 1.0
O3' A:ADP3001 4.2 18.7 1.0
NH2 A:ARG316 4.3 17.5 1.0
C5' A:ADP3001 4.3 19.1 1.0
O5' A:ADP3001 4.3 19.5 1.0
O1A A:ADP3001 4.3 15.1 1.0
O1B A:ADP3001 4.4 19.2 1.0
O A:HOH7003 4.5 22.1 1.0
OD1 A:ASN332 4.5 16.5 1.0
CG A:ASN332 4.7 18.2 1.0
OE1 A:GLN582 4.7 21.6 1.0
O A:HOH7120 4.8 25.2 1.0
C3' A:ADP3001 4.8 20.2 1.0

Magnesium binding site 3 out of 4 in 2io9

Go back to Magnesium Binding Sites List in 2io9
Magnesium binding site 3 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp


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+ ,Gsh and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7003

b:21.4
occ:1.00
 O2B B:ADP3002 2.0 22.4 1.0
O B:HOH7613 2.0 20.2 1.0
OD1 B:ASN332 2.0 18.0 1.0
O B:HOH7612 2.0 20.1 1.0
OE1 B:GLU330 2.1 23.6 1.0
OE2 B:GLU330 2.2 21.8 1.0
CD B:GLU330 2.5 23.1 1.0
CG B:ASN332 3.0 17.2 1.0
O B:HOH7614 3.0 20.1 1.0
PB B:ADP3002 3.1 20.5 1.0
O3B B:ADP3002 3.4 20.2 1.0
ND2 B:ASN332 3.4 14.9 1.0
MG B:MG7004 3.5 21.8 1.0
O3A B:ADP3002 3.9 17.3 1.0
CA B:ARG538 4.0 28.7 1.0
CG B:GLU330 4.0 21.9 1.0
CB B:ARG538 4.1 31.1 1.0
NZ B:LYS498 4.1 17.6 1.0
N1 B:GSH5002 4.2 31.6 1.0
O1B B:ADP3002 4.3 20.9 1.0
O B:HOH7074 4.3 22.1 1.0
CB B:ASN332 4.4 17.3 1.0
O B:GLY537 4.4 28.0 1.0
O11 B:GSH5002 4.5 33.4 1.0
OD2 B:ASP318 4.5 18.9 1.0
O2A B:ADP3002 4.6 18.2 1.0
N B:CYS539 4.6 26.1 1.0
O B:HOH7172 4.7 36.9 1.0
CE B:LYS498 4.8 15.1 1.0
C1 B:GSH5002 4.8 32.3 1.0
PA B:ADP3002 4.8 21.8 1.0
CA1 B:GSH5002 4.8 31.7 1.0
C B:ARG538 4.9 26.9 1.0
CB B:GLU330 4.9 22.6 1.0
CA B:ASN332 5.0 20.0 1.0

Magnesium binding site 4 out of 4 in 2io9

Go back to Magnesium Binding Sites List in 2io9
Magnesium binding site 4 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ ,Gsh and Adp


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+ ,Gsh and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7004

b:21.8
occ:1.00
 OE2 B:GLU330 1.8 21.8 1.0
OD2 B:ASP318 1.9 18.9 1.0
O3B B:ADP3002 2.0 20.2 1.0
O2A B:ADP3002 2.0 18.2 1.0
O B:HOH7614 2.0 20.1 1.0
O B:HOH7615 2.1 20.6 1.0
CD B:GLU330 3.0 23.1 1.0
PB B:ADP3002 3.1 20.5 1.0
CG B:ASP318 3.2 22.4 1.0
PA B:ADP3002 3.2 21.8 1.0
O3A B:ADP3002 3.4 17.3 1.0
MG B:MG7003 3.5 21.4 1.0
O B:HOH7613 3.6 20.2 1.0
O2B B:ADP3002 3.6 22.4 1.0
O B:HOH7171 3.7 7.5 1.0
CG B:GLU330 3.7 21.9 1.0
ND2 B:ASN332 3.8 14.9 1.0
OE1 B:GLU330 3.9 23.6 1.0
CB B:ASP318 4.0 20.4 1.0
N1 B:GSH5002 4.0 31.6 1.0
OD1 B:ASP318 4.0 19.7 1.0
NH2 B:ARG316 4.2 26.2 1.0
O1A B:ADP3002 4.3 17.4 1.0
O3' B:ADP3002 4.3 21.3 1.0
O1B B:ADP3002 4.3 20.9 1.0
O5' B:ADP3002 4.3 22.9 1.0
C5' B:ADP3002 4.3 22.5 1.0
O B:HOH7062 4.5 28.3 1.0
OD1 B:ASN332 4.5 18.0 1.0
CG B:ASN332 4.6 17.2 1.0
O B:HOH7071 4.7 25.1 1.0
C3' B:ADP3002 4.8 23.4 1.0
NE2 B:GLN582 4.9 25.5 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 00:13:20 2024

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