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Magnesium in PDB 2io8: E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp

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

All present enzymatic activity of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ 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+ and Adp, PDB code: 2io8 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 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.200, 75.610, 84.440, 70.17, 73.92, 77.77
R / Rfree (%) 17.3 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Adp (pdb code 2io8). 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, PDB code: 2io8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2io8

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Magnesium binding site 1 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ 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+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7001

b:16.3
occ:1.00
 O A:HOH4001 1.9 9.8 1.0
O A:HOH4002 1.9 15.0 1.0
O2B A:ADP5001 2.0 16.3 1.0
OE1 A:GLU330 2.0 13.0 1.0
OD1 A:ASN332 2.1 15.3 1.0
OE2 A:GLU330 2.2 17.6 1.0
CD A:GLU330 2.4 13.8 1.0
CG A:ASN332 3.2 16.6 1.0
PB A:ADP5001 3.2 15.2 1.0
O3B A:ADP5001 3.6 10.9 1.0
ND2 A:ASN332 3.6 19.4 1.0
NZ A:LYS498 3.7 16.5 1.0
O A:HOH4003 3.7 19.6 1.0
MG A:MG7002 3.8 16.4 1.0
O3A A:ADP5001 4.0 17.6 1.0
CG A:GLU330 4.0 14.4 1.0
CA A:ARG538 4.2 25.2 1.0
O A:HOH3646 4.2 50.4 1.0
O A:HOH3447 4.3 38.3 1.0
O A:GLY537 4.3 22.6 1.0
O A:HOH3073 4.4 25.7 1.0
O1B A:ADP5001 4.4 17.9 1.0
CE A:LYS498 4.5 17.4 1.0
CB A:ASN332 4.5 16.4 1.0
CB A:ARG538 4.6 26.8 1.0
N A:CYS539 4.7 23.4 1.0
O2A A:ADP5001 4.7 14.6 1.0
OD2 A:ASP318 4.8 21.4 1.0
CB A:GLU330 4.9 17.1 1.0
PA A:ADP5001 4.9 17.2 1.0
C A:ARG538 4.9 24.7 1.0
CA A:ASN332 5.0 18.0 1.0

Magnesium binding site 2 out of 4 in 2io8

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Magnesium binding site 2 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ 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+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg7002

b:16.4
occ:1.00
 OD2 A:ASP318 1.9 21.4 1.0
O2A A:ADP5001 2.0 14.6 1.0
O A:HOH4004 2.0 16.9 1.0
OE2 A:GLU330 2.1 17.6 1.0
O3B A:ADP5001 2.1 10.9 1.0
O A:HOH4003 2.2 19.6 1.0
CD A:GLU330 3.2 13.8 1.0
CG A:ASP318 3.2 24.1 1.0
PA A:ADP5001 3.2 17.2 1.0
PB A:ADP5001 3.2 15.2 1.0
O3A A:ADP5001 3.5 17.6 1.0
O A:HOH4002 3.6 15.0 1.0
O A:HOH3027 3.6 23.7 1.0
CG A:GLU330 3.7 14.4 1.0
O2B A:ADP5001 3.7 16.3 1.0
MG A:MG7001 3.8 16.3 1.0
ND2 A:ASN332 4.0 19.4 1.0
CB A:ASP318 4.1 17.6 1.0
OD1 A:ASP318 4.1 24.8 1.0
O A:HOH3119 4.1 33.0 1.0
OE1 A:GLU330 4.2 13.0 1.0
C5' A:ADP5001 4.2 19.6 1.0
O5' A:ADP5001 4.2 20.6 1.0
O3' A:ADP5001 4.3 17.5 1.0
O1A A:ADP5001 4.3 16.9 1.0
O1B A:ADP5001 4.5 17.9 1.0
NH1 A:ARG316 4.5 36.5 1.0
O A:HOH3910 4.5 50.1 1.0
OE1 A:GLN582 4.6 21.5 1.0
OD1 A:ASN332 4.7 15.3 1.0
C3' A:ADP5001 4.8 17.2 1.0
CG A:ASN332 4.8 16.6 1.0
C4' A:ADP5001 5.0 18.7 1.0

Magnesium binding site 3 out of 4 in 2io8

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Magnesium binding site 3 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ 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+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7003

b:17.6
occ:1.00
 O B:HOH4005 2.0 17.0 1.0
O2B B:ADP5002 2.0 18.8 1.0
OE1 B:GLU330 2.0 17.8 1.0
O B:HOH4006 2.1 18.4 1.0
OE2 B:GLU330 2.1 21.4 1.0
OD1 B:ASN332 2.1 11.0 1.0
CD B:GLU330 2.4 18.9 1.0
CG B:ASN332 3.1 15.4 1.0
PB B:ADP5002 3.1 18.0 1.0
ND2 B:ASN332 3.4 13.8 1.0
O3B B:ADP5002 3.4 17.8 1.0
O B:HOH4007 3.5 19.7 1.0
MG B:MG7004 3.6 20.5 1.0
NZ B:LYS498 3.8 17.4 1.0
O3A B:ADP5002 3.9 16.0 1.0
CG B:GLU330 3.9 17.9 1.0
CA B:ARG538 4.3 29.7 1.0
CB B:ARG538 4.3 32.8 1.0
O1B B:ADP5002 4.3 20.1 1.0
O B:GLY537 4.4 25.2 1.0
CB B:ASN332 4.5 14.8 1.0
O2A B:ADP5002 4.5 14.5 1.0
OD2 B:ASP318 4.5 23.8 1.0
O B:HOH3911 4.5 32.2 1.0
PA B:ADP5002 4.7 17.3 1.0
CB B:GLU330 4.8 18.5 1.0
O B:HOH3104 4.9 28.4 1.0
N B:CYS539 4.9 28.2 1.0
O B:HOH3307 4.9 50.8 1.0
CA B:ASN332 5.0 20.6 1.0
CE B:LYS498 5.0 19.2 1.0

Magnesium binding site 4 out of 4 in 2io8

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Magnesium binding site 4 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ 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+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg7004

b:20.5
occ:1.00
 OD2 B:ASP318 1.9 23.8 1.0
O3B B:ADP5002 2.0 17.8 1.0
OE2 B:GLU330 2.1 21.4 1.0
O B:HOH4007 2.1 19.7 1.0
O B:HOH4008 2.1 22.2 1.0
O2A B:ADP5002 2.1 14.5 1.0
CG B:ASP318 3.1 24.1 1.0
PB B:ADP5002 3.2 18.0 1.0
CD B:GLU330 3.2 18.9 1.0
PA B:ADP5002 3.3 17.3 1.0
O B:HOH3100 3.3 26.8 1.0
O B:HOH4006 3.6 18.4 1.0
O3A B:ADP5002 3.6 16.0 1.0
MG B:MG7003 3.6 17.6 1.0
O2B B:ADP5002 3.7 18.8 1.0
OD1 B:ASP318 3.8 26.5 1.0
CG B:GLU330 3.9 17.9 1.0
ND2 B:ASN332 4.0 13.8 1.0
NH1 B:ARG316 4.1 32.3 1.0
CB B:ASP318 4.2 20.5 1.0
OE1 B:GLU330 4.2 17.8 1.0
O3' B:ADP5002 4.3 21.2 1.0
O5' B:ADP5002 4.4 18.6 1.0
C5' B:ADP5002 4.4 20.0 1.0
O B:HOH3685 4.4 40.0 1.0
O B:HOH3911 4.4 32.2 1.0
O1B B:ADP5002 4.5 20.1 1.0
O1A B:ADP5002 4.5 16.1 1.0
O B:HOH3329 4.5 39.0 1.0
NE2 B:GLN582 4.6 24.9 1.0
OD1 B:ASN332 4.7 11.0 1.0
CG B:ASN332 4.8 15.4 1.0
C3' B:ADP5002 4.9 21.9 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: Sun Aug 10 11:38:02 2025

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