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Magnesium in PDB 2io7: E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Amppnp

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

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

Protein crystallography data

The structure of E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Amppnp, PDB code: 2io7 was solved by C.H.Pai, B.Y.Chiang, T.P.Ko, 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 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.010, 75.540, 84.060, 70.67, 74.36, 78.22
R / Rfree (%) 19.8 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Amppnp (pdb code 2io7). 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 Amppnp, PDB code: 2io7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2io7

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Magnesium binding site 1 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Amppnp


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 Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5001

b:1.0
occ:1.00
 OE1 A:GLU330 2.1 2.8 1.0
OD1 A:ASN332 2.2 1.5 1.0
O2B A:ANP964 2.3 3.7 1.0
O3G A:ANP964 2.3 4.5 1.0
CD A:GLU330 2.8 2.8 1.0
OE2 A:GLU330 3.0 2.8 1.0
CG A:ASN332 3.3 2.2 1.0
PG A:ANP964 3.4 4.0 1.0
PB A:ANP964 3.4 4.1 1.0
N3B A:ANP964 3.4 4.2 1.0
O A:GLY537 3.6 7.9 1.0
ND2 A:ASN332 3.8 1.4 1.0
NZ A:LYS498 3.9 1.8 1.0
O A:HOH5265 4.0 18.2 1.0
CA A:ARG538 4.0 12.4 1.0
CB A:ARG538 4.1 14.4 1.0
CG A:GLU330 4.1 2.9 1.0
O A:HOH5034 4.2 1.0 1.0
O2G A:ANP964 4.4 3.3 1.0
O1B A:ANP964 4.5 3.5 1.0
CB A:ASN332 4.5 3.4 1.0
O1G A:ANP964 4.6 5.0 1.0
C A:GLY537 4.6 8.8 1.0
O A:HOH5039 4.6 32.6 1.0
O3A A:ANP964 4.6 3.5 1.0
N A:ARG538 4.8 10.8 1.0
MG A:MG5002 4.8 1.0 1.0
CB A:GLU330 4.9 3.3 1.0
CA A:ASN332 5.0 4.1 1.0

Magnesium binding site 2 out of 4 in 2io7

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


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 Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5002

b:1.0
occ:1.00
 O2A A:ANP964 1.9 4.7 1.0
OE2 A:GLU330 2.2 2.8 1.0
OD2 A:ASP318 2.3 5.8 1.0
N3B A:ANP964 2.3 4.2 1.0
O2G A:ANP964 2.4 3.3 1.0
PG A:ANP964 2.9 4.0 1.0
O A:HOH5036 3.2 32.9 1.0
CD A:GLU330 3.3 2.8 1.0
CG A:ASP318 3.3 6.3 1.0
PA A:ANP964 3.3 4.1 1.0
PB A:ANP964 3.7 4.1 1.0
O3A A:ANP964 3.7 3.5 1.0
O1G A:ANP964 3.9 5.0 1.0
CG A:GLU330 4.0 2.9 1.0
O3G A:ANP964 4.0 4.5 1.0
OD1 A:ASP318 4.0 7.3 1.0
O3' A:ANP964 4.0 9.4 1.0
CB A:ASP318 4.1 5.8 1.0
OE1 A:GLU330 4.1 2.8 1.0
ND2 A:ASN332 4.1 1.4 1.0
O1A A:ANP964 4.2 3.9 1.0
NH1 A:ARG316 4.2 14.6 1.0
O5' A:ANP964 4.3 5.0 1.0
C5' A:ANP964 4.5 6.2 1.0
O2B A:ANP964 4.5 3.7 1.0
NE2 A:GLN582 4.6 16.8 1.0
O1B A:ANP964 4.7 3.5 1.0
OE1 A:GLN582 4.7 16.1 1.0
C3' A:ANP964 4.7 9.2 1.0
MG A:MG5001 4.8 1.0 1.0
OD1 A:ASN332 5.0 1.5 1.0

Magnesium binding site 3 out of 4 in 2io7

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Magnesium binding site 3 out of 4 in the E. Coli Bifunctional Glutathionylspermidine Synthetase/Amidase Incomplex with MG2+ and Amppnp


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 Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5003

b:1.1
occ:1.00
 OE1 B:GLU330 1.8 1.4 1.0
O2B B:ANP965 1.9 8.8 1.0
OD1 B:ASN332 2.3 2.0 1.0
CD B:GLU330 2.4 1.6 1.0
OE2 B:GLU330 2.4 1.4 1.0
O3G B:ANP965 2.5 7.1 1.0
PB B:ANP965 3.0 8.9 1.0
N3B B:ANP965 3.0 8.5 1.0
CG B:ASN332 3.3 2.8 1.0
PG B:ANP965 3.3 7.9 1.0
ND2 B:ASN332 3.6 2.0 1.0
NZ B:LYS498 3.8 1.0 1.0
CG B:GLU330 3.9 1.7 1.0
O B:GLY537 3.9 13.4 1.0
O3A B:ANP965 4.0 9.3 1.0
O1B B:ANP965 4.2 8.5 1.0
O2G B:ANP965 4.2 7.7 1.0
CA B:ARG538 4.3 18.1 1.0
CB B:ARG538 4.3 20.2 1.0
MG B:MG5004 4.4 2.0 1.0
O B:HOH5081 4.4 5.8 1.0
O1G B:ANP965 4.5 9.1 1.0
CB B:GLU330 4.5 2.3 1.0
O2A B:ANP965 4.6 10.7 1.0
CB B:ASN332 4.6 3.2 1.0
O B:HOH5330 4.6 15.9 1.0
PA B:ANP965 4.8 9.8 1.0
CE B:LYS498 4.8 1.0 1.0
C B:GLY537 4.9 13.8 1.0

Magnesium binding site 4 out of 4 in 2io7

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


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 Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5004

b:2.0
occ:1.00
 OD2 B:ASP318 1.8 9.9 1.0
O2A B:ANP965 2.0 10.7 1.0
OE2 B:GLU330 2.2 1.4 1.0
N3B B:ANP965 2.5 8.5 1.0
O2G B:ANP965 2.6 7.7 1.0
CG B:ASP318 2.9 9.7 1.0
PG B:ANP965 3.2 7.9 1.0
CD B:GLU330 3.2 1.6 1.0
PA B:ANP965 3.4 9.8 1.0
CG B:GLU330 3.6 1.7 1.0
CB B:ASP318 3.8 9.2 1.0
OD1 B:ASP318 3.8 10.7 1.0
PB B:ANP965 3.9 8.9 1.0
O3A B:ANP965 4.0 9.3 1.0
O3' B:ANP965 4.0 14.1 1.0
ND2 B:ASN332 4.1 2.0 1.0
O1G B:ANP965 4.1 9.1 1.0
NE2 B:GLN582 4.2 24.3 1.0
NH1 B:ARG316 4.2 14.5 1.0
O3G B:ANP965 4.3 7.1 1.0
OE1 B:GLN582 4.3 25.1 1.0
OE1 B:GLU330 4.3 1.4 1.0
O1A B:ANP965 4.4 9.5 1.0
MG B:MG5003 4.4 1.1 1.0
O5' B:ANP965 4.5 10.8 1.0
C5' B:ANP965 4.6 12.2 1.0
C3' B:ANP965 4.6 14.0 1.0
O2B B:ANP965 4.6 8.8 1.0
CD B:GLN582 4.7 23.4 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 00:13:07 2024

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