Atomistry » Magnesium » PDB 2iec-2ivn » 2io8
Atomistry »
  Magnesium »
    PDB 2iec-2ivn »
      2io8 »

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

Go back to Magnesium Binding Sites List in 2io8
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

Go back to Magnesium Binding Sites List in 2io8
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

Go back to Magnesium Binding Sites List in 2io8
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

Go back to Magnesium Binding Sites List in 2io8
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: Wed Aug 14 00:13:12 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy