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Magnesium in PDB 3ig8: Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp

Enzymatic activity of Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp

All present enzymatic activity of Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp:
6.3.2.2;

Protein crystallography data

The structure of Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp, PDB code: 3ig8 was solved by E.Biterova, J.J.Barycki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.90 / 2.69
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.849, 117.849, 164.444, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp (pdb code 3ig8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp, PDB code: 3ig8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3ig8

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Magnesium binding site 1 out of 3 in the Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg695

b:51.6
occ:1.00
OE1 A:GLU103 2.2 53.6 1.0
OE2 A:GLU52 2.2 44.5 1.0
OE2 A:GLU693 2.2 49.6 1.0
OE2 A:GLU96 2.2 47.8 1.0
CD A:GLU103 3.2 49.1 1.0
CD A:GLU96 3.3 43.8 1.0
CD A:GLU52 3.3 43.2 1.0
CD A:GLU693 3.3 46.1 1.0
MG A:MG697 3.4 48.4 1.0
O A:HOH808 3.7 60.8 1.0
O A:HOH705 3.7 35.7 1.0
OE1 A:GLN268 3.7 36.0 1.0
OE2 A:GLU103 3.7 49.9 1.0
CG A:GLU52 3.8 38.0 1.0
CG A:GLU96 3.8 41.1 1.0
OE1 A:GLU693 3.9 47.3 1.0
OE2 A:GLU50 3.9 45.7 1.0
OE1 A:GLU96 4.3 39.4 1.0
OE1 A:GLU52 4.3 43.8 1.0
CG A:GLU693 4.3 42.8 1.0
CG A:GLU103 4.4 42.8 1.0
CB A:GLU693 4.4 39.6 1.0
CD A:GLN268 4.5 31.4 1.0
NE2 A:GLN268 4.7 33.5 1.0
MG A:MG696 4.8 42.2 1.0
CD A:GLU50 4.8 40.8 1.0
O3B A:ADP694 4.8 56.8 1.0
CB A:GLU103 4.9 39.4 1.0
N A:GLU693 4.9 39.5 1.0

Magnesium binding site 2 out of 3 in 3ig8

Go back to Magnesium Binding Sites List in 3ig8
Magnesium binding site 2 out of 3 in the Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg696

b:42.2
occ:1.00
OE1 A:GLU50 2.2 39.7 1.0
O2B A:ADP694 2.2 54.2 1.0
OE2 A:GLU470 2.2 40.9 1.0
OE1 A:GLN268 2.2 36.0 1.0
CD A:GLU50 2.7 40.8 1.0
OE2 A:GLU50 2.8 45.7 1.0
CD A:GLN268 2.9 31.4 1.0
PB A:ADP694 3.2 61.0 1.0
CD A:GLU470 3.2 38.5 1.0
O3B A:ADP694 3.3 56.8 1.0
NE2 A:GLN268 3.4 33.5 1.0
OE1 A:GLU470 3.7 39.4 1.0
CG A:GLN268 4.0 30.7 1.0
O A:HOH805 4.1 34.3 1.0
CB A:GLN268 4.1 30.9 1.0
MG A:MG697 4.1 48.4 1.0
O A:HOH798 4.1 37.1 1.0
CG A:GLU50 4.2 36.9 1.0
NH1 A:ARG472 4.2 33.5 1.0
O1B A:ADP694 4.2 59.5 1.0
O3A A:ADP694 4.4 58.4 1.0
O A:HOH704 4.5 38.0 1.0
OE1 A:GLU693 4.5 47.3 1.0
CG A:GLU470 4.5 35.8 1.0
O2A A:ADP694 4.5 60.1 1.0
CB A:GLU50 4.6 33.9 1.0
MG A:MG695 4.8 51.6 1.0

Magnesium binding site 3 out of 3 in 3ig8

Go back to Magnesium Binding Sites List in 3ig8
Magnesium binding site 3 out of 3 in the Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Saccharomyces Cerevisiae Glutamate Cysteine Ligase in Complex with MG2+, L-Glutamate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg697

b:48.4
occ:1.00
OE2 A:GLU103 2.2 49.9 1.0
O3B A:ADP694 2.2 56.8 1.0
OE2 A:GLU50 2.2 45.7 1.0
O2A A:ADP694 2.7 60.1 1.0
O A:HOH808 2.9 60.8 1.0
CD A:GLU103 3.0 49.1 1.0
OE1 A:GLU103 3.1 53.6 1.0
MG A:MG695 3.4 51.6 1.0
CD A:GLU50 3.5 40.8 1.0
PB A:ADP694 3.5 61.0 1.0
PA A:ADP694 3.8 59.3 1.0
O3A A:ADP694 4.0 58.4 1.0
MG A:MG696 4.1 42.2 1.0
O2B A:ADP694 4.1 54.2 1.0
OE2 A:GLU96 4.2 47.8 1.0
CG A:GLU50 4.3 36.9 1.0
OE1 A:GLU50 4.4 39.7 1.0
CG A:GLU103 4.4 42.8 1.0
CD2 A:HIS94 4.6 49.4 1.0
OE1 A:GLN268 4.6 36.0 1.0
OE2 A:GLU693 4.7 49.6 1.0
O1A A:ADP694 4.7 57.2 1.0
O1B A:ADP694 4.7 59.5 1.0

Reference:

E.I.Biterova, J.J.Barycki. Mechanistic Details of Glutathione Biosynthesis Revealed By Crystal Structures of Saccharomyces Cerevisiae Glutamate Cysteine Ligase. J.Biol.Chem. V. 284 32700 2009.
ISSN: ISSN 0021-9258
PubMed: 19726687
DOI: 10.1074/JBC.M109.025114
Page generated: Mon Dec 14 08:16:56 2020

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