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Magnesium in PDB 3kal: Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound

Enzymatic activity of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound

All present enzymatic activity of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound:
6.3.2.23;

Protein crystallography data

The structure of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound, PDB code: 3kal was solved by A.Galant, K.A.J.Arkus, C.Zubieta, R.E.Cahoon, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.26 / 1.90
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 115.700, 115.700, 101.760, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 25

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound (pdb code 3kal). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound, PDB code: 3kal:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3kal

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Magnesium binding site 1 out of 6 in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:39.4
occ:1.00
 O2 A:SO4505 2.0 37.2 1.0
OE1 A:GLU392 2.1 33.5 1.0
OD1 A:ASN171 2.2 33.0 1.0
O3B A:ADP500 2.2 37.1 1.0
OE2 A:GLU169 2.3 35.1 1.0
OE1 A:GLU169 2.3 30.4 1.0
CD A:GLU169 2.6 33.7 1.0
CD A:GLU392 3.2 36.2 1.0
S A:SO4505 3.2 49.3 1.0
PB A:ADP500 3.3 32.7 1.0
CG A:ASN171 3.3 24.6 1.0
O1B A:ADP500 3.3 29.1 1.0
OE2 A:GLU392 3.6 40.4 1.0
O1 A:SO4505 3.6 29.3 1.0
MG A:MG503 3.8 27.7 1.0
ND2 A:ASN171 3.8 25.0 1.0
NZ A:LYS334 4.0 32.4 1.0
CG A:GLU169 4.0 25.7 1.0
O3 A:SO4505 4.2 41.9 1.0
MG A:MG504 4.2 36.8 1.0
CB2 A:HGS501 4.2 37.9 1.0
CA A:GLU392 4.2 36.6 1.0
O3A A:ADP500 4.3 34.0 1.0
O4 A:SO4505 4.3 46.4 1.0
O2B A:ADP500 4.3 29.6 1.0
CB A:GLU392 4.3 35.4 1.0
O A:HOH508 4.3 24.9 1.0
N A:GLY393 4.4 45.3 1.0
CG A:GLU392 4.4 28.1 1.0
CE A:LYS334 4.4 28.0 1.0
CB A:ASN171 4.6 29.4 1.0
O2A A:ADP500 4.7 29.6 1.0
C A:GLU392 4.8 39.5 1.0
CB A:GLU169 4.9 21.4 1.0
PA A:ADP500 5.0 33.6 1.0
CA A:ASN171 5.0 27.0 1.0
SG2 A:HGS501 5.0 48.6 1.0

Magnesium binding site 2 out of 6 in 3kal

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Magnesium binding site 2 out of 6 in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:27.7
occ:1.00
 O1B A:ADP500 2.1 29.1 1.0
O A:HOH588 2.1 25.5 1.0
O2A A:ADP500 2.1 29.6 1.0
O A:HOH710 2.1 32.5 1.0
OE2 A:GLU169 2.2 35.1 1.0
O1 A:SO4505 2.2 29.3 1.0
S A:SO4505 3.1 49.3 1.0
PB A:ADP500 3.2 32.7 1.0
CD A:GLU169 3.2 33.7 1.0
PA A:ADP500 3.2 33.6 1.0
O3A A:ADP500 3.5 34.0 1.0
O3 A:SO4505 3.7 41.9 1.0
CG A:GLU169 3.7 25.7 1.0
O2 A:SO4505 3.8 37.2 1.0
MG A:MG502 3.8 39.4 1.0
O3B A:ADP500 3.9 37.1 1.0
O5' A:ADP500 4.0 30.1 1.0
NH2 A:ARG475 4.1 45.8 1.0
C5' A:ADP500 4.1 31.4 1.0
OD2 A:ASP155 4.1 28.2 1.0
O3' A:ADP500 4.1 33.7 1.0
OE1 A:GLU169 4.2 30.4 1.0
OE2 A:GLU450 4.2 45.0 1.0
O2B A:ADP500 4.4 29.6 1.0
O4 A:SO4505 4.4 46.4 1.0
O1A A:ADP500 4.4 36.1 1.0
CZ A:ARG475 4.4 49.3 1.0
NH1 A:ARG475 4.5 49.6 1.0
C3' A:ADP500 4.5 29.1 1.0
ND2 A:ASN171 4.6 25.0 1.0
C4' A:ADP500 4.8 30.4 1.0
OD1 A:ASN171 4.8 33.0 1.0
OE1 A:GLU450 4.9 42.8 1.0
CB A:GLU169 5.0 21.4 1.0
CD A:GLU450 5.0 27.7 1.0

Magnesium binding site 3 out of 6 in 3kal

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Magnesium binding site 3 out of 6 in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:36.8
occ:1.00
 O A:MET170 2.1 28.9 1.0
O A:GLY332 2.2 32.2 1.0
OE2 A:GLU392 2.2 40.4 1.0
O A:HOH566 2.8 27.5 1.0
O A:HOH634 2.9 27.7 1.0
OE1 A:GLU169 3.1 30.4 1.0
CD A:GLU392 3.1 36.2 1.0
C A:GLY332 3.3 32.5 1.0
C A:MET170 3.3 25.9 1.0
OE1 A:GLU392 3.4 33.5 1.0
CA A:GLY332 3.8 29.5 1.0
CA A:ASN171 4.0 27.0 1.0
MG A:MG502 4.2 39.4 1.0
N A:ASN171 4.2 26.9 1.0
OD1 A:ASN171 4.2 33.0 1.0
O A:HOH681 4.2 28.8 1.0
N A:MET170 4.3 29.7 1.0
CD A:GLU169 4.3 33.7 1.0
CE A:LYS334 4.3 28.0 1.0
CA A:MET170 4.3 30.1 1.0
NZ A:LYS334 4.3 32.4 1.0
CD A:LYS334 4.4 31.8 1.0
O A:HOH647 4.4 36.5 1.0
N A:THR333 4.4 31.1 1.0
O A:HOH508 4.5 24.9 1.0
CG A:GLU392 4.5 28.1 1.0
O A:HOH654 4.6 36.8 1.0
CB A:GLU169 4.7 21.4 1.0
CG A:ASN171 4.7 24.6 1.0
N A:THR172 4.8 28.1 1.0
CA A:THR333 4.8 31.9 1.0
C A:THR333 4.9 30.4 1.0
CB A:MET170 4.9 29.4 1.0
CG A:GLU169 5.0 25.7 1.0
C A:ASN171 5.0 25.5 1.0

Magnesium binding site 4 out of 6 in 3kal

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Magnesium binding site 4 out of 6 in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:34.0
occ:1.00
 O2 B:SO4505 2.0 35.8 1.0
OE1 B:GLU392 2.1 32.3 1.0
OD1 B:ASN171 2.1 28.5 1.0
O3B B:ADP500 2.2 35.2 1.0
OE2 B:GLU169 2.3 35.7 1.0
OE1 B:GLU169 2.4 33.0 1.0
CD B:GLU169 2.7 33.4 1.0
CD B:GLU392 3.2 35.4 1.0
CG B:ASN171 3.2 27.9 1.0
S B:SO4505 3.2 45.4 1.0
PB B:ADP500 3.3 32.9 1.0
O1B B:ADP500 3.4 29.0 1.0
OE2 B:GLU392 3.7 41.8 1.0
O1 B:SO4505 3.7 31.4 1.0
MG B:MG503 3.8 29.9 1.0
ND2 B:ASN171 3.8 24.0 1.0
NZ B:LYS334 3.9 32.6 1.0
CG B:GLU169 4.1 23.1 1.0
O3 B:SO4505 4.2 39.0 1.0
CA B:GLU392 4.2 36.0 1.0
CB B:GLU392 4.3 33.7 1.0
CB2 B:HGS501 4.3 38.6 1.0
O3A B:ADP500 4.3 35.7 1.0
O B:HOH516 4.3 23.1 1.0
CG B:GLU392 4.4 31.7 1.0
O2B B:ADP500 4.4 27.3 1.0
O4 B:SO4505 4.4 42.9 1.0
N B:GLY393 4.5 43.8 1.0
CB B:ASN171 4.5 28.0 1.0
CE B:LYS334 4.7 30.8 1.0
O2A B:ADP500 4.7 31.2 1.0
C B:GLU392 4.8 39.4 1.0
CB B:GLU169 4.9 24.8 1.0
CA B:ASN171 4.9 27.1 1.0
CA2 B:HGS501 5.0 53.5 1.0

Magnesium binding site 5 out of 6 in 3kal

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Magnesium binding site 5 out of 6 in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:29.9
occ:1.00
 O B:HOH663 2.0 26.0 1.0
O1B B:ADP500 2.1 29.0 1.0
O1 B:SO4505 2.1 31.4 1.0
O2A B:ADP500 2.1 31.2 1.0
OE2 B:GLU169 2.2 35.7 1.0
O B:HOH627 2.2 30.4 1.0
S B:SO4505 3.1 45.4 1.0
PA B:ADP500 3.2 33.7 1.0
PB B:ADP500 3.2 32.9 1.0
CD B:GLU169 3.2 33.4 1.0
O3A B:ADP500 3.5 35.7 1.0
O3 B:SO4505 3.6 39.0 1.0
O2 B:SO4505 3.7 35.8 1.0
CG B:GLU169 3.7 23.1 1.0
MG B:MG502 3.8 34.0 1.0
O3B B:ADP500 3.9 35.2 1.0
OD2 B:ASP155 4.0 28.7 1.0
O3' B:ADP500 4.0 33.2 1.0
O5' B:ADP500 4.0 31.0 1.0
C5' B:ADP500 4.1 34.8 1.0
NH2 B:ARG475 4.2 41.9 1.0
OE1 B:GLU169 4.2 33.0 1.0
OE2 B:GLU450 4.4 44.1 1.0
NH1 B:ARG475 4.4 44.5 1.0
O B:HOH629 4.4 46.7 1.0
O1A B:ADP500 4.4 39.1 1.0
O2B B:ADP500 4.4 27.3 1.0
O4 B:SO4505 4.4 42.9 1.0
CZ B:ARG475 4.5 46.2 1.0
C3' B:ADP500 4.6 29.4 1.0
ND2 B:ASN171 4.6 24.0 1.0
OD1 B:ASN171 4.7 28.5 1.0
C4' B:ADP500 4.8 28.0 1.0
CB B:GLU169 5.0 24.8 1.0
NH2 B:ARG153 5.0 26.4 1.0

Magnesium binding site 6 out of 6 in 3kal

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Magnesium binding site 6 out of 6 in the Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Homoglutathione Synthetase From Glycine Max in Closed Conformation with Homoglutathione, Adp, A Sulfate Ion, and Three Magnesium Ions Bound within 5.0Å range:

Reference:

A.Galant, K.A.Arkus, C.Zubieta, R.E.Cahoon, J.M.Jez. Structural Basis For Evolution of Product Diversity in Soybean Glutathione Biosynthesis. Plant Cell V. 21 3450 2009.
ISSN: ISSN 1040-4651
PubMed: 19948790
DOI: 10.1105/TPC.109.071183
Page generated: Wed Aug 14 17:59:57 2024

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