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Magnesium in PDB 1m0w: Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions

Enzymatic activity of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions

All present enzymatic activity of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions:
6.3.2.3;

Protein crystallography data

The structure of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions, PDB code: 1m0w was solved by A.Gogos, L.Shapiro, S.K.Burley, New York Sgx Research Centerfor Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.661, 52.006, 100.636, 82.08, 86.77, 77.49
R / Rfree (%) 17.2 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions (pdb code 1m0w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions, PDB code: 1m0w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1m0w

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Magnesium binding site 1 out of 4 in the Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:21.1
occ:1.00
 OE1 A:GLU146 2.1 16.3 1.0
O2A A:ANP504 2.1 14.9 0.5
O A:HOH2603 2.2 18.5 1.0
O A:HOH2517 2.2 19.5 1.0
O2G A:ANP504 2.2 16.9 0.5
O A:HOH2585 2.2 15.9 1.0
O2A A:ANP504 2.3 24.1 0.5
O1B A:ANP504 2.4 24.8 0.5
CD A:GLU146 3.2 16.0 1.0
PA A:ANP504 3.4 24.0 0.5
PA A:ANP504 3.5 14.8 0.5
PG A:ANP504 3.6 17.6 0.5
PB A:ANP504 3.6 24.1 0.5
O3A A:ANP504 3.6 24.4 0.5
CG A:GLU146 3.8 14.5 1.0
O A:HOH2724 3.9 35.8 1.0
NH2 A:ARG467 3.9 12.0 0.5
O3A A:ANP504 4.0 15.9 0.5
MG A:MG503 4.1 30.7 1.0
O1G A:ANP504 4.1 17.3 0.5
OD1 A:ASP130 4.1 12.8 1.0
O3' A:ANP504 4.2 22.8 0.5
OD1 A:ASN148 4.2 16.5 1.0
O1B A:ANP504 4.2 15.4 0.5
OE2 A:GLU146 4.2 16.4 1.0
N3B A:ANP504 4.3 16.8 0.5
O3' A:ANP504 4.3 12.1 0.5
OE1 A:GLU442 4.3 19.2 1.0
O1A A:ANP504 4.4 23.7 0.5
O2B A:ANP504 4.4 24.5 0.5
O1A A:ANP504 4.4 14.5 0.5
PB A:ANP504 4.4 16.7 0.5
C5' A:ANP504 4.5 23.2 0.5
C5' A:ANP504 4.5 13.1 0.5
O5' A:ANP504 4.5 14.2 0.5
O5' A:ANP504 4.6 23.7 0.5
N3B A:ANP504 4.6 24.9 0.5
O3 A:3GC501 4.6 14.9 0.5
O3 A:3GC501 4.7 16.4 0.5
O3G A:ANP504 4.7 16.9 0.5
NH1 A:ARG467 4.7 11.4 0.5
C3' A:ANP504 4.8 23.0 0.5
CZ A:ARG467 4.8 12.8 0.5
C3' A:ANP504 4.8 12.3 0.5
O A:HOH2001 5.0 27.7 1.0

Magnesium binding site 2 out of 4 in 1m0w

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Magnesium binding site 2 out of 4 in the Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:30.7
occ:1.00
 O1G A:ANP504 2.2 17.3 0.5
O1B A:ANP504 2.2 15.4 0.5
OE2 A:GLU146 2.3 16.4 1.0
O A:HOH2001 2.3 27.7 1.0
OE1 A:GLU386 2.4 29.0 0.8
OE1 A:GLU146 2.4 16.3 1.0
CD A:GLU146 2.7 16.0 1.0
O2B A:ANP504 2.8 24.5 0.5
PG A:ANP504 3.1 17.6 0.5
CD A:GLU386 3.2 29.6 0.8
O1B A:ANP504 3.4 24.8 0.5
PB A:ANP504 3.4 16.7 0.5
N3B A:ANP504 3.4 16.8 0.5
O2G A:ANP504 3.5 16.9 0.5
PB A:ANP504 3.6 24.1 0.5
CG A:GLU386 3.8 30.4 0.8
O A:HOH2045 3.8 22.9 1.0
OD1 A:ASN148 3.8 16.5 1.0
O A:HOH2233 4.0 30.4 1.0
OE2 A:GLU386 4.0 28.6 0.8
NZ A:LYS324 4.0 21.4 1.0
MG A:MG502 4.1 21.1 1.0
O3A A:ANP504 4.2 24.4 0.5
CG A:GLU146 4.2 14.5 1.0
CB A:GLU386 4.3 31.4 0.8
O A:HOH2517 4.3 19.5 1.0
O3A A:ANP504 4.4 15.9 0.5
O2B A:ANP504 4.5 16.0 0.5
O3G A:ANP504 4.5 16.9 0.5
O2A A:ANP504 4.6 14.9 0.5
CE A:LYS324 4.7 22.1 1.0
O A:HOH2539 4.8 40.5 1.0
PA A:ANP504 4.9 14.8 0.5
O A:HOH2038 4.9 16.1 1.0
CG A:ASN148 4.9 14.9 1.0
O2A A:ANP504 4.9 24.1 0.5
O A:HOH2298 4.9 28.8 1.0
CB A:GLU146 4.9 13.5 1.0
O1A A:ANP504 5.0 14.5 0.5
PA A:ANP504 5.0 24.0 0.5

Magnesium binding site 3 out of 4 in 1m0w

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Magnesium binding site 3 out of 4 in the Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:20.8
occ:1.00
 OE1 B:GLU1146 2.2 18.0 1.0
O2A B:ANP1504 2.2 20.8 0.5
O B:HOH2674 2.2 22.4 1.0
O B:HOH2559 2.2 19.0 1.0
O B:HOH2673 2.2 17.9 1.0
O1B B:ANP1504 2.3 18.3 0.5
O2A B:ANP1504 2.3 16.0 0.5
O2G B:ANP1504 2.4 25.7 0.5
CD B:GLU1146 3.2 19.0 1.0
PA B:ANP1504 3.4 16.0 0.5
PA B:ANP1504 3.4 21.0 0.5
PB B:ANP1504 3.5 17.5 0.5
O3A B:ANP1504 3.5 17.0 0.5
PG B:ANP1504 3.7 25.6 0.5
CG B:GLU1146 3.7 17.0 1.0
O3A B:ANP1504 3.8 22.7 0.5
NH2 B:ARG1467 3.9 14.2 0.5
OD1 B:ASP1130 4.1 12.5 1.0
O2B B:ANP1504 4.2 18.1 0.5
O3' B:ANP1504 4.2 18.5 0.5
OE2 B:GLU1146 4.3 20.7 1.0
O3' B:ANP1504 4.3 14.0 0.5
MG B:MG1503 4.3 30.1 0.6
OD1 B:ASN1148 4.3 20.1 1.0
O1B B:ANP1504 4.3 23.9 0.5
O1G B:ANP1504 4.3 26.1 0.5
OE1 B:GLU1442 4.4 18.0 1.0
N3B B:ANP1504 4.4 25.2 0.5
C5' B:ANP1504 4.4 19.6 0.5
O1A B:ANP1504 4.4 15.6 0.5
O1A B:ANP1504 4.4 21.1 0.5
PB B:ANP1504 4.4 24.1 0.5
C5' B:ANP1504 4.4 14.6 0.5
O5' B:ANP1504 4.5 20.3 0.5
N3B B:ANP1504 4.5 18.3 0.5
O5' B:ANP1504 4.5 15.0 0.5
NH1 B:ARG1467 4.6 13.5 0.5
C3' B:ANP1504 4.7 18.6 0.5
CZ B:ARG1467 4.7 14.3 0.5
O3 B:3GC1501 4.8 12.6 0.5
C3' B:ANP1504 4.8 14.0 0.5
O3G B:ANP1504 4.8 25.4 0.5
O3 B:3GC1501 4.9 24.8 0.5
CG1 B:VAL1145 5.0 12.1 1.0

Magnesium binding site 4 out of 4 in 1m0w

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Magnesium binding site 4 out of 4 in the Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Glutathione Synthase Bound to Gamma-Glutamyl-Cysteine, Amp-Pnp and 2 Magnesium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1503

b:30.1
occ:0.60
 OE1 B:GLU1386 2.2 37.6 0.7
O1G B:ANP1504 2.2 26.1 0.5
O1B B:ANP1504 2.2 23.9 0.5
O B:HOH2732 2.3 31.9 0.7
OE2 B:GLU1146 2.5 20.7 1.0
OE1 B:GLU1146 2.7 18.0 1.0
O2B B:ANP1504 2.8 18.1 0.5
CD B:GLU1146 2.9 19.0 1.0
PG B:ANP1504 3.1 25.6 0.5
N3B B:ANP1504 3.2 25.2 0.5
CD B:GLU1386 3.2 37.9 0.7
PB B:ANP1504 3.3 24.1 0.5
O2G B:ANP1504 3.5 25.7 0.5
O B:HOH2244 3.7 26.6 1.0
O1B B:ANP1504 3.7 18.3 0.5
PB B:ANP1504 3.8 17.5 0.5
NZ B:LYS1324 3.8 24.8 1.0
O B:HOH2554 3.9 38.4 1.0
CB B:GLU1386 4.0 38.1 0.7
OD1 B:ASN1148 4.0 20.1 1.0
CG B:GLU1386 4.0 38.1 0.7
OE2 B:GLU1386 4.1 37.2 0.7
MG B:MG1502 4.3 20.8 1.0
O3A B:ANP1504 4.3 17.0 0.5
O3A B:ANP1504 4.3 22.7 0.5
CG B:GLU1146 4.4 17.0 1.0
O2B B:ANP1504 4.4 23.8 0.5
O B:HOH2674 4.5 22.4 1.0
O3G B:ANP1504 4.5 25.4 0.5
O2A B:ANP1504 4.8 20.8 0.5
PA B:ANP1504 5.0 21.0 0.5

Reference:

A.Gogos, L.Shapiro. Large Conformational Changes in the Catalytic Cycle of Glutathione Synthase Structure V. 10 1669 2002.
ISSN: ISSN 0969-2126
PubMed: 12467574
DOI: 10.1016/S0969-2126(02)00906-1
Page generated: Tue Aug 13 08:35:53 2024

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