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Magnesium in PDB 1va6: Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue

Enzymatic activity of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue

All present enzymatic activity of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue:
6.3.2.2;

Protein crystallography data

The structure of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue, PDB code: 1va6 was solved by T.Hibi, H.Nii, T.Nakatsu, H.Kato, J.Hiratake, J.Oda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.468, 97.360, 102.185, 90.00, 109.63, 90.00
R / Rfree (%) 20 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue (pdb code 1va6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue, PDB code: 1va6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1va6

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Magnesium binding site 1 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg522

b:18.9
occ:1.00
 NS A:P2S520 2.0 15.4 1.0
OP1 A:P2S520 2.1 9.0 1.0
OE1 A:GLU67 2.2 20.4 1.0
OE2 A:GLU29 2.2 15.2 1.0
OD1 A:ASP60 2.2 15.5 1.0
O A:HOH571 2.5 36.7 1.0
P A:P2S520 2.6 15.1 1.0
CD A:GLU67 3.1 18.1 1.0
CG A:ASP60 3.3 14.9 1.0
OE2 A:GLU67 3.3 14.9 1.0
S A:P2S520 3.3 14.4 1.0
CD A:GLU29 3.3 17.1 1.0
OP3 A:P2S520 3.6 16.6 1.0
MG A:MG524 3.7 14.2 1.0
CG A:P2S520 3.8 19.1 1.0
O A:HOH544 3.9 37.6 1.0
OP2 A:P2S520 3.9 16.8 1.0
CD A:P2S520 3.9 18.7 1.0
CG A:GLU29 4.0 14.7 1.0
OD2 A:ASP60 4.0 18.2 1.0
OE1 A:GLU27 4.1 11.6 1.0
CB A:ASP60 4.2 17.4 1.0
O A:HOH705 4.2 43.1 1.0
CB A:P2S520 4.2 20.8 1.0
OE1 A:GLU29 4.3 13.7 1.0
CG A:GLU67 4.4 18.3 1.0
OS A:P2S520 4.6 14.2 1.0
CE1 A:HIS150 4.6 14.6 1.0
O A:HOH537 4.6 40.8 1.0
MG A:MG523 4.7 15.0 1.0
O1B A:ADP521 4.9 7.3 1.0
ND1 A:HIS150 4.9 9.6 1.0

Magnesium binding site 2 out of 8 in 1va6

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Magnesium binding site 2 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg523

b:15.0
occ:1.00
 ND1 A:HIS150 2.0 9.6 1.0
O3B A:ADP521 2.1 10.6 1.0
OP3 A:P2S520 2.1 16.6 1.0
OE1 A:GLU27 2.1 11.6 1.0
OE2 A:GLU328 2.2 8.0 1.0
OE2 A:GLU27 2.2 10.7 1.0
CD A:GLU27 2.4 12.4 1.0
CE1 A:HIS150 3.0 14.6 1.0
CG A:HIS150 3.1 14.9 1.0
CD A:GLU328 3.3 16.0 1.0
CB A:HIS150 3.5 10.7 1.0
P A:P2S520 3.5 15.1 1.0
PB A:ADP521 3.5 11.3 1.0
O A:HOH571 3.6 36.7 1.0
MG A:MG524 3.7 14.2 1.0
O1B A:ADP521 3.8 7.3 1.0
OP1 A:P2S520 3.9 9.0 1.0
CG A:GLU27 3.9 10.8 1.0
CG A:GLU328 3.9 12.3 1.0
NH1 A:ARG330 4.1 19.1 1.0
NE2 A:HIS150 4.1 9.6 1.0
CD2 A:HIS150 4.2 9.0 1.0
OE1 A:GLU328 4.2 8.2 1.0
O A:HOH538 4.3 35.2 1.0
NS A:P2S520 4.3 15.4 1.0
O2B A:ADP521 4.4 9.8 1.0
CB A:GLU27 4.4 10.2 1.0
O3A A:ADP521 4.7 12.3 1.0
NH2 A:ARG304 4.7 24.8 1.0
OP2 A:P2S520 4.7 16.8 1.0
MG A:MG522 4.7 18.9 1.0
O2A A:ADP521 4.8 6.4 1.0
O A:HOH537 4.9 40.8 1.0
NZ A:LYS306 4.9 28.1 1.0
CA A:HIS150 5.0 9.5 1.0
OE2 A:GLU67 5.0 14.9 1.0
CG A:ARG330 5.0 12.7 1.0

Magnesium binding site 3 out of 8 in 1va6

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Magnesium binding site 3 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg524

b:14.2
occ:1.00
 OE1 A:GLU27 2.1 11.6 1.0
O2A A:ADP521 2.1 6.4 1.0
OE2 A:GLU67 2.1 14.9 1.0
OP1 A:P2S520 2.2 9.0 1.0
O1B A:ADP521 2.2 7.3 1.0
O A:HOH705 2.2 43.1 1.0
PB A:ADP521 3.1 11.3 1.0
CD A:GLU27 3.1 12.4 1.0
CD A:GLU67 3.2 18.1 1.0
O3B A:ADP521 3.3 10.6 1.0
PA A:ADP521 3.4 12.8 1.0
P A:P2S520 3.4 15.1 1.0
OP3 A:P2S520 3.5 16.6 1.0
O A:HOH571 3.5 36.7 1.0
O3A A:ADP521 3.6 12.3 1.0
MG A:MG522 3.7 18.9 1.0
OE1 A:GLU67 3.7 20.4 1.0
MG A:MG523 3.7 15.0 1.0
O A:HOH584 3.8 43.1 1.0
CG A:GLU27 3.8 10.8 1.0
OE2 A:GLU27 4.0 10.7 1.0
O A:HOH544 4.1 37.6 1.0
O5' A:ADP521 4.3 10.9 1.0
O A:HOH693 4.3 61.1 1.0
OP2 A:P2S520 4.4 16.8 1.0
O1A A:ADP521 4.4 11.5 1.0
CB A:GLU27 4.4 10.2 1.0
O2B A:ADP521 4.4 9.8 1.0
CG A:GLU67 4.5 18.3 1.0
NS A:P2S520 4.5 15.4 1.0
CD1 A:ILE69 4.6 11.0 1.0
CG1 A:ILE69 4.9 9.4 1.0

Magnesium binding site 4 out of 8 in 1va6

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Magnesium binding site 4 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg525

b:15.0
occ:1.00
 O B:HOH1628 1.9 36.8 1.0
O B:HOH1643 2.0 29.0 1.0
O A:HOH696 2.1 48.9 1.0
OD1 A:ASP408 2.2 18.3 1.0
O A:HOH546 2.2 37.1 1.0
O A:HOH574 2.3 31.3 1.0
CG A:ASP408 3.2 13.3 1.0
OD2 A:ASP408 3.4 11.7 1.0
O A:HOH533 3.9 31.9 1.0
O A:HOH576 4.0 42.6 1.0
OD2 B:ASP487 4.1 10.3 1.0
OD1 B:ASP487 4.1 15.1 1.0
O A:ASP408 4.2 5.2 1.0
OD1 A:ASP412 4.2 5.8 1.0
OD2 A:ASP412 4.2 13.7 1.0
NE B:ARG484 4.3 26.5 1.0
O A:PRO3 4.3 22.7 1.0
NH2 A:ARG411 4.4 17.2 1.0
CB A:ASP408 4.5 9.9 1.0
O A:ILE2 4.5 12.1 1.0
CG B:ASP487 4.6 14.9 1.0
CG A:ASP412 4.6 10.1 1.0
C A:ASP408 4.7 6.8 1.0
CD B:ARG484 4.8 24.2 1.0
CA A:ASP408 4.8 5.3 1.0
CG2 A:ILE2 4.9 19.3 1.0
CB A:ILE2 4.9 21.7 1.0

Magnesium binding site 5 out of 8 in 1va6

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Magnesium binding site 5 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1522

b:21.9
occ:1.00
 NS B:P2S1520 2.0 20.2 1.0
OE2 B:GLU29 2.1 14.2 1.0
OP1 B:P2S1520 2.2 15.9 1.0
OD1 B:ASP60 2.2 19.1 1.0
OE1 B:GLU67 2.2 13.3 1.0
O B:HOH1657 2.2 52.4 1.0
P B:P2S1520 2.6 15.8 1.0
CD B:GLU67 3.1 14.7 1.0
CG B:ASP60 3.2 24.6 1.0
CD B:GLU29 3.3 12.9 1.0
S B:P2S1520 3.3 20.0 1.0
OE2 B:GLU67 3.4 9.0 1.0
OP3 B:P2S1520 3.6 13.3 1.0
MG B:MG1524 3.7 15.4 1.0
CG B:P2S1520 3.8 19.4 1.0
OD2 B:ASP60 3.8 21.4 1.0
CG B:GLU29 3.9 6.3 1.0
OP2 B:P2S1520 3.9 18.1 1.0
CD B:P2S1520 4.0 26.3 1.0
OE1 B:GLU27 4.1 9.6 1.0
CB B:ASP60 4.1 18.9 1.0
CB B:P2S1520 4.2 20.5 1.0
OE1 B:GLU29 4.3 19.4 1.0
O B:HOH1677 4.3 31.3 1.0
CG B:GLU67 4.4 9.8 1.0
OS B:P2S1520 4.5 14.6 1.0
O B:HOH1536 4.6 37.1 1.0
CE1 B:HIS150 4.8 13.7 1.0
MG B:MG1523 4.8 11.8 1.0
O1B B:ADP1521 4.9 11.3 1.0
ND1 B:HIS150 5.0 10.4 1.0

Magnesium binding site 6 out of 8 in 1va6

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Magnesium binding site 6 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1523

b:11.8
occ:1.00
 O3B B:ADP1521 2.0 18.6 1.0
ND1 B:HIS150 2.1 10.4 1.0
OP3 B:P2S1520 2.1 13.3 1.0
OE2 B:GLU27 2.1 6.3 1.0
OE2 B:GLU328 2.2 13.1 1.0
OE1 B:GLU27 2.2 9.6 1.0
CD B:GLU27 2.4 9.1 1.0
CE1 B:HIS150 3.0 13.7 1.0
CG B:HIS150 3.1 14.4 1.0
CD B:GLU328 3.3 16.6 1.0
CB B:HIS150 3.5 11.4 1.0
PB B:ADP1521 3.5 12.0 1.0
P B:P2S1520 3.6 15.8 1.0
O B:HOH1657 3.7 52.4 1.0
CG B:GLU27 3.9 8.0 1.0
MG B:MG1524 3.9 15.4 1.0
O1B B:ADP1521 4.0 11.3 1.0
CG B:GLU328 4.0 10.9 1.0
OP1 B:P2S1520 4.0 15.9 1.0
NH1 B:ARG330 4.0 17.7 1.0
NE2 B:HIS150 4.2 8.8 1.0
CD2 B:HIS150 4.2 7.0 1.0
OE1 B:GLU328 4.3 14.7 1.0
CB B:GLU27 4.4 10.0 1.0
NS B:P2S1520 4.4 20.2 1.0
O B:HOH1541 4.4 31.6 1.0
O2B B:ADP1521 4.4 10.7 1.0
O3A B:ADP1521 4.5 12.6 1.0
OP2 B:P2S1520 4.6 18.1 1.0
MG B:MG1522 4.8 21.9 1.0
NH2 B:ARG304 4.9 23.8 1.0
O B:HOH1536 4.9 37.1 1.0
O2A B:ADP1521 4.9 8.1 1.0
NZ B:LYS306 4.9 27.9 1.0
CG B:ARG330 5.0 11.2 1.0
CA B:HIS150 5.0 11.3 1.0

Magnesium binding site 7 out of 8 in 1va6

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Magnesium binding site 7 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1524

b:15.4
occ:1.00
 O B:HOH1677 2.0 31.3 1.0
OE1 B:GLU27 2.1 9.6 1.0
O2A B:ADP1521 2.2 8.1 1.0
O1B B:ADP1521 2.2 11.3 1.0
OE2 B:GLU67 2.2 9.0 1.0
OP1 B:P2S1520 2.2 15.9 1.0
PB B:ADP1521 3.1 12.0 1.0
CD B:GLU27 3.1 9.1 1.0
CD B:GLU67 3.2 14.7 1.0
O3B B:ADP1521 3.3 18.6 1.0
PA B:ADP1521 3.4 10.2 1.0
P B:P2S1520 3.4 15.8 1.0
OP3 B:P2S1520 3.6 13.3 1.0
O B:HOH1657 3.6 52.4 1.0
O3A B:ADP1521 3.6 12.6 1.0
OE1 B:GLU67 3.6 13.3 1.0
MG B:MG1522 3.7 21.9 1.0
CG B:GLU27 3.7 8.0 1.0
MG B:MG1523 3.9 11.8 1.0
O B:HOH1658 4.0 59.7 1.0
O B:HOH1661 4.0 69.8 1.0
OE2 B:GLU27 4.1 6.3 1.0
OP2 B:P2S1520 4.3 18.1 1.0
O1A B:ADP1521 4.3 16.7 1.0
O5' B:ADP1521 4.4 13.8 1.0
CD1 B:ILE69 4.4 13.7 1.0
O2B B:ADP1521 4.5 10.7 1.0
CG B:GLU67 4.5 9.8 1.0
NS B:P2S1520 4.5 20.2 1.0
CB B:GLU27 4.6 10.0 1.0
CG1 B:ILE69 4.7 13.4 1.0

Magnesium binding site 8 out of 8 in 1va6

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Magnesium binding site 8 out of 8 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Gamma-Glutamylcysteine Synthetase From Escherichia Coli B Complexed with Transition-State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1525

b:31.4
occ:1.00
 O B:HOH1664 1.8 61.2 1.0
O B:HOH1667 1.9 61.5 1.0
OD1 B:ASP408 2.1 32.0 1.0
O B:HOH1678 2.1 50.5 1.0
O B:HOH1666 2.3 59.8 1.0
CG B:ASP408 3.1 29.6 1.0
OD2 B:ASP408 3.3 31.9 1.0
O B:ASP408 4.3 23.1 1.0
OD2 B:ASP412 4.3 20.5 1.0
OD1 B:ASP412 4.4 27.4 1.0
NH2 B:ARG411 4.4 24.6 1.0
O B:ILE2 4.4 46.3 1.0
CB B:ASP408 4.4 25.9 1.0
O B:PRO3 4.4 48.0 1.0
C B:ASP408 4.6 23.4 1.0
CG B:ASP412 4.7 24.1 1.0
CG2 B:ILE2 4.7 40.9 1.0
CA B:ASP408 4.7 22.7 1.0

Reference:

T.Hibi, H.Nii, T.Nakatsu, A.Kimura, H.Kato, J.Hiratake, J.Oda. Crystal Structure of Gamma-Glutamylcysteine Synthetase: Insights Into the Mechanism of Catalysis By A Key Enzyme For Glutathione Homeostasis Proc.Natl.Acad.Sci.Usa V. 101 15052 2004.
ISSN: ISSN 0027-8424
PubMed: 15477603
DOI: 10.1073/PNAS.0403277101
Page generated: Tue Aug 13 15:02:02 2024

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