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Magnesium in PDB 2d33: Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride

Enzymatic activity of Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride

All present enzymatic activity of Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride:
6.3.2.2;

Protein crystallography data

The structure of Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride, PDB code: 2d33 was solved by T.Hibi, M.Nakayama, H.Nii, Y.Kurokawa, H.Katano, J.Oda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 325.226, 325.226, 105.181, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 19.1

Other elements in 2d33:

The structure of Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Aluminium (Al) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride (pdb code 2d33). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride, PDB code: 2d33:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 2d33

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Magnesium binding site 1 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg523

b:40.9
occ:1.00
 O A:HOH700 2.0 43.0 1.0
F1 A:AF3522 2.2 52.0 1.0
OE2 A:GLU519 2.3 71.5 1.0
OE1 A:GLU67 2.4 34.9 1.0
OD1 A:ASP60 2.4 37.3 1.0
OE2 A:GLU29 2.7 32.5 1.0
AL A:AF3522 3.0 55.6 1.0
CD A:GLU67 3.0 32.0 1.0
MG A:MG525 3.2 26.8 1.0
CD A:GLU519 3.3 71.2 1.0
OE2 A:GLU67 3.4 34.2 1.0
CG A:ASP60 3.4 35.4 1.0
F3 A:AF3522 3.5 49.7 1.0
CG A:GLU519 3.8 70.4 1.0
CD A:GLU29 3.8 30.9 1.0
N A:CYS520 4.0 52.9 1.0
OE1 A:GLU27 4.1 30.1 1.0
CG A:GLU67 4.1 30.2 1.0
CE1 A:HIS150 4.2 25.5 1.0
CB A:ASP60 4.2 32.2 1.0
CG A:GLU29 4.2 27.5 1.0
OD2 A:ASP60 4.2 37.0 1.0
OE1 A:GLU519 4.4 71.4 1.0
F2 A:AF3522 4.5 51.6 1.0
O A:HOH560 4.5 25.1 1.0
O1B A:ADP521 4.5 33.9 1.0
MG A:MG524 4.5 34.6 1.0
ND1 A:HIS150 4.7 26.6 1.0
CB A:GLU519 4.8 69.8 1.0
OE1 A:GLU29 4.9 28.5 1.0
CB A:GLU67 4.9 24.9 1.0
CA A:ASP60 5.0 28.7 1.0

Magnesium binding site 2 out of 13 in 2d33

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Magnesium binding site 2 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg524

b:34.6
occ:1.00
 OE2 A:GLU328 2.1 34.6 1.0
O3B A:ADP521 2.2 30.9 1.0
OE2 A:GLU27 2.2 30.1 1.0
ND1 A:HIS150 2.3 26.6 1.0
F3 A:AF3522 2.4 49.7 1.0
OE1 A:GLU27 2.5 30.1 1.0
CD A:GLU27 2.7 30.1 1.0
CE1 A:HIS150 2.8 25.5 1.0
PB A:ADP521 3.0 33.3 1.0
O1B A:ADP521 3.1 33.9 1.0
CD A:GLU328 3.3 34.1 1.0
CG A:HIS150 3.5 25.9 1.0
MG A:MG525 3.7 26.8 1.0
AL A:AF3522 3.7 55.6 1.0
OE1 A:GLU328 4.0 36.0 1.0
O2B A:ADP521 4.0 33.8 1.0
NH2 A:ARG330 4.0 46.0 1.0
NE2 A:HIS150 4.0 25.1 1.0
CB A:HIS150 4.2 24.5 1.0
CG A:GLU27 4.2 28.8 1.0
O A:HOH700 4.2 43.0 1.0
OE2 A:GLU519 4.3 71.5 1.0
NE A:ARG330 4.3 46.0 1.0
O3A A:ADP521 4.3 32.5 1.0
CD2 A:HIS150 4.4 25.2 1.0
CG A:GLU328 4.4 32.4 1.0
CZ A:ARG330 4.5 45.8 1.0
MG A:MG523 4.5 40.9 1.0
O A:HOH546 4.6 29.6 1.0
O2A A:ADP521 4.6 34.5 1.0
F2 A:AF3522 4.9 51.6 1.0
CB A:GLU27 4.9 25.4 1.0
CD A:GLU519 4.9 71.2 1.0
PA A:ADP521 4.9 34.8 1.0
OE1 A:GLU519 5.0 71.4 1.0

Magnesium binding site 3 out of 13 in 2d33

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Magnesium binding site 3 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg525

b:26.8
occ:1.00
 O1B A:ADP521 2.1 33.9 1.0
OE2 A:GLU67 2.1 34.2 1.0
OE1 A:GLU27 2.2 30.1 1.0
O A:HOH560 2.3 25.1 1.0
O2A A:ADP521 2.3 34.5 1.0
AL A:AF3522 2.5 55.6 1.0
F1 A:AF3522 2.8 52.0 1.0
CD A:GLU67 2.9 32.0 1.0
OE1 A:GLU67 3.1 34.9 1.0
MG A:MG523 3.2 40.9 1.0
F3 A:AF3522 3.3 49.7 1.0
PB A:ADP521 3.4 33.3 1.0
CD A:GLU27 3.4 30.1 1.0
F2 A:AF3522 3.5 51.6 1.0
PA A:ADP521 3.6 34.8 1.0
MG A:MG524 3.7 34.6 1.0
O A:HOH700 3.9 43.0 1.0
O3A A:ADP521 3.9 32.5 1.0
O3B A:ADP521 4.0 30.9 1.0
CG A:GLU27 4.3 28.8 1.0
OE2 A:GLU27 4.3 30.1 1.0
CG A:GLU67 4.4 30.2 1.0
CD1 A:ILE69 4.4 19.9 1.0
O2B A:ADP521 4.5 33.8 1.0
OE2 A:GLU519 4.5 71.5 1.0
O5' A:ADP521 4.6 35.6 1.0
CB A:GLU27 4.6 25.4 1.0
O1A A:ADP521 4.7 35.6 1.0
CG1 A:ILE69 4.9 20.1 1.0
ND1 A:HIS150 5.0 26.6 1.0
OD1 A:ASP60 5.0 37.3 1.0

Magnesium binding site 4 out of 13 in 2d33

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Magnesium binding site 4 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg526

b:44.1
occ:1.00
 OD1 A:ASN442 2.3 28.5 1.0
OD2 A:ASP444 2.3 27.7 1.0
O A:HOH601 2.4 20.7 1.0
O A:HOH586 2.5 21.9 1.0
CG A:ASN442 3.1 27.5 1.0
CG A:ASP444 3.3 27.3 1.0
ND2 A:ASN442 3.4 25.8 1.0
O A:HOH606 3.6 35.1 1.0
CB A:ASP444 3.6 24.1 1.0
O A:HOH636 4.0 31.5 1.0
N A:ASP444 4.3 22.5 1.0
CB A:ASN442 4.4 26.2 1.0
OD1 A:ASP444 4.5 27.8 1.0
CA A:ASP444 4.6 23.3 1.0
CA A:ASN442 4.7 27.4 1.0
O A:HOH672 4.8 46.7 1.0
CD A:PRO443 4.8 23.8 1.0

Magnesium binding site 5 out of 13 in 2d33

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Magnesium binding site 5 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1523

b:45.8
occ:1.00
 F1 B:AF31522 2.1 58.0 1.0
OE2 B:GLU1519 2.1 51.0 1.0
OE2 B:GLU29 2.2 41.5 1.0
O B:HOH1591 2.2 47.7 1.0
OD1 B:ASP60 2.2 43.1 1.0
OE1 B:GLU67 2.3 38.7 1.0
CG B:ASP60 3.1 42.4 1.0
AL B:AF31522 3.1 60.7 1.0
CD B:GLU1519 3.2 51.1 1.0
CD B:GLU29 3.3 41.2 1.0
CD B:GLU67 3.3 38.1 1.0
OE2 B:GLU67 3.7 39.8 1.0
MG B:MG1525 3.7 37.8 1.0
CG B:GLU1519 3.7 51.3 1.0
OD2 B:ASP60 3.8 43.5 1.0
CG B:GLU29 3.9 38.6 1.0
F3 B:AF31522 3.9 58.3 1.0
CB B:ASP60 4.0 40.7 1.0
N B:CYS1520 4.0 48.0 1.0
OE1 B:GLU27 4.1 36.7 1.0
CB B:GLU1519 4.1 52.6 1.0
OE1 B:GLU1519 4.2 50.0 1.0
F2 B:AF31522 4.2 59.6 1.0
OE1 B:GLU29 4.4 41.5 1.0
CE1 B:HIS150 4.5 31.1 1.0
O B:HOH1588 4.5 52.8 1.0
CG B:GLU67 4.6 37.5 1.0
MG B:MG1524 4.7 36.4 1.0
O B:HOH1589 4.7 44.1 1.0
O1B B:ADP1521 4.8 38.8 1.0
ND1 B:HIS150 4.9 30.3 1.0
CA B:ASP60 4.9 39.4 1.0
CB B:GLU67 5.0 35.1 1.0

Magnesium binding site 6 out of 13 in 2d33

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Magnesium binding site 6 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1524

b:36.4
occ:1.00
 OE2 B:GLU328 2.1 37.8 1.0
OE2 B:GLU27 2.1 35.6 1.0
O3B B:ADP1521 2.1 37.7 1.0
ND1 B:HIS150 2.2 30.3 1.0
F3 B:AF31522 2.3 58.3 1.0
OE1 B:GLU27 2.4 36.7 1.0
CD B:GLU27 2.6 35.6 1.0
CE1 B:HIS150 2.8 31.1 1.0
PB B:ADP1521 3.3 36.7 1.0
CD B:GLU328 3.3 36.9 1.0
AL B:AF31522 3.3 60.7 1.0
CG B:HIS150 3.4 30.4 1.0
O1B B:ADP1521 3.4 38.8 1.0
O B:HOH1591 3.6 47.7 1.0
MG B:MG1525 3.8 37.8 1.0
NH1 B:ARG330 3.9 36.1 1.0
OE2 B:GLU1519 4.0 51.0 1.0
CB B:HIS150 4.0 31.1 1.0
NE2 B:HIS150 4.0 32.2 1.0
OE1 B:GLU328 4.1 37.7 1.0
F1 B:AF31522 4.1 58.0 1.0
CG B:GLU27 4.1 35.2 1.0
O B:HOH1541 4.2 42.7 1.0
O2B B:ADP1521 4.3 37.2 1.0
CG B:GLU328 4.3 35.9 1.0
CD2 B:HIS150 4.3 31.5 1.0
O2A B:ADP1521 4.4 37.3 1.0
O3A B:ADP1521 4.5 36.3 1.0
MG B:MG1523 4.7 45.8 1.0
F2 B:AF31522 4.7 59.6 1.0
CB B:GLU27 4.7 33.6 1.0
CD B:GLU1519 4.8 51.1 1.0
OE1 B:GLU1519 4.8 50.0 1.0

Magnesium binding site 7 out of 13 in 2d33

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Magnesium binding site 7 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1525

b:37.8
occ:1.00
 F1 B:AF31522 1.8 58.0 1.0
O2A B:ADP1521 2.0 37.3 1.0
OE1 B:GLU27 2.0 36.7 1.0
O1B B:ADP1521 2.1 38.8 1.0
OE2 B:GLU67 2.2 39.8 1.0
O B:HOH1589 2.4 44.1 1.0
AL B:AF31522 2.6 60.7 1.0
CD B:GLU27 3.1 35.6 1.0
CD B:GLU67 3.1 38.1 1.0
PA B:ADP1521 3.3 37.2 1.0
PB B:ADP1521 3.3 36.7 1.0
OE1 B:GLU67 3.4 38.7 1.0
F2 B:AF31522 3.4 59.6 1.0
O B:HOH1591 3.6 47.7 1.0
MG B:MG1523 3.7 45.8 1.0
O3A B:ADP1521 3.7 36.3 1.0
O3B B:ADP1521 3.7 37.7 1.0
F3 B:AF31522 3.8 58.3 1.0
MG B:MG1524 3.8 36.4 1.0
CG B:GLU27 3.9 35.2 1.0
OE2 B:GLU27 4.0 35.6 1.0
O1A B:ADP1521 4.3 37.8 1.0
CD1 B:ILE69 4.3 34.5 1.0
O5' B:ADP1521 4.3 37.5 1.0
CB B:GLU27 4.4 33.6 1.0
CG B:GLU67 4.5 37.5 1.0
CG1 B:ILE69 4.5 34.8 1.0
O2B B:ADP1521 4.6 37.2 1.0
OE2 B:GLU1519 4.6 51.0 1.0

Magnesium binding site 8 out of 13 in 2d33

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Magnesium binding site 8 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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 Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2523

b:46.3
occ:1.00
 O C:HOH2552 2.1 46.4 1.0
OE1 C:GLU67 2.2 45.0 1.0
OE2 C:GLU2519 2.2 67.2 1.0
OD1 C:ASP60 2.2 49.9 1.0
F1 C:AF32522 2.2 59.9 1.0
OE2 C:GLU29 2.3 46.3 1.0
CD C:GLU67 3.0 43.5 1.0
CG C:ASP60 3.2 49.9 1.0
AL C:AF32522 3.2 62.6 1.0
OE2 C:GLU67 3.3 44.1 1.0
CD C:GLU2519 3.3 67.6 1.0
CD C:GLU29 3.4 46.6 1.0
MG C:MG2525 3.7 45.8 1.0
CG C:GLU29 4.0 45.2 1.0
OD2 C:ASP60 4.0 50.2 1.0
CB C:ASP60 4.0 49.1 1.0
CG C:GLU2519 4.0 68.0 1.0
F3 C:AF32522 4.1 60.2 1.0
N C:CYS2520 4.1 55.2 1.0
F2 C:AF32522 4.1 60.3 1.0
OE1 C:GLU27 4.2 39.9 1.0
OE1 C:GLU2519 4.2 67.4 1.0
CG C:GLU67 4.4 43.0 1.0
OE1 C:GLU29 4.5 46.4 1.0
CE1 C:HIS150 4.6 38.9 1.0
CB C:GLU2519 4.6 68.4 1.0
O1B C:ADP2521 4.6 42.2 1.0
CB C:GLU67 4.7 42.3 1.0
CA C:ASP60 4.8 48.0 1.0
MG C:MG2524 4.8 47.3 1.0
ND1 C:HIS150 5.0 38.5 1.0

Magnesium binding site 9 out of 13 in 2d33

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Magnesium binding site 9 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2524

b:47.3
occ:1.00
 OE2 C:GLU328 2.1 41.0 1.0
O3B C:ADP2521 2.2 42.0 1.0
OE2 C:GLU27 2.3 40.2 1.0
OE1 C:GLU27 2.3 39.9 1.0
F3 C:AF32522 2.4 60.2 1.0
ND1 C:HIS150 2.4 38.5 1.0
CD C:GLU27 2.6 39.9 1.0
O1B C:ADP2521 3.0 42.2 1.0
PB C:ADP2521 3.0 41.6 1.0
CE1 C:HIS150 3.1 38.9 1.0
AL C:AF32522 3.1 62.6 1.0
CD C:GLU328 3.3 40.3 1.0
CG C:HIS150 3.6 38.5 1.0
F1 C:AF32522 3.8 59.9 1.0
O C:HOH2552 3.8 46.4 1.0
MG C:MG2525 3.9 45.8 1.0
OE1 C:GLU328 4.0 39.6 1.0
NH1 C:ARG330 4.0 44.0 1.0
CB C:HIS150 4.1 37.8 1.0
O2B C:ADP2521 4.1 41.9 1.0
CG C:GLU27 4.1 38.9 1.0
O C:HOH2528 4.1 38.9 1.0
O3A C:ADP2521 4.2 43.3 1.0
O2A C:ADP2521 4.3 46.0 1.0
NE2 C:HIS150 4.3 39.2 1.0
OE2 C:GLU2519 4.3 67.2 1.0
CG C:GLU328 4.4 38.7 1.0
CD2 C:HIS150 4.5 38.5 1.0
F2 C:AF32522 4.6 60.3 1.0
CB C:GLU27 4.8 38.4 1.0
PA C:ADP2521 4.8 45.4 1.0
MG C:MG2523 4.8 46.3 1.0
OE2 C:GLU67 4.9 44.1 1.0

Magnesium binding site 10 out of 13 in 2d33

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Magnesium binding site 10 out of 13 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2525

b:45.8
occ:1.00
 F1 C:AF32522 1.7 59.9 1.0
O2A C:ADP2521 1.9 46.0 1.0
O1B C:ADP2521 2.0 42.2 1.0
OE2 C:GLU67 2.2 44.1 1.0
OE1 C:GLU27 2.3 39.9 1.0
AL C:AF32522 2.8 62.6 1.0
CD C:GLU67 3.1 43.5 1.0
PA C:ADP2521 3.3 45.4 1.0
PB C:ADP2521 3.3 41.6 1.0
CD C:GLU27 3.4 39.9 1.0
OE1 C:GLU67 3.5 45.0 1.0
O3A C:ADP2521 3.7 43.3 1.0
MG C:MG2523 3.7 46.3 1.0
F2 C:AF32522 3.7 60.3 1.0
O C:HOH2552 3.8 46.4 1.0
MG C:MG2524 3.9 47.3 1.0
CG C:GLU27 4.0 38.9 1.0
O3B C:ADP2521 4.1 42.0 1.0
CD1 C:ILE69 4.1 39.3 1.0
F3 C:AF32522 4.1 60.2 1.0
O1A C:ADP2521 4.2 45.6 1.0
OE2 C:GLU27 4.3 40.2 1.0
CG C:GLU67 4.4 43.0 1.0
O5' C:ADP2521 4.4 45.5 1.0
CB C:GLU27 4.4 38.4 1.0
O2B C:ADP2521 4.5 41.9 1.0
CG1 C:ILE69 4.6 38.8 1.0
OE2 C:GLU2519 4.8 67.2 1.0

Reference:

T.Hibi, M.Nakayama, H.Nii, Y.Kurokawa, H.Katano, J.Oda. Structural Basis of Efficient Coupling Between Peptide Ligation and Atp Hydrolysis By Gamma-Gluatamylcysteine Synthetase To Be Published.
Page generated: Tue Aug 13 22:25:07 2024

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