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Fluorine 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:

Magnesium (Mg) 13 atoms
Aluminium (Al) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride, PDB code: 2d33:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 2d33

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Fluorine binding site 1 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F522

b:52.0
occ:1.00
 F1 A:AF3522 0.0 52.0 1.0
AL A:AF3522 1.8 55.6 1.0
MG A:MG523 2.2 40.9 1.0
OD1 A:ASP60 2.6 37.3 1.0
OE1 A:GLU67 2.6 34.9 1.0
MG A:MG525 2.8 26.8 1.0
F2 A:AF3522 2.8 51.6 1.0
O A:HOH560 3.0 25.1 1.0
N A:CYS520 3.2 52.9 1.0
OE2 A:GLU519 3.2 71.5 1.0
F3 A:AF3522 3.3 49.7 1.0
CD A:GLU67 3.5 32.0 1.0
OE2 A:GLU67 3.7 34.2 1.0
O1B A:ADP521 3.7 33.9 1.0
CG A:ASP60 3.8 35.4 1.0
O A:HOH700 4.0 43.0 1.0
CD A:GLU519 4.3 71.2 1.0
CB A:ASP60 4.4 32.2 1.0
CA A:CYS520 4.6 53.3 1.0
OE1 A:GLU27 4.6 30.1 1.0
CA A:ASP60 4.6 28.7 1.0
OE2 A:GLU29 4.6 32.5 1.0
OD2 A:ASP60 4.8 37.0 1.0
CG A:GLU67 4.9 30.2 1.0
O A:THR59 4.9 28.2 1.0
O2A A:ADP521 4.9 34.5 1.0

Fluorine binding site 2 out of 12 in 2d33

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Fluorine binding site 2 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F522

b:51.6
occ:1.00
 F2 A:AF3522 0.0 51.6 1.0
AL A:AF3522 1.6 55.6 1.0
O1B A:ADP521 2.8 33.9 1.0
F1 A:AF3522 2.8 52.0 1.0
F3 A:AF3522 2.8 49.7 1.0
MG A:MG525 3.5 26.8 1.0
O A:HOH560 3.5 25.1 1.0
N A:CYS520 3.6 52.9 1.0
O2B A:ADP521 3.7 33.8 1.0
PB A:ADP521 3.8 33.3 1.0
ND2 A:ASN297 4.2 52.3 1.0
OE2 A:GLU519 4.3 71.5 1.0
MG A:MG523 4.5 40.9 1.0
OXT A:CYS520 4.5 53.5 1.0
CG A:ASN297 4.8 51.1 1.0
O3A A:ADP521 4.8 32.5 1.0
MG A:MG524 4.9 34.6 1.0
O2A A:ADP521 4.9 34.5 1.0
OD1 A:ASP60 4.9 37.3 1.0
CA A:CYS520 5.0 53.3 1.0
O3B A:ADP521 5.0 30.9 1.0

Fluorine binding site 3 out of 12 in 2d33

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Fluorine binding site 3 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


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Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F522

b:49.7
occ:1.00
 F3 A:AF3522 0.0 49.7 1.0
AL A:AF3522 1.8 55.6 1.0
MG A:MG524 2.4 34.6 1.0
O1B A:ADP521 2.6 33.9 1.0
OE2 A:GLU519 2.7 71.5 1.0
F2 A:AF3522 2.8 51.6 1.0
MG A:MG525 3.3 26.8 1.0
PB A:ADP521 3.3 33.3 1.0
F1 A:AF3522 3.3 52.0 1.0
MG A:MG523 3.5 40.9 1.0
NH2 A:ARG330 3.5 46.0 1.0
O3B A:ADP521 3.5 30.9 1.0
CD A:GLU519 3.6 71.2 1.0
OE1 A:GLU27 3.6 30.1 1.0
CE1 A:HIS150 3.7 25.5 1.0
O2B A:ADP521 3.7 33.8 1.0
OE1 A:GLU519 3.7 71.4 1.0
ND1 A:HIS150 4.0 26.6 1.0
OE2 A:GLU328 4.1 34.6 1.0
N A:CYS520 4.2 52.9 1.0
O A:HOH700 4.3 43.0 1.0
OE2 A:GLU27 4.5 30.1 1.0
CD A:GLU27 4.5 30.1 1.0
CZ A:ARG330 4.6 45.8 1.0
O3A A:ADP521 4.8 32.5 1.0
NH1 A:ARG304 4.8 46.9 1.0
O A:HOH560 4.9 25.1 1.0
NE2 A:HIS150 4.9 25.1 1.0
O2A A:ADP521 4.9 34.5 1.0
OD1 A:ASP60 5.0 37.3 1.0
NE A:ARG330 5.0 46.0 1.0

Fluorine binding site 4 out of 12 in 2d33

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Fluorine binding site 4 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F1522

b:58.0
occ:1.00
 F1 B:AF31522 0.0 58.0 1.0
AL B:AF31522 1.8 60.7 1.0
MG B:MG1525 1.8 37.8 1.0
MG B:MG1523 2.1 45.8 1.0
OE1 B:GLU67 2.5 38.7 1.0
OE2 B:GLU67 2.7 39.8 1.0
F2 B:AF31522 2.8 59.6 1.0
O B:HOH1589 2.9 44.1 1.0
O1B B:ADP1521 2.9 38.8 1.0
O B:HOH1591 2.9 47.7 1.0
OE1 B:GLU27 3.0 36.7 1.0
CD B:GLU67 3.0 38.1 1.0
OE2 B:GLU1519 3.2 51.0 1.0
OD1 B:ASP60 3.2 43.1 1.0
F3 B:AF31522 3.3 58.3 1.0
O2A B:ADP1521 3.8 37.3 1.0
MG B:MG1524 4.1 36.4 1.0
OE2 B:GLU29 4.2 41.5 1.0
CD B:GLU27 4.2 35.6 1.0
PB B:ADP1521 4.3 36.7 1.0
CD B:GLU1519 4.3 51.1 1.0
CG B:ASP60 4.4 42.4 1.0
N B:CYS1520 4.4 48.0 1.0
CG B:GLU67 4.5 37.5 1.0
O3B B:ADP1521 4.6 37.7 1.0
OE1 B:GLU1519 5.0 50.0 1.0
OE2 B:GLU27 5.0 35.6 1.0

Fluorine binding site 5 out of 12 in 2d33

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Fluorine binding site 5 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1522

b:59.6
occ:1.00
 F2 B:AF31522 0.0 59.6 1.0
AL B:AF31522 1.6 60.7 1.0
O1B B:ADP1521 2.5 38.8 1.0
F1 B:AF31522 2.8 58.0 1.0
F3 B:AF31522 2.9 58.3 1.0
MG B:MG1525 3.4 37.8 1.0
PB B:ADP1521 3.5 36.7 1.0
O B:HOH1589 3.5 44.1 1.0
O2B B:ADP1521 3.7 37.2 1.0
N B:CYS1520 3.8 48.0 1.0
OE2 B:GLU1519 4.2 51.0 1.0
MG B:MG1523 4.2 45.8 1.0
OD1 B:ASP60 4.4 43.1 1.0
O3B B:ADP1521 4.5 37.7 1.0
OE1 B:GLU27 4.6 36.7 1.0
O3A B:ADP1521 4.7 36.3 1.0
MG B:MG1524 4.7 36.4 1.0
O2A B:ADP1521 4.7 37.3 1.0
OE1 B:GLU1519 4.8 50.0 1.0
CD B:GLU1519 4.8 51.1 1.0
OXT B:CYS1520 4.8 48.0 1.0
O B:HOH1554 4.8 45.6 1.0
ND2 B:ASN297 5.0 52.5 1.0

Fluorine binding site 6 out of 12 in 2d33

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Fluorine binding site 6 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1522

b:58.3
occ:1.00
 F3 B:AF31522 0.0 58.3 1.0
AL B:AF31522 1.8 60.7 1.0
MG B:MG1524 2.3 36.4 1.0
OE2 B:GLU1519 2.8 51.0 1.0
F2 B:AF31522 2.9 59.6 1.0
O1B B:ADP1521 3.0 38.8 1.0
O3B B:ADP1521 3.1 37.7 1.0
OE1 B:GLU1519 3.2 50.0 1.0
F1 B:AF31522 3.3 58.0 1.0
PB B:ADP1521 3.3 36.7 1.0
CD B:GLU1519 3.4 51.1 1.0
NH1 B:ARG330 3.5 36.1 1.0
CE1 B:HIS150 3.6 31.1 1.0
OE1 B:GLU27 3.6 36.7 1.0
OE2 B:GLU328 3.7 37.8 1.0
O2B B:ADP1521 3.8 37.2 1.0
MG B:MG1525 3.8 37.8 1.0
ND1 B:HIS150 3.8 30.3 1.0
O B:HOH1554 3.9 45.6 1.0
MG B:MG1523 3.9 45.8 1.0
O B:HOH1591 4.0 47.7 1.0
OE2 B:GLU27 4.3 35.6 1.0
CD B:GLU27 4.4 35.6 1.0
N B:CYS1520 4.5 48.0 1.0
NH1 B:ARG304 4.6 39.7 1.0
CD B:GLU328 4.7 36.9 1.0
CZ B:ARG330 4.7 36.4 1.0
NE2 B:HIS150 4.8 32.2 1.0
CG B:GLU1519 4.9 51.3 1.0
O3A B:ADP1521 4.9 36.3 1.0
OE1 B:GLU328 4.9 37.7 1.0

Fluorine binding site 7 out of 12 in 2d33

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Fluorine binding site 7 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
C:F2522

b:59.9
occ:1.00
 F1 C:AF32522 0.0 59.9 1.0
MG C:MG2525 1.7 45.8 1.0
AL C:AF32522 1.8 62.6 1.0
MG C:MG2523 2.2 46.3 1.0
O1B C:ADP2521 2.5 42.2 1.0
OE2 C:GLU67 2.7 44.1 1.0
F2 C:AF32522 2.8 60.3 1.0
OE1 C:GLU67 2.9 45.0 1.0
OE1 C:GLU27 2.9 39.9 1.0
O C:HOH2552 3.0 46.4 1.0
CD C:GLU67 3.1 43.5 1.0
F3 C:AF32522 3.2 60.2 1.0
OE2 C:GLU2519 3.3 67.2 1.0
OD1 C:ASP60 3.6 49.9 1.0
O2A C:ADP2521 3.6 46.0 1.0
MG C:MG2524 3.8 47.3 1.0
PB C:ADP2521 4.0 41.6 1.0
CD C:GLU27 4.2 39.9 1.0
N C:CYS2520 4.4 55.2 1.0
CD C:GLU2519 4.4 67.6 1.0
OE2 C:GLU29 4.5 46.3 1.0
CG C:GLU67 4.6 43.0 1.0
O3B C:ADP2521 4.6 42.0 1.0
OE1 C:GLU2519 4.8 67.4 1.0
PA C:ADP2521 4.8 45.4 1.0
CG C:ASP60 4.8 49.9 1.0
O3A C:ADP2521 4.8 43.3 1.0
O2B C:ADP2521 4.9 41.9 1.0
ND1 C:HIS150 5.0 38.5 1.0
OE2 C:GLU27 5.0 40.2 1.0
CE1 C:HIS150 5.0 38.9 1.0

Fluorine binding site 8 out of 12 in 2d33

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Fluorine binding site 8 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F2522

b:60.3
occ:1.00
 F2 C:AF32522 0.0 60.3 1.0
AL C:AF32522 1.6 62.6 1.0
F1 C:AF32522 2.8 59.9 1.0
O1B C:ADP2521 2.9 42.2 1.0
F3 C:AF32522 2.9 60.2 1.0
N C:CYS2520 3.0 55.2 1.0
MG C:MG2525 3.7 45.8 1.0
O2B C:ADP2521 3.8 41.9 1.0
PB C:ADP2521 3.8 41.6 1.0
OE2 C:GLU2519 4.1 67.2 1.0
MG C:MG2523 4.1 46.3 1.0
OE1 C:GLU2519 4.2 67.4 1.0
OXT C:CYS2520 4.3 55.5 1.0
CA C:CYS2520 4.4 55.4 1.0
OD1 C:ASP60 4.4 49.9 1.0
CD C:GLU2519 4.5 67.6 1.0
MG C:MG2524 4.6 47.3 1.0
C C:CYS2520 4.8 55.8 1.0
O3B C:ADP2521 4.8 42.0 1.0
OE1 C:GLU27 4.9 39.9 1.0
ND2 C:ASN297 4.9 56.3 1.0

Fluorine binding site 9 out of 12 in 2d33

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Fluorine binding site 9 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F2522

b:60.2
occ:1.00
 F3 C:AF32522 0.0 60.2 1.0
AL C:AF32522 1.8 62.6 1.0
MG C:MG2524 2.4 47.3 1.0
F2 C:AF32522 2.9 60.3 1.0
OE2 C:GLU2519 3.0 67.2 1.0
O1B C:ADP2521 3.0 42.2 1.0
OE1 C:GLU2519 3.1 67.4 1.0
F1 C:AF32522 3.2 59.9 1.0
NH1 C:ARG330 3.3 44.0 1.0
CD C:GLU2519 3.4 67.6 1.0
CE1 C:HIS150 3.4 38.9 1.0
O3B C:ADP2521 3.5 42.0 1.0
PB C:ADP2521 3.5 41.6 1.0
ND1 C:HIS150 3.7 38.5 1.0
OE2 C:GLU328 3.7 41.0 1.0
OE1 C:GLU27 3.8 39.9 1.0
O2B C:ADP2521 3.9 41.9 1.0
O C:HOH2552 4.1 46.4 1.0
MG C:MG2523 4.1 46.3 1.0
MG C:MG2525 4.1 45.8 1.0
NH1 C:ARG304 4.3 45.2 1.0
CZ C:ARG330 4.3 44.8 1.0
N C:CYS2520 4.4 55.2 1.0
NH2 C:ARG330 4.6 44.6 1.0
OE2 C:GLU27 4.6 40.2 1.0
CD C:GLU328 4.6 40.3 1.0
CD C:GLU27 4.6 39.9 1.0
OE1 C:GLU328 4.6 39.6 1.0
NE2 C:HIS150 4.7 39.2 1.0
CG C:GLU2519 4.9 68.0 1.0

Fluorine binding site 10 out of 12 in 2d33

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Fluorine binding site 10 out of 12 in the Crystal Structure of Gamma-Glutamylcysteine Synthetase Complexed with Aluminum Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
D:F3522

b:58.8
occ:1.00
 F1 D:AF33522 0.0 58.8 1.0
AL D:AF33522 1.8 62.7 1.0
MG D:MG3525 1.9 37.6 1.0
MG D:MG3523 2.1 38.2 1.0
OE2 D:GLU67 2.3 37.8 1.0
OE1 D:GLU67 2.5 39.4 1.0
O D:HOH3555 2.6 30.2 1.0
CD D:GLU67 2.7 37.8 1.0
F2 D:AF33522 2.7 58.8 1.0
O D:HOH3593 2.9 37.7 1.0
O1B D:ADP3521 3.0 37.2 1.0
OE1 D:GLU27 3.1 33.1 1.0
OD1 D:ASP60 3.3 40.1 1.0
F3 D:AF33522 3.3 57.0 1.0
OE2 D:GLU3519 3.3 49.5 1.0
O2A D:ADP3521 3.9 37.4 1.0
OE2 D:GLU29 4.2 38.1 1.0
CG D:GLU67 4.2 36.4 1.0
MG D:MG3524 4.3 35.6 1.0
N D:CYS3520 4.3 53.0 1.0
CD D:GLU27 4.4 32.2 1.0
PB D:ADP3521 4.4 37.0 1.0
CG D:ASP60 4.4 39.6 1.0
CD D:GLU3519 4.5 49.3 1.0
O3B D:ADP3521 4.9 36.8 1.0
CB D:ASP60 4.9 38.2 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: Wed Jul 31 14:00:58 2024

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