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Iron in PDB 4y0d: Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115)

Enzymatic activity of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115)

All present enzymatic activity of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115):
2.6.1.19; 2.6.1.22;

Protein crystallography data

The structure of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115), PDB code: 4y0d was solved by W.Rui, S.Ruslan, L.Hyunbeom, H.D.Emma, I.J.Jose, K.Neil, B.S.Richard, L.Dali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.12 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.555, 227.280, 70.999, 90.00, 108.83, 90.00
R / Rfree (%) 16.8 / 20.9

Iron Binding Sites:

The binding sites of Iron atom in the Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115) (pdb code 4y0d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115), PDB code: 4y0d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4y0d

Go back to Iron Binding Sites List in 4y0d
Iron binding site 1 out of 4 in the Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:25.4
occ:1.00
 FE1 A:FES501 0.0 25.4 1.0
S1 A:FES501 2.2 29.4 1.0
S2 A:FES501 2.2 26.3 1.0
SG B:CYS135 2.3 24.7 1.0
SG B:CYS138 2.3 28.2 1.0
FE2 A:FES501 3.0 27.1 1.0
CB B:CYS138 3.2 19.2 1.0
CB B:CYS135 3.4 25.2 1.0
N B:CYS135 3.6 26.0 1.0
N B:CYS138 3.7 22.2 1.0
CA B:CYS135 4.0 24.6 1.0
CA B:CYS138 4.0 21.3 1.0
C B:CYS135 4.4 22.3 1.0
C B:ALA134 4.5 23.7 1.0
O B:CYS135 4.5 22.5 1.0
SG A:CYS135 4.5 26.7 1.0
CB B:ALA134 4.5 20.8 1.0
C B:SER137 4.8 23.8 1.0
N B:ALA134 4.8 21.9 1.0
CA B:ALA134 4.8 22.8 1.0
CB B:SER137 4.8 25.0 1.0
O B:HOH886 4.9 41.7 1.0
SG A:CYS138 5.0 29.7 1.0
N B:SER137 5.0 23.1 1.0

Iron binding site 2 out of 4 in 4y0d

Go back to Iron Binding Sites List in 4y0d
Iron binding site 2 out of 4 in the Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:27.1
occ:1.00
 FE2 A:FES501 0.0 27.1 1.0
S1 A:FES501 2.2 29.4 1.0
S2 A:FES501 2.2 26.3 1.0
SG A:CYS135 2.3 26.7 1.0
SG A:CYS138 2.3 29.7 1.0
FE1 A:FES501 3.0 25.4 1.0
CB A:CYS138 3.2 28.6 1.0
CB A:CYS135 3.5 20.1 1.0
N A:CYS135 3.5 19.7 1.0
N A:CYS138 3.8 25.5 1.0
CA A:CYS135 4.0 24.9 1.0
CA A:CYS138 4.1 28.4 1.0
CB A:ALA134 4.3 24.8 1.0
C A:ALA134 4.3 24.5 1.0
C A:CYS135 4.4 23.1 1.0
O A:CYS135 4.4 27.8 1.0
SG B:CYS135 4.5 24.7 1.0
O A:HOH856 4.6 40.0 1.0
CA A:ALA134 4.7 24.1 1.0
N A:ALA134 4.7 25.1 1.0
O B:HOH642 4.9 23.7 1.0
CB A:SER137 4.9 25.4 1.0
C A:SER137 4.9 24.3 1.0
SG B:CYS138 4.9 28.2 1.0

Iron binding site 3 out of 4 in 4y0d

Go back to Iron Binding Sites List in 4y0d
Iron binding site 3 out of 4 in the Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:26.7
occ:1.00
 FE1 C:FES501 0.0 26.7 1.0
S1 C:FES501 2.2 30.1 1.0
S2 C:FES501 2.2 27.4 1.0
SG C:CYS138 2.3 23.1 1.0
SG C:CYS135 2.3 21.9 1.0
FE2 C:FES501 2.9 19.7 1.0
CB C:CYS138 3.3 17.9 1.0
CB C:CYS135 3.4 23.3 1.0
O D:HOH876 3.5 50.5 1.0
N C:CYS135 3.7 16.2 1.0
N C:CYS138 3.8 24.1 1.0
CA C:CYS135 4.0 24.5 1.0
CA C:CYS138 4.2 26.7 1.0
C C:ALA134 4.3 23.8 1.0
CB C:ALA134 4.4 16.0 1.0
C C:CYS135 4.5 22.4 1.0
SG D:CYS135 4.5 23.1 1.0
O C:CYS135 4.6 27.0 1.0
O C:HOH907 4.6 25.4 1.0
CA C:ALA134 4.7 24.3 1.0
SG D:CYS138 4.8 22.5 1.0
N C:ALA134 4.8 21.0 1.0
C C:SER137 4.9 17.7 1.0
CB C:SER137 5.0 25.9 1.0

Iron binding site 4 out of 4 in 4y0d

Go back to Iron Binding Sites List in 4y0d
Iron binding site 4 out of 4 in the Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Gamma-Aminobutyric Acid Aminotransferase Inactivated By (1S,3S)-3- Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:19.7
occ:1.00
 FE2 C:FES501 0.0 19.7 1.0
S1 C:FES501 2.2 30.1 1.0
S2 C:FES501 2.2 27.4 1.0
SG D:CYS135 2.3 23.1 1.0
SG D:CYS138 2.3 22.5 1.0
FE1 C:FES501 2.9 26.7 1.0
CB D:CYS138 3.3 17.0 1.0
O D:HOH876 3.4 50.5 1.0
CB D:CYS135 3.4 22.9 1.0
N D:CYS135 3.6 24.1 1.0
N D:CYS138 3.7 13.8 1.0
CA D:CYS135 4.0 24.2 1.0
CA D:CYS138 4.1 18.8 1.0
C D:ALA134 4.4 20.9 1.0
CB D:ALA134 4.4 17.3 1.0
C D:CYS135 4.5 23.2 1.0
SG C:CYS135 4.5 21.9 1.0
O D:CYS135 4.5 25.1 1.0
SG C:CYS138 4.7 23.1 1.0
CA D:ALA134 4.8 21.1 1.0
N D:ALA134 4.8 22.4 1.0
C D:SER137 4.9 14.5 1.0
O D:HOH809 4.9 38.4 1.0
O D:HOH807 4.9 32.1 1.0
CB D:SER137 4.9 17.7 1.0

Reference:

L.Hyunbeom, H.D.Emma, W.Rui, S.Ruslan, I.J.Jose, L.Dali, K.Neil, B.S.Richard. Mechanism of Inactivation of Gamma-Aminobutyric Acid Aminotransferase By (1S,3S)-3-Amino-4-Difluoromethylenyl-1-Cyclopentanoic Acid (Cpp-115) J. Am. Chem. Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25616005
DOI: 10.1021/JA512299N
Page generated: Mon Aug 5 16:02:35 2024

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