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Iron in PDB 4y0h: 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: 4y0h 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) 53.96 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.496, 226.924, 71.436, 90.00, 108.67, 90.00
R / Rfree (%) 17.6 / 20.3

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 4y0h). 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: 4y0h:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4y0h

Go back to Iron Binding Sites List in 4y0h
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:13.1
occ:1.00
FE1 A:FES501 0.0 13.1 1.0
S1 A:FES501 2.2 13.7 1.0
S2 A:FES501 2.2 13.6 1.0
SG A:CYS135 2.3 14.3 1.0
SG A:CYS138 2.4 11.9 1.0
FE2 A:FES501 2.7 13.1 1.0
CB A:CYS138 3.2 12.8 1.0
CB A:CYS135 3.3 15.1 1.0
N A:CYS135 3.7 12.4 1.0
N A:CYS138 3.8 11.4 1.0
CA A:CYS135 4.0 13.6 1.0
CA A:CYS138 4.1 12.0 1.0
SG B:CYS135 4.4 14.0 1.0
C A:ALA134 4.4 11.7 1.0
C A:CYS135 4.5 13.7 1.0
SG B:CYS138 4.6 11.9 1.0
O A:CYS135 4.6 13.3 1.0
CB A:ALA134 4.7 13.2 1.0
CA A:ALA134 4.8 12.3 1.0
N A:ALA134 4.9 11.7 1.0
C A:SER137 4.9 10.5 0.7
C A:SER137 5.0 12.1 0.3

Iron binding site 2 out of 4 in 4y0h

Go back to Iron Binding Sites List in 4y0h
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:13.1
occ:1.00
FE2 A:FES501 0.0 13.1 1.0
S2 A:FES501 2.2 13.6 1.0
S1 A:FES501 2.2 13.7 1.0
SG B:CYS135 2.3 14.0 1.0
SG B:CYS138 2.4 11.9 1.0
FE1 A:FES501 2.7 13.1 1.0
CB B:CYS138 3.3 13.3 1.0
CB B:CYS135 3.4 13.1 1.0
N B:CYS135 3.7 11.8 1.0
N B:CYS138 3.8 11.0 1.0
CA B:CYS135 4.0 12.5 1.0
CA B:CYS138 4.1 11.7 1.0
SG A:CYS135 4.4 14.3 1.0
C B:ALA134 4.4 11.5 1.0
C B:CYS135 4.5 12.7 1.0
O B:CYS135 4.6 12.6 1.0
O B:HOH620 4.6 14.5 1.0
SG A:CYS138 4.6 11.9 1.0
CB B:ALA134 4.7 12.3 1.0
CA B:ALA134 4.8 12.1 1.0
N B:ALA134 4.8 12.6 1.0
C B:SER137 4.9 13.5 1.0
O A:HOH649 5.0 17.5 1.0

Iron binding site 3 out of 4 in 4y0h

Go back to Iron Binding Sites List in 4y0h
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:11.5
occ:1.00
FE1 C:FES501 0.0 11.5 1.0
S1 C:FES501 2.2 11.3 1.0
SG D:CYS135 2.3 12.0 1.0
S2 C:FES501 2.3 12.4 1.0
SG D:CYS138 2.4 10.5 1.0
FE2 C:FES501 2.8 11.2 1.0
CB D:CYS138 3.3 10.0 1.0
CB D:CYS135 3.4 9.9 1.0
N D:CYS138 3.7 9.5 1.0
N D:CYS135 3.8 9.6 1.0
CA D:CYS135 4.0 10.1 1.0
CA D:CYS138 4.1 9.5 1.0
SG C:CYS135 4.4 11.2 1.0
C D:ALA134 4.5 11.8 1.0
C D:CYS135 4.5 11.4 1.0
O D:HOH840 4.6 12.6 1.0
O D:CYS135 4.6 10.6 1.0
SG C:CYS138 4.6 10.4 1.0
CB D:ALA134 4.7 12.3 1.0
N D:ALA134 4.9 9.6 1.0
CA D:ALA134 4.9 11.1 1.0
C D:SER137 4.9 9.0 1.0

Iron binding site 4 out of 4 in 4y0h

Go back to Iron Binding Sites List in 4y0h
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:11.2
occ:1.00
FE2 C:FES501 0.0 11.2 1.0
S2 C:FES501 2.2 12.4 1.0
SG C:CYS135 2.3 11.2 1.0
S1 C:FES501 2.3 11.3 1.0
SG C:CYS138 2.3 10.4 1.0
FE1 C:FES501 2.8 11.5 1.0
CB C:CYS138 3.3 9.4 1.0
CB C:CYS135 3.4 11.3 1.0
N C:CYS135 3.7 9.2 1.0
N C:CYS138 3.7 8.8 1.0
CA C:CYS135 4.0 9.3 1.0
CA C:CYS138 4.1 9.7 1.0
C C:ALA134 4.3 10.4 1.0
SG D:CYS135 4.4 12.0 1.0
C C:CYS135 4.5 9.9 1.0
O C:HOH727 4.5 11.6 1.0
O C:CYS135 4.6 10.0 1.0
SG D:CYS138 4.7 10.5 1.0
CB C:ALA134 4.7 10.6 1.0
N C:ALA134 4.8 10.0 1.0
CA C:ALA134 4.8 9.9 1.0
O C:HOH777 4.8 16.8 1.0
C C:SER137 4.9 10.1 0.3
C C:SER137 4.9 9.1 0.7

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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