Fluorine in PDB 7y02: Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid

Enzymatic activity of Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid

All present enzymatic activity of Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid:
3.2.2.22;

Protein crystallography data

The structure of Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid, PDB code: 7y02 was solved by M.Goto, S.Higashi, T.Ohba, R.Kawata, K.Nagatsu, S.Suzuki, R.Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.86 / 1.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.688, 67.688, 141.205, 90, 90, 90
R / Rfree (%) 20.8 / 22.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid (pdb code 7y02). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid, PDB code: 7y02:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7y02

Go back to Fluorine Binding Sites List in 7y02
Fluorine binding site 1 out of 2 in the Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:52.6
occ:1.00
 FAX A:IEZ501 0.0 52.6 1.0
CZ A:IEZ501 1.4 49.2 1.0
CE1 A:IEZ501 2.4 47.5 1.0
CE2 A:IEZ501 2.4 47.8 1.0
CD1 A:IEZ501 3.7 45.5 1.0
CD2 A:IEZ501 3.7 45.6 1.0
CG A:IEZ501 4.2 44.0 1.0
O A:HOH781 4.4 44.0 1.0
O A:ASN209 4.9 23.2 1.0

Fluorine binding site 2 out of 2 in 7y02

Go back to Fluorine Binding Sites List in 7y02
Fluorine binding site 2 out of 2 in the Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ricin A Chain Bound with (S)-2-(2-Amino-4-Oxo-3, 4-Dihydropteridine-7-Carboxamido)-3-(4-Fluorophenyl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:43.2
occ:1.00
 FAX A:IEZ502 0.0 43.2 1.0
CZ A:IEZ502 1.3 40.2 1.0
CE1 A:IEZ502 2.3 40.3 1.0
CE2 A:IEZ502 2.3 40.3 1.0
O A:HOH621 3.0 27.0 1.0
C6 A:IEZ501 3.1 22.8 1.0
CD1 A:IEZ502 3.6 39.3 1.0
CD2 A:IEZ502 3.6 39.4 1.0
N5 A:IEZ501 3.6 21.9 1.0
N A:IEZ501 3.7 30.3 1.0
CE3 A:TRP211 3.7 19.3 1.0
O A:HOH763 3.8 30.0 1.0
NH1 A:ARG180 4.0 19.2 1.0
C7 A:IEZ501 4.0 23.6 1.0
CG A:IEZ502 4.1 38.7 1.0
CZ A:ARG180 4.1 19.1 1.0
NH2 A:ARG180 4.3 19.2 1.0
CZ3 A:TRP211 4.3 19.3 1.0
OXT A:IEZ501 4.3 42.9 1.0
CAL A:IEZ501 4.4 26.1 1.0
CA A:IEZ501 4.6 37.3 1.0
CB A:IEZ501 4.6 40.3 1.0
O A:GLU208 4.6 20.4 1.0
NE A:ARG180 4.7 18.4 1.0
CD2 A:TRP211 4.7 19.3 1.0
CB A:TRP211 4.7 19.2 1.0
OE2 A:GLU177 4.8 20.6 1.0
C4A A:IEZ501 4.8 21.1 1.0
C A:IEZ501 5.0 40.2 1.0

Reference:

M.Goto, S.Higashi, T.Ohba, R.Kawata, K.Nagatsu, S.Suzuki, E.V.Anslyn, R.Saito. Conformational Change in Ricin Toxin A-Chain: A Critical Factor For Inhibitor Binding to the Secondary Pocket. Biochem.Biophys.Res.Commun. V. 627 1 2022.
ISSN: ESSN 1090-2104
PubMed: 35998389
DOI: 10.1016/J.BBRC.2022.08.008
Page generated: Wed Apr 5 01:53:40 2023

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