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Fluorine in PDB 4amx: Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride

Enzymatic activity of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride

All present enzymatic activity of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride:
4.2.2.13;

Protein crystallography data

The structure of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride, PDB code: 4amx was solved by H.J.Rozeboom, S.Yu, S.Madrid, K.H.Kalk, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.74 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 91.643, 97.008, 135.708, 80.38, 83.11, 85.22
R / Rfree (%) 22 / 26.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride (pdb code 4amx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride, PDB code: 4amx:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4amx

Go back to Fluorine Binding Sites List in 4amx
Fluorine binding site 1 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride


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 the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1039

b:39.3
occ:1.00
 F A:5GF1039 0.0 39.3 1.0
C5 A:5GF1039 1.3 36.6 1.0
O5 A:5GF1039 2.3 35.3 1.0
C4 A:5GF1039 2.3 36.2 1.0
C6 A:5GF1039 2.3 36.2 1.0
O4 A:5GF1039 2.7 36.3 1.0
C3 A:5GF1039 2.8 37.4 1.0
CZ A:PHE698 3.2 23.8 1.0
C1 A:5GF1039 3.4 35.6 1.0
O1 A:GOL1040 3.5 47.3 1.0
C2 A:GOL1040 3.5 50.7 1.0
C2 A:5GF1039 3.5 37.2 1.0
O6 A:5GF1039 3.6 35.8 1.0
CD2 A:PHE373 3.7 28.9 1.0
CE2 A:PHE698 3.8 24.6 1.0
CE2 A:PHE373 4.0 29.7 1.0
C3 A:GOL1040 4.0 50.4 1.0
O3 A:5GF1039 4.0 38.4 1.0
CE1 A:PHE698 4.1 23.1 1.0
C1 A:GOL1040 4.1 50.0 1.0
O2 A:5GF1039 4.1 36.2 1.0
O3 A:GOL1040 4.2 48.5 1.0
CG A:PHE373 4.3 28.8 1.0
O2 A:GOL1040 4.5 52.8 1.0
OD2 A:ASP553 4.6 36.0 1.0
OD1 A:ASP665 4.7 28.9 1.0
CD1 A:TYR513 4.7 42.5 1.0
CE1 A:TYR513 4.7 41.2 1.0
OD2 A:ASP412 4.8 26.4 1.0
CB A:PHE373 4.8 28.8 1.0
CZ A:PHE373 4.8 29.8 1.0

Fluorine binding site 2 out of 4 in 4amx

Go back to Fluorine Binding Sites List in 4amx
Fluorine binding site 2 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride


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 the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1039

b:46.6
occ:1.00
 F B:5GF1039 0.0 46.6 1.0
C5 B:5GF1039 1.3 44.6 1.0
O5 B:5GF1039 2.2 44.0 1.0
C4 B:5GF1039 2.3 44.7 1.0
C6 B:5GF1039 2.3 44.7 1.0
O4 B:5GF1039 2.7 44.8 1.0
C3 B:5GF1039 2.9 44.7 1.0
C1 B:5GF1039 3.4 42.0 1.0
CZ B:PHE698 3.4 32.8 1.0
O6 B:5GF1039 3.5 47.1 1.0
C2 B:5GF1039 3.6 44.4 1.0
CD2 B:PHE373 3.7 32.1 1.0
CE2 B:PHE373 3.9 33.4 1.0
CE2 B:PHE698 4.0 33.4 1.0
O2 B:5GF1039 4.1 44.0 1.0
O3 B:5GF1039 4.1 44.7 1.0
CG B:PHE373 4.2 31.6 1.0
CE1 B:PHE698 4.3 32.6 1.0
CZ B:PHE373 4.5 33.5 1.0
OD2 B:ASP553 4.5 48.8 1.0
OD1 B:ASP665 4.7 32.5 1.0
CD1 B:PHE373 4.8 32.0 1.0
CB B:PHE373 4.8 31.1 1.0
CE1 B:PHE373 4.9 32.9 1.0
OD2 B:ASP412 4.9 29.2 1.0

Fluorine binding site 3 out of 4 in 4amx

Go back to Fluorine Binding Sites List in 4amx
Fluorine binding site 3 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1039

b:46.8
occ:1.00
 F C:5GF1039 0.0 46.8 1.0
C5 C:5GF1039 1.3 44.5 1.0
O5 C:5GF1039 2.2 44.2 1.0
C4 C:5GF1039 2.3 44.0 1.0
C6 C:5GF1039 2.3 44.1 1.0
O4 C:5GF1039 2.6 43.2 1.0
C3 C:5GF1039 2.9 44.0 1.0
O C:HOH2102 3.4 35.4 1.0
C1 C:5GF1039 3.4 42.1 1.0
O6 C:5GF1039 3.5 44.6 1.0
CZ C:PHE698 3.5 29.4 1.0
C2 C:5GF1039 3.6 43.8 1.0
CD2 C:PHE373 3.7 36.2 1.0
CE2 C:PHE373 3.8 36.7 1.0
O2 C:5GF1039 4.1 42.5 1.0
CE2 C:PHE698 4.2 29.1 1.0
CG C:PHE373 4.2 35.6 1.0
O3 C:5GF1039 4.2 44.2 1.0
CE1 C:PHE698 4.4 29.3 1.0
CZ C:PHE373 4.5 35.8 1.0
OD2 C:ASP553 4.6 50.6 1.0
OD2 C:ASP412 4.8 32.9 1.0
CB C:PHE373 4.8 35.0 1.0
CD1 C:PHE373 4.8 34.3 1.0
OD1 C:ASP665 4.9 30.7 1.0
OD2 C:ASP665 4.9 31.8 1.0
CE1 C:PHE373 4.9 33.9 1.0

Fluorine binding site 4 out of 4 in 4amx

Go back to Fluorine Binding Sites List in 4amx
Fluorine binding site 4 out of 4 in the Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- 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 the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Glucosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1041

b:48.9
occ:1.00
 F1 D:AFR1041 0.0 48.9 1.0
C5 D:AFR1041 1.3 47.5 1.0
O5 D:AFR1041 2.3 47.7 1.0
C4 D:AFR1041 2.3 47.3 1.0
C6 D:AFR1041 2.3 46.1 1.0
C3 D:AFR1041 2.7 47.6 1.0
O4 D:AFR1041 2.8 46.5 1.0
C1 D:AFR1041 3.0 49.3 1.0
C2 D:AFR1041 3.2 48.6 1.0
CZ D:PHE698 3.3 24.4 1.0
O D:HOH2186 3.5 26.4 1.0
O6 D:AFR1041 3.6 45.6 1.0
CD2 D:PHE373 3.6 32.9 1.0
CE2 D:PHE698 3.9 25.4 1.0
CE2 D:PHE373 3.9 33.6 1.0
O3 D:AFR1041 4.1 48.1 1.0
CE1 D:PHE698 4.2 23.5 1.0
CG D:PHE373 4.3 31.7 1.0
O2 D:AFR1041 4.4 48.1 1.0
OD2 D:ASP665 4.5 31.6 1.0
CZ D:PHE373 4.7 34.6 1.0
CB D:PHE373 4.7 31.0 1.0
OD2 D:ASP553 4.8 38.7 1.0
OD2 D:ASP412 4.8 30.4 1.0
OD1 D:ASP665 4.8 29.9 1.0

Reference:

H.J.Rozeboom, S.Yu, S.Madrid, K.H.Kalk, R.Zhang, B.W.Dijkstra. Crystal Structure of Alpha-1,4-Glucan Lyase, A Unique Glycoside Hydrolase Family Member with A Novel Catalytic Mechanism. J.Biol.Chem. V. 288 26764 2013.
ISSN: ISSN 0021-9258
PubMed: 23902768
DOI: 10.1074/JBC.M113.485896
Page generated: Mon Jul 14 20:25:20 2025

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