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

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

All present enzymatic activity of Crystal Structure of the Gracilariopsis Lemaneiformis Alpha-1,4- Glucan Lyase Covalent Intermediate Complex with 5-Fluoro-Idosyl- 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-Idosyl- Fluoride, PDB code: 4amw 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) 43.57 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.100, 97.300, 136.280, 80.31, 83.29, 85.21
R / Rfree (%) 20.7 / 25.4

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-Idosyl- Fluoride (pdb code 4amw). 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-Idosyl- Fluoride, PDB code: 4amw:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4amw

Go back to Fluorine Binding Sites List in 4amw
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-Idosyl- 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-Idosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1039

b:30.5
occ:1.00
 F1 A:B9D1039 0.0 30.5 1.0
C5 A:B9D1039 1.3 28.2 1.0
O A:B9D1039 2.2 27.9 1.0
C6 A:B9D1039 2.3 28.4 1.0
C4 A:B9D1039 2.4 27.7 1.0
OD1 A:ASP412 2.9 16.8 1.0
C1 A:B9D1039 3.0 26.7 1.0
O4 A:B9D1039 3.2 25.4 1.0
OD2 A:ASP553 3.2 19.8 1.0
ND2 A:ASN459 3.2 19.1 1.0
O6 A:B9D1039 3.6 29.4 1.0
C3 A:B9D1039 3.6 28.7 1.0
CE1 A:TYR513 3.7 23.7 1.0
CG A:ASP412 3.8 19.3 1.0
C2 A:B9D1039 3.9 28.5 1.0
OD2 A:ASP412 3.9 17.9 1.0
CG A:ASN459 4.1 14.0 1.0
CD1 A:TYR513 4.3 24.7 1.0
CZ A:TYR513 4.3 22.4 1.0
OH A:TYR513 4.4 24.6 1.0
CG A:ASP553 4.5 14.1 1.0
CG2 A:VAL413 4.5 17.1 1.0
CG1 A:VAL413 4.5 13.5 1.0
OD1 A:ASN459 4.6 14.2 1.0
CD1 A:PHE373 4.7 15.0 1.0
CE1 A:PHE373 4.7 17.4 1.0
O3 A:B9D1039 4.8 28.1 1.0
CZ A:PHE373 4.8 16.8 1.0
CG A:PHE373 4.8 14.4 1.0
CE2 A:PHE373 5.0 17.7 1.0
CD2 A:PHE373 5.0 16.4 1.0

Fluorine binding site 2 out of 4 in 4amw

Go back to Fluorine Binding Sites List in 4amw
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-Idosyl- 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-Idosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1039

b:42.4
occ:1.00
 F1 B:B9D1039 0.0 42.4 1.0
C5 B:B9D1039 1.3 42.1 1.0
O B:B9D1039 2.2 41.8 1.0
C6 B:B9D1039 2.3 42.9 1.0
C4 B:B9D1039 2.4 42.0 1.0
OD1 B:ASP412 3.0 18.7 1.0
C1 B:B9D1039 3.0 40.4 1.0
O4 B:B9D1039 3.1 40.7 1.0
OD2 B:ASP553 3.3 32.9 1.0
ND2 B:ASN459 3.3 18.3 1.0
O6 B:B9D1039 3.6 45.1 1.0
C3 B:B9D1039 3.7 42.5 1.0
CG B:ASP412 3.8 21.6 1.0
CE1 B:TYR513 3.8 43.0 1.0
OD2 B:ASP412 3.9 20.3 1.0
C2 B:B9D1039 3.9 42.0 1.0
CD1 B:TYR513 4.4 44.2 1.0
CG B:ASN459 4.4 20.4 1.0
CE B:MET554 4.4 34.0 1.0
CE1 B:PHE373 4.4 24.1 1.0
CD1 B:PHE373 4.5 21.7 1.0
CG1 B:VAL413 4.5 23.3 1.0
CG B:ASP553 4.5 24.9 1.0
CZ B:PHE373 4.6 21.9 1.0
CG2 B:VAL413 4.8 24.9 1.0
O3 B:B9D1039 4.8 42.4 1.0
CG B:PHE373 4.8 20.5 1.0
CZ B:TYR513 4.8 41.2 1.0
CE2 B:PHE373 4.9 22.0 1.0
OH B:TYR513 4.9 37.9 1.0
CD2 B:PHE373 5.0 21.4 1.0
OD1 B:ASN459 5.0 21.4 1.0

Fluorine binding site 3 out of 4 in 4amw

Go back to Fluorine Binding Sites List in 4amw
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-Idosyl- 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-Idosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1039

b:38.2
occ:1.00
 F1 C:B9D1039 0.0 38.2 1.0
C5 C:B9D1039 1.3 39.8 1.0
O C:B9D1039 2.3 38.9 1.0
C6 C:B9D1039 2.3 39.5 1.0
C4 C:B9D1039 2.4 38.7 1.0
O C:HOH2303 2.7 41.1 1.0
C1 C:B9D1039 3.0 37.4 1.0
OD1 C:ASP412 3.1 20.7 1.0
O4 C:B9D1039 3.1 40.1 1.0
ND2 C:ASN459 3.2 24.1 1.0
OD2 C:ASP553 3.3 35.2 1.0
O6 C:B9D1039 3.6 40.7 1.0
C3 C:B9D1039 3.7 39.2 1.0
CE2 C:TYR513 3.8 47.0 1.0
CG C:ASP412 3.9 20.6 1.0
C2 C:B9D1039 4.0 39.0 1.0
OD2 C:ASP412 4.1 21.6 1.0
CG C:ASN459 4.3 22.3 1.0
CB C:VAL413 4.4 24.1 1.0
CG1 C:VAL413 4.5 23.3 1.0
CG C:ASP553 4.5 26.8 1.0
CE1 C:PHE373 4.5 22.2 1.0
CD2 C:TYR513 4.6 49.4 1.0
CD1 C:PHE373 4.6 21.6 1.0
CE C:MET554 4.7 38.0 1.0
CZ C:PHE373 4.8 22.8 1.0
O3 C:B9D1039 4.8 36.8 1.0
CZ C:TYR513 4.8 43.8 1.0
OH C:TYR513 4.8 40.3 1.0
OD1 C:ASN459 4.9 22.3 1.0
CG C:PHE373 5.0 21.3 1.0

Fluorine binding site 4 out of 4 in 4amw

Go back to Fluorine Binding Sites List in 4amw
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-Idosyl- 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-Idosyl- Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1041

b:39.5
occ:1.00
 F1 D:5DI1041 0.0 39.5 1.0
C5 D:5DI1041 1.3 40.7 1.0
O5 D:5DI1041 2.2 41.8 1.0
C6 D:5DI1041 2.3 42.2 1.0
C4 D:5DI1041 2.4 40.5 1.0
OD1 D:ASP412 2.8 18.7 1.0
O4 D:5DI1041 3.0 38.5 1.0
O D:HOH2467 3.2 32.4 1.0
ND2 D:ASN459 3.4 23.5 1.0
C1 D:5DI1041 3.5 43.4 1.0
CG D:ASP412 3.5 20.0 1.0
O6 D:5DI1041 3.6 43.0 1.0
OD2 D:ASP553 3.6 29.0 1.0
CE1 D:TYR513 3.6 40.1 1.0
OD2 D:ASP412 3.6 22.9 1.0
C3 D:5DI1041 3.7 41.9 1.0
C2 D:5DI1041 4.1 42.7 1.0
CD1 D:TYR513 4.1 42.4 1.0
CD1 D:PHE373 4.2 19.3 1.0
CE1 D:PHE373 4.3 23.4 1.0
CG D:ASN459 4.3 21.2 1.0
CZ D:TYR513 4.4 39.4 1.0
CG1 D:VAL413 4.4 20.8 1.0
CG2 D:VAL413 4.4 20.6 1.0
OH D:TYR513 4.6 37.0 1.0
CG D:PHE373 4.6 20.1 1.0
CZ D:PHE373 4.6 21.6 1.0
OD1 D:ASN459 4.8 22.9 1.0
CG D:ASP553 4.8 22.9 1.0
CE D:MET554 4.8 36.2 1.0
O3 D:5DI1041 4.8 43.1 1.0
N D:VAL413 4.8 20.4 1.0
CB D:VAL413 4.9 21.8 1.0
CB D:ASP412 4.9 17.9 1.0
CD2 D:PHE373 4.9 21.4 1.0
CE2 D:PHE373 4.9 23.6 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: Thu Aug 1 00:00:04 2024

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