Atomistry » Fluorine » PDB 461d-4azy » 4amw
Atomistry »
  Fluorine »
    PDB 461d-4azy »
      4amw »

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: Sun Dec 13 11:58:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy