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

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: Thu Aug 1 00:00:36 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy