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Fluorine in PDB 3ij9: Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase

Enzymatic activity of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase

All present enzymatic activity of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase:
3.2.1.1;

Protein crystallography data

The structure of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase, PDB code: 3ij9 was solved by C.Li, R.Zhang, S.G.Withers, G.D.Brayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.38 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.380, 68.000, 129.950, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.7

Other elements in 3ij9:

The structure of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase (pdb code 3ij9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase, PDB code: 3ij9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 3ij9

Go back to Fluorine Binding Sites List in 3ij9
Fluorine binding site 1 out of 5 in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:23.9
occ:1.00
 F1 A:B9D501 0.0 23.9 1.0
C5 A:B9D501 1.4 25.5 1.0
O A:B9D501 2.3 23.8 1.0
C6 A:B9D501 2.3 23.6 1.0
C4 A:B9D501 2.4 26.1 1.0
O4 A:B9D501 2.9 28.3 1.0
CB A:TYR62 3.1 14.4 1.0
O5 A:BGC502 3.3 31.9 1.0
C5 A:BGC502 3.3 32.9 1.0
NE2 A:HIS101 3.6 12.9 1.0
C1 A:BGC502 3.6 30.9 1.0
O6 A:B9D501 3.6 26.0 1.0
O A:TYR62 3.6 14.1 1.0
C1 A:B9D501 3.7 25.0 1.0
CE1 A:HIS101 3.7 13.6 1.0
C3 A:B9D501 3.7 25.2 1.0
C6 A:BGC502 3.8 31.8 1.0
CG A:TYR62 3.9 15.2 1.0
CD2 A:LEU165 3.9 19.0 1.0
C2 A:B9D501 4.2 24.6 1.0
CA A:TYR62 4.3 13.3 1.0
C A:TYR62 4.3 14.2 1.0
CD1 A:TYR62 4.4 14.0 1.0
OD2 A:ASP197 4.5 14.6 1.0
O A:HOH721 4.6 52.8 1.0
OD1 A:ASP197 4.7 15.1 1.0
C4 A:BGC502 4.7 33.0 1.0
CD2 A:HIS101 4.7 12.7 1.0
O3 A:B9D501 4.8 25.6 1.0
C3 A:BGC502 4.9 33.5 1.0
C2 A:BGC502 4.9 32.3 1.0
CD2 A:TYR62 4.9 14.2 1.0
CG A:LEU165 4.9 21.3 1.0
O6 A:BGC502 4.9 30.6 1.0
ND1 A:HIS101 4.9 13.5 1.0
CG A:ASP197 5.0 16.0 1.0

Fluorine binding site 2 out of 5 in 3ij9

Go back to Fluorine Binding Sites List in 3ij9
Fluorine binding site 2 out of 5 in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:44.7
occ:1.00
 F1 A:B0D503 0.0 44.7 1.0
CX1 A:B0D503 1.4 45.3 1.0
OX5 A:B0D503 2.3 45.2 1.0
CX2 A:B0D503 2.4 45.2 1.0
OX2 A:B0D503 2.8 45.8 1.0
CX6 A:B0D503 2.9 45.8 1.0
CX5 A:B0D503 3.0 45.6 1.0
CX3 A:B0D503 3.0 45.2 1.0
OX6 A:B0D503 3.1 47.2 1.0
CX4 A:B0D503 3.6 44.9 1.0
F2 A:B0D503 4.2 45.3 1.0
OX3 A:B0D503 4.3 46.9 1.0
CE3 A:TRP203 4.7 17.6 1.0
OX4 A:B0D503 4.7 44.3 1.0
CD2 A:TRP203 4.8 16.8 1.0
CZ3 A:TRP203 4.8 18.8 1.0
O A:HOH570 5.0 18.8 1.0

Fluorine binding site 3 out of 5 in 3ij9

Go back to Fluorine Binding Sites List in 3ij9
Fluorine binding site 3 out of 5 in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:45.3
occ:1.00
 F2 A:B0D503 0.0 45.3 1.0
CX5 A:B0D503 1.4 45.6 1.0
CX6 A:B0D503 2.3 45.8 1.0
OX5 A:B0D503 2.3 45.2 1.0
CX4 A:B0D503 2.4 44.9 1.0
OX6 A:B0D503 2.8 47.2 1.0
OX4 A:B0D503 2.9 44.3 1.0
O A:HOH570 3.3 18.8 1.0
N A:ASP206 3.4 13.5 1.0
OD1 A:ASP206 3.4 17.3 1.0
CA A:GLY205 3.4 14.6 1.0
CB A:TRP203 3.5 15.1 1.0
C A:GLY205 3.6 14.0 1.0
CX1 A:B0D503 3.7 45.3 1.0
CX3 A:B0D503 3.8 45.2 1.0
N A:GLY205 3.8 15.1 1.0
CG A:ASP206 3.8 16.7 1.0
CG A:TRP203 4.2 15.4 1.0
CX2 A:B0D503 4.2 45.2 1.0
F1 A:B0D503 4.2 44.7 1.0
CA A:ASP206 4.3 14.4 1.0
OD2 A:ASP206 4.3 16.2 1.0
CB A:ASP206 4.4 14.6 1.0
O A:GLY205 4.4 12.2 1.0
C A:TRP203 4.7 14.1 1.0
CA A:TRP203 4.8 14.0 1.0
CD2 A:TRP203 4.8 16.8 1.0
O A:TRP203 4.8 14.2 1.0
OX3 A:B0D503 4.8 46.9 1.0
CD1 A:TRP203 4.9 16.3 1.0

Fluorine binding site 4 out of 5 in 3ij9

Go back to Fluorine Binding Sites List in 3ij9
Fluorine binding site 4 out of 5 in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:40.8
occ:1.00
 F1 A:B0D504 0.0 40.8 1.0
CX1 A:B0D504 1.3 41.3 1.0
OX5 A:B0D504 2.3 39.1 1.0
CX2 A:B0D504 2.3 41.9 1.0
OX2 A:B0D504 2.8 44.0 1.0
CX6 A:B0D504 2.8 37.7 1.0
OX6 A:B0D504 2.9 32.6 1.0
CX5 A:B0D504 2.9 40.1 1.0
CX3 A:B0D504 2.9 41.6 1.0
CX4 A:B0D504 3.5 40.9 1.0
CD A:LYS208 3.6 24.4 1.0
CA A:GLY249 3.7 12.8 1.0
O A:GLY249 3.7 15.1 1.0
C A:GLY249 3.9 13.6 1.0
F2 A:B0D504 4.1 41.1 1.0
OX3 A:B0D504 4.2 44.1 1.0
CG A:LYS208 4.3 20.2 1.0
O A:HOH509 4.3 16.3 1.0
OD1 A:ASN250 4.3 14.7 1.0
OX4 A:B0D504 4.6 41.6 1.0
N A:GLY249 4.8 11.4 1.0
CE A:LYS208 4.8 26.4 1.0
NZ A:LYS208 4.8 27.1 1.0
CB A:LYS208 4.9 17.2 1.0
N A:ASN250 4.9 14.0 1.0

Fluorine binding site 5 out of 5 in 3ij9

Go back to Fluorine Binding Sites List in 3ij9
Fluorine binding site 5 out of 5 in the Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Directed 'in Situ' Elongation As A Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic A-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:41.1
occ:1.00
 F2 A:B0D504 0.0 41.1 1.0
CX5 A:B0D504 1.4 40.1 1.0
OX5 A:B0D504 2.3 39.1 1.0
CX6 A:B0D504 2.4 37.7 1.0
CX4 A:B0D504 2.4 40.9 1.0
OX4 A:B0D504 2.9 41.6 1.0
OX6 A:B0D504 3.0 32.6 1.0
O A:HOH509 3.5 16.3 1.0
CX1 A:B0D504 3.6 41.3 1.0
CB A:PRO204 3.7 14.6 1.0
CX3 A:B0D504 3.8 41.6 1.0
F1 A:B0D504 4.1 40.8 1.0
O A:ASP246 4.1 13.6 1.0
CX2 A:B0D504 4.2 41.9 1.0
C A:PRO204 4.4 14.2 1.0
N A:GLY205 4.5 15.1 1.0
CA A:PRO204 4.7 14.2 1.0
O A:PRO204 4.7 15.0 1.0
CG A:PRO204 4.8 14.1 1.0
CA A:GLY205 4.9 14.6 1.0
OX3 A:B0D504 4.9 44.1 1.0
O A:HOH570 4.9 18.8 1.0

Reference:

R.Zhang, C.Li, L.K.Williams, B.P.Rempel, G.D.Brayer, S.G.Withers. Directed "in Situ" Inhibitor Elongation As A Strategy to Structurally Characterize the Covalent Glycosyl-Enzyme Intermediate of Human Pancreatic Alpha-Amylase Biochemistry V. 48 10752 2009.
ISSN: ISSN 0006-2960
PubMed: 19803533
DOI: 10.1021/BI901400P
Page generated: Mon Jul 14 17:02:21 2025

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