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Fluorine in PDB 3ij8: 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: 3ij8 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) 29.33 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.000, 68.470, 129.860, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 21.3

Other elements in 3ij8:

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 3ij8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 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: 3ij8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 3ij8

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Fluorine binding site 1 out of 7 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:26.5
occ:1.00
 F1 A:B0D501 0.0 26.5 1.0
CX1 A:B0D501 1.4 27.8 1.0
OX5 A:B0D501 2.3 28.0 1.0
CX2 A:B0D501 2.4 27.0 1.0
CX6 A:B0D501 2.8 29.4 1.0
OX2 A:B0D501 2.8 26.5 1.0
CX5 A:B0D501 3.0 28.6 1.0
CX3 A:B0D501 3.0 27.6 1.0
O A:HOH733 3.2 27.7 1.0
OX6 A:B0D501 3.2 30.1 1.0
O A:HOH755 3.3 41.1 1.0
CD1 A:ILE235 3.4 22.1 1.0
CX4 A:B0D501 3.6 27.4 1.0
F2 A:B0D501 4.2 29.2 1.0
OX3 A:B0D501 4.3 27.0 1.0
OX4 A:B0D501 4.6 27.4 1.0
O A:HOH645 4.6 24.7 1.0
CG1 A:ILE235 4.7 21.6 1.0
CB A:ILE235 4.9 20.7 1.0

Fluorine binding site 2 out of 7 in 3ij8

Go back to Fluorine Binding Sites List in 3ij8
Fluorine binding site 2 out of 7 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:F501

b:29.2
occ:1.00
 F2 A:B0D501 0.0 29.2 1.0
CX5 A:B0D501 1.4 28.6 1.0
CX6 A:B0D501 2.3 29.4 1.0
OX5 A:B0D501 2.3 28.0 1.0
CX4 A:B0D501 2.4 27.4 1.0
O6 A:B9D504 2.7 36.5 1.0
OX6 A:B0D501 2.7 30.1 1.0
OX4 A:B0D501 2.9 27.4 1.0
O A:HOH742 3.1 46.1 1.0
CX1 A:B0D501 3.7 27.8 1.0
O4 A:B9D504 3.7 35.5 1.0
C3 A:B9D504 3.7 33.5 1.0
CX3 A:B0D501 3.8 27.6 1.0
OD2 A:ASP300 4.0 22.8 1.0
C6 A:B9D504 4.0 34.5 1.0
O A:HIS305 4.0 42.2 1.0
O3 A:B9D504 4.1 31.6 1.0
CX2 A:B0D501 4.2 27.0 1.0
F1 A:B0D501 4.2 26.5 1.0
OD1 A:ASP300 4.2 23.4 1.0
CG A:ASP300 4.3 20.8 1.0
C4 A:B9D504 4.3 34.1 1.0
C5 A:B9D504 4.8 33.8 1.0
OX3 A:B0D501 4.9 27.0 1.0
C2 A:B9D504 4.9 33.1 1.0

Fluorine binding site 3 out of 7 in 3ij8

Go back to Fluorine Binding Sites List in 3ij8
Fluorine binding site 3 out of 7 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:F502

b:38.0
occ:1.00
 F1 A:B0D502 0.0 38.0 1.0
CX1 A:B0D502 1.4 38.2 1.0
OX5 A:B0D502 2.4 38.0 1.0
CX2 A:B0D502 2.5 38.4 1.0
OX2 A:B0D502 2.8 38.1 1.0
CX6 A:B0D502 2.9 38.7 1.0
OX6 A:B0D502 3.0 39.8 1.0
CX5 A:B0D502 3.1 38.4 1.0
CX3 A:B0D502 3.1 38.3 1.0
CX4 A:B0D502 3.7 38.2 1.0
F2 A:B0D502 4.3 37.8 1.0
OX3 A:B0D502 4.4 40.1 1.0
CE3 A:TRP203 4.6 17.0 1.0
CZ3 A:TRP203 4.7 18.4 1.0
CD2 A:TRP203 4.7 16.6 1.0
OX4 A:B0D502 4.8 37.8 1.0
O A:HOH546 4.9 19.8 1.0

Fluorine binding site 4 out of 7 in 3ij8

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Fluorine binding site 4 out of 7 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:F502

b:37.8
occ:1.00
 F2 A:B0D502 0.0 37.8 1.0
CX5 A:B0D502 1.4 38.4 1.0
CX6 A:B0D502 2.3 38.7 1.0
OX5 A:B0D502 2.3 38.0 1.0
CX4 A:B0D502 2.4 38.2 1.0
OX6 A:B0D502 2.8 39.8 1.0
OX4 A:B0D502 2.9 37.8 1.0
O A:HOH546 3.2 19.8 1.0
N A:ASP206 3.4 13.1 1.0
CA A:GLY205 3.4 13.7 1.0
CB A:TRP203 3.5 14.5 1.0
OD1 A:ASP206 3.5 16.5 1.0
C A:GLY205 3.6 13.0 1.0
CX1 A:B0D502 3.7 38.2 1.0
N A:GLY205 3.7 13.7 1.0
CX3 A:B0D502 3.8 38.3 1.0
CG A:ASP206 3.9 15.1 1.0
CG A:TRP203 4.1 14.9 1.0
CX2 A:B0D502 4.2 38.4 1.0
F1 A:B0D502 4.3 38.0 1.0
CA A:ASP206 4.3 13.6 1.0
OD2 A:ASP206 4.3 15.6 1.0
CB A:ASP206 4.5 14.3 1.0
O A:GLY205 4.5 14.0 1.0
C A:TRP203 4.7 13.7 1.0
O A:HOH860 4.7 49.4 1.0
CA A:TRP203 4.7 14.0 1.0
CD2 A:TRP203 4.8 16.6 1.0
O A:TRP203 4.8 13.7 1.0
CD1 A:TRP203 4.8 15.4 1.0
OX3 A:B0D502 4.9 40.1 1.0
C A:PRO204 5.0 13.1 1.0

Fluorine binding site 5 out of 7 in 3ij8

Go back to Fluorine Binding Sites List in 3ij8
Fluorine binding site 5 out of 7 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:F503

b:18.0
occ:1.00
 F1 A:B0D503 0.0 18.0 1.0
CX1 A:B0D503 1.4 19.5 1.0
OX5 A:B0D503 2.3 19.2 1.0
CX2 A:B0D503 2.4 19.9 1.0
OX2 A:B0D503 2.8 20.9 1.0
CX6 A:B0D503 2.8 19.1 1.0
CX3 A:B0D503 3.0 20.7 1.0
CX5 A:B0D503 3.0 20.2 1.0
OX6 A:B0D503 3.2 17.0 1.0
CX4 A:B0D503 3.6 20.5 1.0
CD A:LYS208 3.6 22.2 1.0
O A:GLY249 3.7 14.1 1.0
CA A:GLY249 3.7 11.7 1.0
C A:GLY249 3.9 11.9 1.0
F2 A:B0D503 4.2 21.2 1.0
OX3 A:B0D503 4.3 22.3 1.0
CG A:LYS208 4.3 18.2 1.0
O A:HOH532 4.5 14.9 1.0
OD1 A:ASN250 4.6 14.4 1.0
OX4 A:B0D503 4.6 22.1 1.0
NZ A:LYS208 4.8 22.7 1.0
N A:GLY249 4.8 11.6 1.0
CE A:LYS208 4.8 24.0 1.0
N A:ASN250 5.0 12.7 1.0
CB A:LYS208 5.0 14.2 1.0

Fluorine binding site 6 out of 7 in 3ij8

Go back to Fluorine Binding Sites List in 3ij8
Fluorine binding site 6 out of 7 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 6 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:21.2
occ:1.00
 F2 A:B0D503 0.0 21.2 1.0
CX5 A:B0D503 1.4 20.2 1.0
CX6 A:B0D503 2.3 19.1 1.0
OX5 A:B0D503 2.3 19.2 1.0
CX4 A:B0D503 2.4 20.5 1.0
OX6 A:B0D503 2.7 17.0 1.0
OX4 A:B0D503 2.9 22.1 1.0
O A:HOH532 3.2 14.9 1.0
CB A:PRO204 3.6 13.8 1.0
CX1 A:B0D503 3.7 19.5 1.0
CX3 A:B0D503 3.7 20.7 1.0
O A:HOH860 4.1 49.4 1.0
O A:ASP246 4.1 12.9 1.0
CX2 A:B0D503 4.2 19.9 1.0
F1 A:B0D503 4.2 18.0 1.0
C A:PRO204 4.4 13.1 1.0
N A:GLY205 4.5 13.7 1.0
CA A:PRO204 4.6 13.0 1.0
CG A:PRO204 4.7 13.2 1.0
O A:PRO204 4.7 12.8 1.0
OX3 A:B0D503 4.8 22.3 1.0
CA A:GLY205 5.0 13.7 1.0

Fluorine binding site 7 out of 7 in 3ij8

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Fluorine binding site 7 out of 7 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 7 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:35.0
occ:1.00
 F1 A:B9D504 0.0 35.0 1.0
C5 A:B9D504 1.4 33.8 1.0
O A:B9D504 2.3 33.3 1.0
C6 A:B9D504 2.4 34.5 1.0
C4 A:B9D504 2.4 34.1 1.0
O4 A:B9D504 2.9 35.5 1.0
CB A:TYR62 2.9 13.3 1.0
O A:TYR62 3.4 14.4 1.0
NE2 A:HIS101 3.4 14.0 1.0
O6 A:B9D504 3.5 36.5 1.0
C1 A:B9D504 3.6 32.8 1.0
C3 A:B9D504 3.7 33.5 1.0
CE1 A:HIS101 3.7 13.6 1.0
CG A:TYR62 3.8 12.2 1.0
CD2 A:LEU165 3.8 18.1 1.0
CA A:TYR62 4.0 13.7 1.0
C A:TYR62 4.1 14.2 1.0
C2 A:B9D504 4.1 33.1 1.0
CD1 A:TYR62 4.2 13.8 1.0
O A:HOH675 4.3 31.6 1.0
OD2 A:ASP197 4.5 18.1 1.0
CD2 A:HIS101 4.6 13.8 1.0
OD1 A:ASP197 4.7 16.2 1.0
CD2 A:TYR62 4.7 13.3 1.0
O3 A:B9D504 4.8 31.6 1.0
ND1 A:HIS101 4.9 13.4 1.0
CG A:ASP197 5.0 14.6 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: Wed Jul 31 19:31:53 2024

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