Atomistry » Fluorine » PDB 3igu-3jx2 » 3ij8
Atomistry »
  Fluorine »
    PDB 3igu-3jx2 »
      3ij8 »

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

Go back to Fluorine Binding Sites List in 3ij8
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

Go back to Fluorine Binding Sites List in 3ij8
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

Go back to Fluorine Binding Sites List in 3ij8
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy