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Calcium in PDB 4b0p: Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium

Enzymatic activity of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium

All present enzymatic activity of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium:
3.1.1.8;

Protein crystallography data

The structure of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium, PDB code: 4b0p was solved by M.Wandhammer, M.De Koning, M.Van Grol, D.Noort, M.Goeldner, F.Nachon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.878 / 2.50
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 154.230, 154.230, 133.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.44 / 21.2

Other elements in 4b0p:

The structure of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium also contains other interesting chemical elements:

Fluorine (F) 5 atoms
Potassium (K) 1 atom
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium (pdb code 4b0p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium, PDB code: 4b0p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4b0p

Go back to Calcium Binding Sites List in 4b0p
Calcium binding site 1 out of 4 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2191

b:83.6
occ:1.00
 OH A:TYR420 3.3 39.6 1.0
NH1 A:ARG515 3.9 52.0 1.0
NZ A:LYS323 4.1 56.8 1.0
O A:HOH3178 4.2 47.2 1.0
CZ A:TYR420 4.3 31.5 1.0
CG A:LYS323 4.4 34.4 1.0
CE2 A:TYR420 4.5 32.2 1.0
CZ A:ARG515 4.6 47.8 1.0
CD A:LYS323 4.6 39.4 1.0
NH2 A:ARG515 4.6 37.7 1.0
CE A:LYS323 4.7 48.5 1.0
O A:HOH3174 4.8 48.9 1.0

Calcium binding site 2 out of 4 in 4b0p

Go back to Calcium Binding Sites List in 4b0p
Calcium binding site 2 out of 4 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2192

b:80.9
occ:1.00
 OG1 A:THR488 3.7 64.9 1.0
N A:THR488 3.7 69.2 1.0
CB A:THR508 3.9 65.7 1.0
O A:HOH3175 3.9 64.6 1.0
CG2 A:THR508 3.9 56.9 1.0
CA A:SER487 4.0 65.4 1.0
C A:SER487 4.3 71.5 1.0
O A:ASN486 4.6 63.9 1.0
CB A:THR488 4.6 62.7 1.0
OG1 A:THR508 4.6 70.4 1.0
O A:HOH3152 4.6 49.3 1.0
CB A:SER487 4.7 63.4 1.0
CA A:THR488 4.7 64.2 1.0
N A:SER487 5.0 54.8 1.0

Calcium binding site 3 out of 4 in 4b0p

Go back to Calcium Binding Sites List in 4b0p
Calcium binding site 3 out of 4 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2197

b:84.6
occ:1.00
 SG A:CYS66 2.7 49.1 1.0
NE2 A:GLN270 3.3 96.1 1.0
O A:HOH3100 3.6 67.0 1.0
CB A:CYS66 3.7 36.9 1.0
CB A:PRO269 3.8 62.8 1.0
CD1 A:LEU273 3.9 70.4 1.0
CD A:GLN270 4.3 93.3 1.0
CA A:CYS66 4.3 35.4 1.0
CB A:LEU88 4.4 38.0 1.0
CG A:PRO269 4.5 57.7 1.0
O A:LEU88 4.6 41.2 1.0
CG A:GLN270 4.7 82.2 1.0
C A:LEU88 4.7 40.2 1.0
N A:GLN270 4.9 65.4 1.0
N A:SER89 4.9 42.2 1.0
C A:PRO269 5.0 55.8 1.0

Calcium binding site 4 out of 4 in 4b0p

Go back to Calcium Binding Sites List in 4b0p
Calcium binding site 4 out of 4 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2198

b:93.0
occ:1.00
 O A:HOH3088 3.3 54.6 1.0
O A:PHE217 3.4 28.8 1.0
C A:PHE217 3.7 28.3 1.0
OG1 A:THR218 3.7 41.6 1.0
O A:PRO189 4.0 35.5 1.0
O A:SER215 4.0 36.3 1.0
N A:PHE217 4.2 37.2 1.0
N A:THR218 4.2 34.7 1.0
CA A:PHE217 4.2 29.5 1.0
CA A:LYS190 4.3 34.6 1.0
O A:LYS190 4.4 42.4 1.0
CA A:THR218 4.4 31.6 1.0
C A:SER215 4.4 34.0 1.0
C A:LYS190 4.5 34.9 1.0
CB A:THR218 4.6 34.4 1.0
C A:LEU216 4.9 36.1 1.0
CA A:SER215 4.9 35.9 1.0
NE2 A:GLN179 4.9 39.3 1.0
C A:PRO189 4.9 38.4 1.0

Reference:

M.Wandhammer, M.De Koning, M.Van Grol, M.Loiodice, L.Saurel, D.Noort, M.Goeldner, F.Nachon. A Step Toward the Reactivation of Aged Cholinesterases - Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase Chem.Biol.Interact V. 203 19 2013.
ISSN: ISSN 0009-2797
PubMed: 22922115
DOI: 10.1016/J.CBI.2012.08.005
Page generated: Sat Jul 13 22:30:29 2024

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