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Sodium in PDB 5ydi: Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing

Enzymatic activity of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing

All present enzymatic activity of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing:
3.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing, PDB code: 5ydi was solved by Q.Han, H.Guan, H.Ding, C.Liao, H.Robinson, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.72 / 3.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 127.440, 235.910, 167.270, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing (pdb code 5ydi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing, PDB code: 5ydi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ydi

Go back to Sodium Binding Sites List in 5ydi
Sodium binding site 1 out of 4 in the Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na805

b:22.7
occ:1.00
 OG A:SER360 2.1 39.7 1.0
O1 A:GOL804 2.7 53.8 1.0
CB A:SER360 3.3 41.6 1.0
N A:GLY280 3.7 46.1 1.0
CA A:GLY280 3.8 45.7 1.0
CZ A:PHE490 3.9 45.4 1.0
NE2 A:HIS600 4.0 45.2 1.0
C1 A:GOL804 4.0 53.6 1.0
CE1 A:PHE490 4.0 45.2 1.0
CZ A:PHE449 4.3 45.2 1.0
CD2 A:HIS600 4.4 45.0 1.0
CA A:SER360 4.5 42.1 1.0
C A:GLY279 4.6 45.8 1.0
CE2 A:PHE449 4.6 45.2 1.0
C3 A:GOL804 4.8 52.1 1.0
N A:ALA361 4.8 41.9 1.0
CZ A:PHE560 4.9 40.2 1.0
CH2 A:TRP393 4.9 43.0 1.0
CE2 A:PHE560 4.9 40.4 1.0
C2 A:GOL804 4.9 53.2 1.0

Sodium binding site 2 out of 4 in 5ydi

Go back to Sodium Binding Sites List in 5ydi
Sodium binding site 2 out of 4 in the Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na811

b:30.6
occ:1.00
 O B:HOH901 2.2 35.2 1.0
OG B:SER360 2.2 39.3 1.0
CB B:SER360 3.5 40.7 1.0
CZ B:PHE490 3.6 54.1 1.0
NE2 B:HIS600 3.9 58.8 1.0
CE2 B:PHE490 4.0 54.0 1.0
N B:GLY280 4.1 52.5 1.0
CZ B:PHE449 4.1 53.0 1.0
CA B:GLY280 4.1 51.0 1.0
CD2 B:HIS600 4.4 58.5 1.0
CE2 B:PHE449 4.5 53.3 1.0
CA B:SER360 4.6 42.0 1.0
CZ B:PHE560 4.6 43.2 1.0
CE1 B:PHE560 4.8 42.6 1.0
CH2 B:TRP393 4.8 43.4 1.0
CE1 B:PHE490 4.8 53.6 1.0
CE1 B:HIS600 4.9 58.4 1.0
N B:ALA361 4.9 43.7 1.0
C B:GLY279 4.9 53.9 1.0
CE1 B:PHE449 4.9 54.0 1.0
CZ3 B:TRP393 5.0 43.4 1.0

Sodium binding site 3 out of 4 in 5ydi

Go back to Sodium Binding Sites List in 5ydi
Sodium binding site 3 out of 4 in the Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na812

b:50.0
occ:1.00
 O3 B:GOL810 2.3 32.3 1.0
C3 B:GOL810 3.3 31.9 1.0
OH B:TYR282 3.9 44.4 1.0
CG B:TYR493 4.1 54.1 1.0
CD2 B:TYR493 4.3 54.2 1.0
CB B:TYR493 4.3 53.5 1.0
CD2 B:PHE490 4.5 54.1 1.0
CD1 B:TYR493 4.5 54.5 1.0
CD1 B:TYR489 4.6 69.1 1.0
C2 B:GOL810 4.6 31.8 1.0
CE2 B:PHE490 4.7 54.0 1.0
CE1 B:TYR489 4.8 71.4 1.0
CE2 B:TYR493 4.8 54.7 1.0
O2 B:GOL810 4.8 31.6 1.0
O B:TYR489 4.9 59.1 1.0

Sodium binding site 4 out of 4 in 5ydi

Go back to Sodium Binding Sites List in 5ydi
Sodium binding site 4 out of 4 in the Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Acetylcholinesterase Catalytic Subunits of the Malaria Vector Anopheles Gambiae, New Crystal Packing within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na806

b:37.2
occ:1.00
 OG C:SER360 2.2 38.8 1.0
O C:HOH901 2.2 29.2 1.0
CB C:SER360 3.4 40.5 1.0
CZ C:PHE490 3.7 44.1 1.0
NE2 C:HIS600 3.9 45.2 1.0
CE1 C:PHE490 3.9 43.7 1.0
N C:GLY280 3.9 49.6 1.0
CA C:GLY280 4.0 48.1 1.0
CD2 C:HIS600 4.1 45.7 1.0
O C:HOH905 4.2 17.8 1.0
CZ C:PHE449 4.6 49.0 1.0
CA C:SER360 4.6 49.9 1.0
C C:GLY279 4.7 50.0 1.0
CE2 C:PHE490 4.9 43.6 1.0
CE2 C:PHE449 5.0 49.1 1.0

Reference:

Q.Han, H.Guan, H.Ding, C.Liao, H.Robinson, J.Li. Crystal Structures of Acetylcholinesterase of the Malaria Vector Anopheles Gambiae Reveal A Polymerization Interface, Ligand Binding Residues and Post Translational Modifications To Be Published.
Page generated: Tue Oct 8 01:22:57 2024

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