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Chlorine in PDB 7a5x: Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.

Enzymatic activity of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.

All present enzymatic activity of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.:
3.2.1.18;

Protein crystallography data

The structure of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group., PDB code: 7a5x was solved by C.Bridot, J.Bouckaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.60 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.203, 96.741, 226.381, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.8

Other elements in 7a5x:

The structure of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group. also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group. (pdb code 7a5x). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group., PDB code: 7a5x:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7a5x

Go back to Chlorine Binding Sites List in 7a5x
Chlorine binding site 1 out of 4 in the Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:37.9
occ:1.00
 HG A:SER511 2.2 56.1 1.0
HZ1 A:LYS509 2.4 40.9 1.0
H A:SER511 2.4 55.6 1.0
H A:ASN502 2.5 53.1 1.0
H A:THR510 2.6 50.8 1.0
HA3 A:GLY501 2.8 49.0 1.0
HB3 A:LYS509 2.9 39.6 1.0
OG A:SER511 3.1 46.8 1.0
HG2 A:LYS509 3.1 41.6 1.0
HB2 A:PHE505 3.2 45.2 1.0
NZ A:LYS509 3.2 34.1 1.0
HA A:LYS509 3.2 46.4 1.0
N A:SER511 3.2 46.3 1.0
N A:THR510 3.3 42.3 1.0
HD2 A:PHE505 3.3 41.7 1.0
N A:ASN502 3.3 44.2 1.0
HE3 A:LYS509 3.4 38.7 1.0
HZ3 A:LYS509 3.5 40.9 1.0
O A:ASN502 3.5 33.8 1.0
CB A:LYS509 3.5 33.0 1.0
HG1 A:THR510 3.6 47.8 1.0
HB3 A:SER511 3.6 53.8 1.0
CA A:GLY501 3.6 40.9 1.0
CB A:SER511 3.7 44.9 1.0
CA A:LYS509 3.7 38.7 1.0
CG A:LYS509 3.7 34.7 1.0
HZ2 A:LYS509 3.8 40.9 1.0
CE A:LYS509 3.8 32.2 1.0
HA2 A:GLY501 3.9 49.0 1.0
CA A:SER511 4.0 34.9 1.0
C A:LYS509 4.0 35.8 1.0
C A:GLY501 4.0 40.2 1.0
OG1 A:THR510 4.0 39.8 1.0
O A:SER511 4.0 43.9 1.0
CB A:PHE505 4.0 37.7 1.0
CD2 A:PHE505 4.1 34.8 1.0
C A:THR510 4.1 48.2 1.0
HB3 A:PHE505 4.2 45.2 1.0
CA A:THR510 4.2 38.2 1.0
C A:ASN502 4.3 38.5 1.0
CD A:LYS509 4.4 41.9 1.0
C A:SER511 4.4 39.6 1.0
CA A:ASN502 4.4 35.3 1.0
HB2 A:LYS509 4.4 39.6 1.0
CG A:PHE505 4.5 33.0 1.0
HG3 A:LYS509 4.6 41.6 1.0
O A:HOH917 4.6 43.1 1.0
HE2 A:LYS509 4.6 38.7 1.0
HB2 A:SER511 4.7 53.8 1.0
CB A:THR510 4.7 40.8 1.0
N A:GLY501 4.8 38.5 1.0
HA A:SER511 4.8 41.9 1.0
HB3 A:ASN502 4.9 42.4 1.0
O A:PHE513 4.9 34.3 1.0
H A:PHE505 4.9 39.1 1.0
O A:LEU500 4.9 36.1 1.0
HD2 A:LYS509 4.9 50.2 1.0
O A:HOH1062 5.0 42.2 1.0

Chlorine binding site 2 out of 4 in 7a5x

Go back to Chlorine Binding Sites List in 7a5x
Chlorine binding site 2 out of 4 in the Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:34.7
occ:1.00
 HZ2 B:LYS509 2.4 40.2 1.0
H B:SER511 2.4 51.5 1.0
HG B:SER511 2.5 53.7 1.0
H B:ASN502 2.6 40.9 1.0
H B:THR510 2.7 58.0 1.0
HA3 B:GLY501 2.9 43.7 1.0
HB3 B:LYS509 3.0 41.6 1.0
NZ B:LYS509 3.1 33.5 1.0
HZ1 B:LYS509 3.1 40.2 1.0
HD2 B:PHE505 3.2 38.1 1.0
HB2 B:PHE505 3.2 39.0 1.0
HG2 B:LYS509 3.2 45.6 1.0
N B:SER511 3.2 42.9 1.0
HA B:LYS509 3.2 50.3 1.0
OG B:SER511 3.2 44.8 1.0
N B:THR510 3.3 48.3 1.0
HE3 B:LYS509 3.4 43.7 1.0
N B:ASN502 3.4 34.1 1.0
O B:ASN502 3.5 35.0 1.0
CB B:LYS509 3.6 34.7 1.0
HB3 B:SER511 3.6 52.9 1.0
HG1 B:THR510 3.7 53.6 1.0
CA B:GLY501 3.7 36.4 1.0
CA B:LYS509 3.7 42.0 1.0
CE B:LYS509 3.8 36.5 1.0
CB B:SER511 3.8 44.1 1.0
HZ3 B:LYS509 3.8 40.2 1.0
CG B:LYS509 3.8 38.0 1.0
CA B:SER511 4.0 35.5 1.0
CD2 B:PHE505 4.0 31.8 1.0
HA2 B:GLY501 4.0 43.7 1.0
O B:SER511 4.0 44.0 1.0
CB B:PHE505 4.0 32.5 1.0
C B:LYS509 4.0 46.5 1.0
OG1 B:THR510 4.0 44.7 1.0
C B:GLY501 4.1 41.9 1.0
HB3 B:PHE505 4.1 39.0 1.0
C B:THR510 4.1 47.4 1.0
CA B:THR510 4.2 46.7 1.0
C B:ASN502 4.3 35.1 1.0
C B:SER511 4.4 36.0 1.0
CD B:LYS509 4.4 39.0 1.0
CG B:PHE505 4.4 34.3 1.0
CA B:ASN502 4.4 38.5 1.0
HB2 B:LYS509 4.5 41.6 1.0
O B:HOH1145 4.5 44.9 1.0
HE2 B:LYS509 4.6 43.7 1.0
HG3 B:LYS509 4.6 45.6 1.0
HB2 B:SER511 4.7 52.9 1.0
CB B:THR510 4.8 48.1 1.0
HA B:SER511 4.8 42.6 1.0
N B:GLY501 4.9 44.2 1.0
O B:PHE513 4.9 32.2 1.0
HB3 B:ASN502 4.9 46.0 1.0
CE2 B:PHE505 4.9 33.2 1.0
H B:PHE505 5.0 38.1 1.0
O B:LEU500 5.0 40.9 1.0
HD2 B:LYS509 5.0 46.7 1.0
HE2 B:PHE505 5.0 39.8 1.0

Chlorine binding site 3 out of 4 in 7a5x

Go back to Chlorine Binding Sites List in 7a5x
Chlorine binding site 3 out of 4 in the Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl804

b:63.2
occ:1.00
 H B:GLY564 2.8 43.5 1.0
HA B:ASN563 3.2 39.4 1.0
HB2 B:ASN563 3.5 32.0 1.0
N B:GLY564 3.6 36.2 1.0
O B:HOH1371 3.8 53.4 1.0
HD2 B:LYS567 3.9 50.8 1.0
CA B:ASN563 4.0 32.9 1.0
CB B:ASN563 4.1 26.7 1.0
C B:ASN563 4.3 35.0 1.0
HB3 B:ASN563 4.3 32.0 1.0
HA2 B:GLY564 4.4 31.9 1.0
CA B:GLY564 4.5 26.6 1.0
O B:GLY564 4.7 31.1 1.0
HB2 B:LYS567 4.8 36.6 1.0
CD B:LYS567 4.8 42.4 1.0
HD3 B:LYS567 4.9 50.8 1.0
HZ2 B:LYS567 4.9 65.2 1.0
C B:GLY564 5.0 26.1 1.0
O B:ARG562 5.0 34.8 1.0

Chlorine binding site 4 out of 4 in 7a5x

Go back to Chlorine Binding Sites List in 7a5x
Chlorine binding site 4 out of 4 in the Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Two Copies of the Catalytic Domain of Nana Sialidase From Streptococcus Pneumoniae Juxtaposed in the P212121 Space Group, in Complex with Dana Derivatized with A Peg Linker on the Glycerol Group. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl805

b:62.2
occ:1.00
 H B:ARG378 2.6 41.9 1.0
HE B:ARG378 3.0 53.9 1.0
HB2 B:ARG378 3.1 37.4 1.0
HH21 B:ARG378 3.2 73.0 1.0
O B:HOH1310 3.3 50.4 1.0
HB3 B:ASP377 3.4 47.9 1.0
N B:ARG378 3.4 34.9 1.0
HA B:ASP377 3.5 38.1 1.0
NE B:ARG378 3.7 44.9 1.0
NH2 B:ARG378 3.9 60.8 1.0
CB B:ARG378 4.0 31.2 1.0
CB B:ASP377 4.0 39.9 1.0
CA B:ASP377 4.1 31.8 1.0
HG3 B:ARG378 4.1 47.5 1.0
OD1 B:ASP377 4.2 33.6 1.0
C B:ASP377 4.3 31.1 1.0
CZ B:ARG378 4.3 51.1 1.0
CA B:ARG378 4.3 42.4 1.0
CG B:ASP377 4.3 39.5 1.0
CG B:ARG378 4.5 39.6 1.0
HH22 B:ARG378 4.6 73.0 1.0
HB3 B:ARG378 4.7 37.4 1.0
CD B:ARG378 4.7 39.0 1.0
O B:HOH1017 4.8 44.9 1.0
O B:ARG378 4.9 35.8 1.0
HB2 B:ASP377 4.9 47.9 1.0
HA B:ARG378 5.0 50.9 1.0

Reference:

C.Assailly, C.Bridot, A.Saumonneau, P.Lottin, B.Roubinet, E.M.Krammer, F.Francois, F.Vena, L.Landemarre, D.Alvarez-Dorta, D.Deniaud, C.Grandjean, C.Tellier, S.Pascual, V.Montembault, L.Fontaine, F.Daligault, J.Bouckaert, S.G.Gouin. Polyvalent Transition-State Analogues of Sialyl Substrates Strongly Inhibit Bacterial Sialidases. Chemistry 2020.
ISSN: ISSN 0947-6539
PubMed: 33150981
DOI: 10.1002/CHEM.202004672
Page generated: Mon Jul 29 18:22:14 2024

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