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Chlorine in PDB 9ayu: Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii

Protein crystallography data

The structure of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii, PDB code: 9ayu was solved by L.J.Worrall, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.326, 164.29, 131.763, 90, 90.2, 90
R / Rfree (%) 16.3 / 18.6

Other elements in 9ayu:

The structure of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii also contains other interesting chemical elements:

Zinc (Zn) 5 atoms
Manganese (Mn) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii (pdb code 9ayu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii, PDB code: 9ayu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 9ayu

Go back to Chlorine Binding Sites List in 9ayu
Chlorine binding site 1 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:21.5
occ:1.00
 O A:HOH1152 1.7 26.6 1.0
NH2 A:ARG541 3.2 14.3 1.0
N A:LEU191 3.4 14.5 1.0
N A:THR190 3.4 13.7 1.0
NE A:ARG541 3.7 13.1 1.0
CA A:GLN538 3.8 14.0 1.0
CZ A:ARG541 3.8 13.8 1.0
CB A:THR190 3.8 12.3 1.0
CD2 A:LEU191 3.9 20.9 1.0
NE A:ARG542 4.0 15.1 1.0
CB A:LEU191 4.0 17.0 1.0
CA A:THR190 4.1 12.7 1.0
CG A:ARG542 4.1 13.7 1.0
O A:GLN538 4.1 12.8 1.0
CG A:GLN538 4.2 14.5 1.0
CB A:ASP189 4.2 13.8 1.0
CB A:ARG541 4.2 13.0 1.0
OG1 A:THR190 4.2 11.8 1.0
C A:THR190 4.2 13.4 1.0
C A:ASP189 4.3 14.3 1.0
O A:ASP537 4.3 13.0 1.0
CB A:GLN538 4.3 14.1 1.0
CA A:LEU191 4.3 15.6 1.0
CA A:ASP189 4.3 13.9 1.0
C A:GLN538 4.4 14.0 1.0
CG A:LEU191 4.5 18.7 1.0
N A:GLN538 4.6 14.6 1.0
CD A:ARG542 4.6 14.4 1.0
O A:LEU191 4.7 14.4 1.0
NH2 A:ARG542 4.7 19.0 1.0
CG A:ASP189 4.7 14.3 1.0
CZ A:ARG542 4.8 16.2 1.0
C A:ASP537 4.8 14.0 1.0
CD A:ARG541 4.8 13.4 1.0
N A:ARG542 4.9 13.0 1.0
NH1 A:ARG541 5.0 13.6 1.0

Chlorine binding site 2 out of 5 in 9ayu

Go back to Chlorine Binding Sites List in 9ayu
Chlorine binding site 2 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:22.4
occ:1.00
 NH2 B:ARG541 3.3 13.8 1.0
N B:THR190 3.3 12.9 1.0
N B:LEU191 3.5 13.7 1.0
CA B:GLN538 3.7 12.3 1.0
CB B:THR190 3.7 12.3 1.0
NE B:ARG541 3.8 13.7 1.0
NE B:ARG542 3.9 15.1 1.0
CZ B:ARG541 3.9 14.3 1.0
CA B:THR190 4.0 13.1 1.0
CG B:ARG542 4.0 13.6 1.0
O B:GLN538 4.0 12.0 1.0
CG B:GLN538 4.1 13.1 1.0
OG1 B:THR190 4.1 12.1 1.0
CD2 B:LEU191 4.1 17.5 1.0
CB B:ASP189 4.2 13.7 1.0
CB B:GLN538 4.2 12.6 1.0
C B:ASP189 4.2 13.3 1.0
CA B:ASP189 4.2 13.3 1.0
CB B:LEU191 4.2 15.5 1.0
C B:THR190 4.3 13.3 1.0
C B:GLN538 4.4 12.3 1.0
O B:ASP537 4.4 12.1 1.0
CB B:ARG541 4.4 12.6 1.0
CA B:LEU191 4.5 14.7 1.0
NH2 B:ARG542 4.5 17.2 1.0
CD B:ARG542 4.5 13.4 1.0
N B:GLN538 4.6 12.9 1.0
CZ B:ARG542 4.6 15.8 1.0
CG B:ASP189 4.7 13.9 1.0
CG B:LEU191 4.7 17.2 1.0
O B:LEU191 4.8 14.0 1.0
C B:ASP537 4.8 12.7 1.0
N B:ARG542 4.9 12.5 1.0
CD B:ARG541 4.9 14.2 1.0
CD B:GLN538 5.0 13.0 1.0

Chlorine binding site 3 out of 5 in 9ayu

Go back to Chlorine Binding Sites List in 9ayu
Chlorine binding site 3 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl703

b:25.2
occ:1.00
 NH2 C:ARG541 3.3 17.5 1.0
N C:THR190 3.4 15.8 1.0
N C:LEU191 3.5 16.2 1.0
CA C:GLN538 3.7 16.8 1.0
NE C:ARG541 3.8 18.2 1.0
CB C:THR190 3.8 16.8 1.0
CZ C:ARG541 3.9 17.9 1.0
NE C:ARG542 4.0 18.0 1.0
CA C:THR190 4.0 16.2 1.0
CD2 C:LEU191 4.0 21.2 1.0
CG C:ARG542 4.1 16.6 1.0
O C:GLN538 4.1 17.9 1.0
CG C:GLN538 4.1 16.1 1.0
CB C:ASP189 4.1 15.9 1.0
CB C:LEU191 4.1 18.0 1.0
OG1 C:THR190 4.2 16.3 1.0
C C:ASP189 4.2 15.5 1.0
CA C:ASP189 4.2 16.0 1.0
CB C:GLN538 4.2 16.1 1.0
C C:THR190 4.2 16.4 1.0
O C:ASP537 4.4 18.4 1.0
CB C:ARG541 4.4 17.8 1.0
CA C:LEU191 4.4 17.1 1.0
C C:GLN538 4.4 17.2 1.0
N C:GLN538 4.6 17.6 1.0
CD C:ARG542 4.6 17.2 1.0
NH2 C:ARG542 4.6 18.4 1.0
CG C:ASP189 4.7 16.4 1.0
CG C:LEU191 4.7 20.0 1.0
O C:LEU191 4.7 17.3 1.0
CZ C:ARG542 4.7 17.9 1.0
C C:ASP537 4.8 17.9 1.0
CD C:ARG541 4.9 18.7 1.0
N C:ARG542 5.0 16.6 1.0
OD1 C:ASP189 5.0 16.8 1.0
CD C:GLN538 5.0 15.9 1.0
NH1 C:ARG541 5.0 18.7 1.0

Chlorine binding site 4 out of 5 in 9ayu

Go back to Chlorine Binding Sites List in 9ayu
Chlorine binding site 4 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl703

b:25.8
occ:1.00
 N D:THR190 3.3 18.2 1.0
NH2 D:ARG541 3.3 19.2 1.0
N D:LEU191 3.5 19.4 1.0
CA D:GLN538 3.7 18.9 1.0
CB D:THR190 3.7 17.6 1.0
NE D:ARG542 3.8 19.1 1.0
NE D:ARG541 3.9 19.3 1.0
CA D:THR190 3.9 18.2 1.0
CZ D:ARG541 4.0 19.4 1.0
CG D:ARG542 4.0 18.9 1.0
CD2 D:LEU191 4.0 24.8 1.0
OG1 D:THR190 4.0 16.6 1.0
O D:GLN538 4.0 18.1 1.0
CG D:GLN538 4.1 18.5 1.0
CB D:ASP189 4.1 19.8 1.0
C D:ASP189 4.1 18.7 1.0
CA D:ASP189 4.2 19.6 1.0
CB D:GLN538 4.2 18.7 1.0
CB D:LEU191 4.2 22.0 1.0
C D:THR190 4.2 18.9 1.0
C D:GLN538 4.4 18.7 1.0
CA D:LEU191 4.4 20.5 1.0
O D:ASP537 4.4 18.7 1.0
NH2 D:ARG542 4.5 21.1 1.0
CB D:ARG541 4.5 19.0 1.0
CD D:ARG542 4.5 19.3 1.0
CZ D:ARG542 4.6 19.7 1.0
N D:GLN538 4.6 19.8 1.0
CG D:ASP189 4.6 20.1 1.0
CG D:LEU191 4.7 23.9 1.0
O D:LEU191 4.7 21.4 1.0
C D:ASP537 4.9 19.6 1.0
OD1 D:ASP189 4.9 19.4 1.0
CD D:GLN538 4.9 17.9 1.0
N D:ARG542 5.0 18.4 1.0

Chlorine binding site 5 out of 5 in 9ayu

Go back to Chlorine Binding Sites List in 9ayu
Chlorine binding site 5 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl703

b:22.9
occ:1.00
 NH2 E:ARG541 3.2 17.1 1.0
N E:THR190 3.3 14.4 1.0
N E:LEU191 3.5 15.2 1.0
CA E:GLN538 3.6 13.9 1.0
CB E:THR190 3.7 14.6 1.0
NE E:ARG542 3.8 16.4 1.0
NE E:ARG541 3.9 16.3 1.0
CZ E:ARG541 4.0 17.2 1.0
CA E:THR190 4.0 14.4 1.0
CG E:GLN538 4.0 14.3 1.0
O E:GLN538 4.0 13.4 1.0
CG E:ARG542 4.0 14.9 1.0
OG1 E:THR190 4.1 14.1 1.0
CB E:GLN538 4.1 14.3 1.0
CD2 E:LEU191 4.1 23.3 1.0
CB E:ASP189 4.1 15.0 1.0
C E:ASP189 4.2 14.7 1.0
CA E:ASP189 4.2 14.7 1.0
CB E:LEU191 4.3 17.2 1.0
C E:THR190 4.3 15.3 1.0
C E:GLN538 4.4 14.2 1.0
O E:ASP537 4.4 13.4 1.0
CB E:ARG541 4.5 14.9 1.0
CA E:LEU191 4.5 16.5 1.0
NH2 E:ARG542 4.5 18.8 1.0
CD E:ARG542 4.5 15.8 1.0
N E:GLN538 4.5 14.5 1.0
CZ E:ARG542 4.6 16.9 1.0
CG E:ASP189 4.6 15.2 1.0
O E:LEU191 4.8 17.2 1.0
CG E:LEU191 4.8 21.6 1.0
C E:ASP537 4.8 14.2 1.0
OD1 E:ASP189 4.9 15.2 1.0
CD E:GLN538 4.9 14.3 1.0
N E:ARG542 5.0 14.3 1.0

Reference:

Y.Tian, L.J.Worrall, L.Sim, F.Liu, S.A.Nasseri, P.Rahfeld, W.Mu, J.N.Kizhakkedathu, N.C.J.Strynadka, S.G.Withers. Cobalt As A Cofactor For Alpha-Galactosaminidase-Catalyzed Cleavage of Blood Group Antigens Acs Catalysis 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C03643
Page generated: Sat Feb 8 17:28:11 2025

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