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Chlorine in PDB 9ay8: Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii

Protein crystallography data

The structure of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii, PDB code: 9ay8 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) 39.44 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.685, 164.568, 131.645, 90, 90.3, 90
R / Rfree (%) 16.8 / 19.3

Other elements in 9ay8:

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

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii (pdb code 9ay8). 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 From Flavonifractor Plautii, PDB code: 9ay8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 9ay8

Go back to Chlorine Binding Sites List in 9ay8
Chlorine binding site 1 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase 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 From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:25.2
occ:1.00
 N A:THR190 3.2 21.0 1.0
NH2 A:ARG541 3.2 23.1 1.0
NE A:ARG542 3.4 22.0 1.0
N A:LEU191 3.5 23.8 1.0
CA A:GLN538 3.6 23.3 1.0
CB A:THR190 3.7 23.1 1.0
CG A:GLN538 3.7 24.6 1.0
CA A:THR190 3.9 21.8 1.0
CG A:ARG542 3.9 22.4 1.0
CD2 A:LEU191 3.9 25.4 1.0
OG1 A:THR190 4.0 21.9 1.0
NH2 A:ARG542 4.0 24.3 1.0
NE A:ARG541 4.0 22.3 1.0
CZ A:ARG541 4.0 23.8 1.0
CB A:GLN538 4.0 24.0 1.0
C A:ASP189 4.0 21.5 1.0
CA A:ASP189 4.0 23.2 1.0
CB A:ASP189 4.1 24.0 1.0
CZ A:ARG542 4.1 25.2 1.0
O A:GLN538 4.1 23.6 1.0
C A:THR190 4.2 22.3 1.0
CD A:ARG542 4.2 21.8 1.0
CB A:LEU191 4.3 25.1 1.0
C A:GLN538 4.4 23.1 1.0
CA A:LEU191 4.4 24.0 1.0
O A:ASP537 4.5 24.2 1.0
N A:GLN538 4.5 24.2 1.0
CG A:ASP189 4.6 24.7 1.0
CD A:GLN538 4.7 27.4 1.0
CG A:LEU191 4.7 25.2 1.0
CB A:ARG541 4.7 22.9 1.0
O A:LEU191 4.7 25.3 1.0
OD1 A:ASP189 4.8 22.6 1.0
C A:ASP537 4.9 25.4 1.0
CG2 A:THR190 5.0 21.6 1.0

Chlorine binding site 2 out of 5 in 9ay8

Go back to Chlorine Binding Sites List in 9ay8
Chlorine binding site 2 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase 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 From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl702

b:26.0
occ:1.00
 N B:THR190 3.1 24.9 1.0
NH2 B:ARG541 3.3 25.1 1.0
NE B:ARG542 3.4 23.1 1.0
N B:LEU191 3.5 24.4 1.0
CA B:GLN538 3.6 25.8 1.0
CB B:THR190 3.6 28.0 1.0
CG B:GLN538 3.7 27.0 1.0
CA B:THR190 3.8 26.4 1.0
NH2 B:ARG542 3.9 23.9 1.0
OG1 B:THR190 3.9 24.6 1.0
CB B:GLN538 3.9 27.0 1.0
NE B:ARG541 4.0 26.3 1.0
CG B:ARG542 4.0 22.5 1.0
C B:ASP189 4.0 25.7 1.0
CA B:ASP189 4.0 23.9 1.0
CZ B:ARG541 4.0 25.0 1.0
CD2 B:LEU191 4.0 26.8 1.0
CB B:ASP189 4.1 22.5 1.0
O B:GLN538 4.1 24.3 1.0
CZ B:ARG542 4.1 24.3 1.0
C B:THR190 4.2 24.8 1.0
CD B:ARG542 4.2 22.6 1.0
C B:GLN538 4.4 25.6 1.0
CB B:LEU191 4.4 25.8 1.0
CA B:LEU191 4.5 25.8 1.0
N B:GLN538 4.6 26.1 1.0
O B:ASP537 4.6 25.2 1.0
CG B:ASP189 4.6 24.6 1.0
CD B:GLN538 4.6 24.9 1.0
CB B:ARG541 4.7 22.2 1.0
CG B:LEU191 4.8 25.5 1.0
O B:LEU191 4.8 24.2 1.0
OD1 B:ASP189 4.9 24.0 1.0
C B:ASP537 4.9 25.5 1.0
CG2 B:THR190 5.0 24.6 1.0

Chlorine binding site 3 out of 5 in 9ay8

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Chlorine binding site 3 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase 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 From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl702

b:30.6
occ:1.00
 N C:THR190 3.2 29.3 1.0
NH2 C:ARG541 3.3 30.5 1.0
NE C:ARG542 3.4 28.0 1.0
N C:LEU191 3.5 30.1 1.0
CA C:GLN538 3.6 29.2 1.0
CB C:THR190 3.7 29.5 1.0
CG C:GLN538 3.7 30.0 1.0
CA C:THR190 3.8 29.4 1.0
OG1 C:THR190 3.9 28.4 1.0
NH2 C:ARG542 4.0 31.5 1.0
CB C:GLN538 4.0 29.1 1.0
NE C:ARG541 4.0 31.2 1.0
CD2 C:LEU191 4.0 31.0 1.0
CG C:ARG542 4.0 29.1 1.0
CZ C:ARG541 4.0 31.8 1.0
C C:ASP189 4.0 28.7 1.0
CA C:ASP189 4.0 28.9 1.0
CB C:ASP189 4.1 28.7 1.0
CZ C:ARG542 4.1 28.5 1.0
O C:GLN538 4.1 30.1 1.0
C C:THR190 4.2 30.0 1.0
CD C:ARG542 4.2 32.0 1.0
CB C:LEU191 4.3 30.1 1.0
C C:GLN538 4.4 30.1 1.0
CA C:LEU191 4.4 30.2 1.0
CG C:ASP189 4.5 29.2 1.0
N C:GLN538 4.6 30.7 1.0
O C:ASP537 4.6 32.4 1.0
CD C:GLN538 4.6 29.8 1.0
O C:LEU191 4.7 31.9 1.0
CG C:LEU191 4.7 30.7 1.0
CB C:ARG541 4.8 31.2 1.0
OD1 C:ASP189 4.8 28.9 1.0
C C:ASP537 4.9 30.4 1.0
NE2 C:GLN538 5.0 32.8 1.0

Chlorine binding site 4 out of 5 in 9ay8

Go back to Chlorine Binding Sites List in 9ay8
Chlorine binding site 4 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase 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 From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl702

b:29.9
occ:1.00
 N D:THR190 3.2 27.7 1.0
NH2 D:ARG541 3.2 31.5 1.0
NE D:ARG542 3.4 27.0 1.0
N D:LEU191 3.5 30.1 1.0
CA D:GLN538 3.6 30.2 1.0
CG D:GLN538 3.7 29.1 1.0
CB D:THR190 3.7 27.5 1.0
CA D:THR190 3.9 28.1 1.0
NE D:ARG541 3.9 31.8 1.0
CZ D:ARG541 3.9 32.5 1.0
CB D:GLN538 4.0 30.7 1.0
OG1 D:THR190 4.0 26.2 1.0
C D:ASP189 4.0 29.3 1.0
NH2 D:ARG542 4.0 29.4 1.0
CA D:ASP189 4.0 30.3 1.0
CD2 D:LEU191 4.0 28.2 1.0
CB D:ASP189 4.0 30.1 1.0
CG D:ARG542 4.1 27.1 1.0
O D:GLN538 4.1 31.2 1.0
CZ D:ARG542 4.2 30.4 1.0
C D:THR190 4.2 28.8 1.0
CB D:LEU191 4.2 28.6 1.0
CD D:ARG542 4.3 27.7 1.0
C D:GLN538 4.4 30.6 1.0
CA D:LEU191 4.4 28.1 1.0
CG D:ASP189 4.5 30.7 1.0
N D:GLN538 4.5 30.2 1.0
O D:ASP537 4.6 28.5 1.0
CD D:GLN538 4.7 28.4 1.0
O D:LEU191 4.7 33.4 1.0
CB D:ARG541 4.7 31.1 1.0
CG D:LEU191 4.7 29.0 1.0
OD1 D:ASP189 4.8 29.4 1.0
C D:ASP537 4.9 33.3 1.0

Chlorine binding site 5 out of 5 in 9ay8

Go back to Chlorine Binding Sites List in 9ay8
Chlorine binding site 5 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase 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 From Flavonifractor Plautii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl702

b:26.5
occ:1.00
 N E:THR190 3.2 25.8 1.0
NH2 E:ARG541 3.2 27.9 1.0
N E:LEU191 3.4 26.7 1.0
NE E:ARG542 3.5 25.3 1.0
CB E:THR190 3.6 25.1 1.0
CA E:GLN538 3.6 28.3 1.0
CG E:GLN538 3.7 29.9 1.0
CA E:THR190 3.8 25.9 1.0
OG1 E:THR190 3.9 22.3 1.0
NE E:ARG541 3.9 28.0 1.0
CZ E:ARG541 3.9 29.8 1.0
CD2 E:LEU191 4.0 29.1 1.0
CB E:GLN538 4.0 29.8 1.0
NH2 E:ARG542 4.0 26.2 1.0
C E:ASP189 4.0 28.4 1.0
CA E:ASP189 4.0 27.8 1.0
CB E:ASP189 4.0 28.0 1.0
CG E:ARG542 4.1 27.9 1.0
O E:GLN538 4.1 26.1 1.0
C E:THR190 4.2 27.2 1.0
CZ E:ARG542 4.2 25.0 1.0
CB E:LEU191 4.3 28.1 1.0
CD E:ARG542 4.3 26.9 1.0
C E:GLN538 4.4 28.5 1.0
CA E:LEU191 4.4 27.7 1.0
O E:ASP537 4.5 26.4 1.0
CG E:ASP189 4.5 27.0 1.0
N E:GLN538 4.5 29.6 1.0
CB E:ARG541 4.7 25.7 1.0
O E:LEU191 4.7 27.6 1.0
CG E:LEU191 4.7 29.6 1.0
CD E:GLN538 4.7 28.2 1.0
OD1 E:ASP189 4.8 27.7 1.0
C E:ASP537 4.9 28.3 1.0
CG2 E:THR190 5.0 24.4 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: Sun Jul 13 15:59:23 2025

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