Atomistry » Chlorine » PDB 9auw-9bni » 9ayu
Atomistry »
  Chlorine »
    PDB 9auw-9bni »
      9ayu »

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: Sun Jul 13 16:00:15 2025

Last articles

Na in 3DDK
Na in 3DFH
Na in 3DEB
Na in 3DAV
Na in 3DDR
Na in 3DBO
Na in 3DC7
Na in 3D97
Na in 3DA9
Na in 3D9R
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy