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Manganese 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:

Chlorine (Cl) 5 atoms
Zinc (Zn) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 5 binding sites of Manganese where determined in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase D463A Mutant From Flavonifractor Plautii, PDB code: 9ayu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 9ayu

Go back to Manganese Binding Sites List in 9ayu
Manganese 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 Manganese with other atoms in the Mn 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:Mn702

b:27.9
occ:1.00
 O A:ASP195 2.2 17.0 1.0
O2 A:EDO705 2.3 20.1 1.0
O A:GLY200 2.3 20.2 1.0
OD1 A:ASP198 2.3 20.0 1.0
OE1 A:GLU245 2.4 17.9 1.0
O A:HOH1030 2.5 13.9 1.0
OE2 A:GLU245 2.5 15.9 1.0
CD A:GLU245 2.8 17.0 1.0
C A:GLY200 3.4 20.8 1.0
CG A:ASP198 3.4 19.7 1.0
C A:ASP195 3.4 17.3 1.0
C2 A:EDO705 3.6 22.6 1.0
OD2 A:ASP198 3.8 19.8 1.0
N A:GLY200 4.2 21.4 1.0
N A:LYS201 4.3 21.5 1.0
CA A:GLY200 4.3 20.8 1.0
N A:LEU196 4.3 18.1 1.0
CA A:LEU196 4.3 18.7 1.0
CG A:GLU245 4.3 16.9 1.0
CA A:LYS201 4.3 21.9 1.0
O A:ASP198 4.4 21.7 1.0
CA A:ASP195 4.4 17.0 1.0
N A:ASP195 4.5 16.1 1.0
C A:ASP198 4.6 21.9 1.0
O1 A:EDO705 4.6 24.6 1.0
N A:ASP198 4.6 19.7 1.0
O A:HOH1175 4.6 34.1 1.0
O A:HOH857 4.7 23.0 1.0
C1 A:EDO705 4.7 23.8 1.0
CB A:ASP198 4.7 20.0 1.0
CB A:ASP195 4.7 18.1 1.0
C A:LEU196 4.7 19.9 1.0
C A:SER199 4.8 23.3 1.0
N A:PHE202 4.8 19.0 1.0
CD A:LYS201 4.8 34.9 1.0
CA A:ASP198 4.8 20.9 1.0

Manganese binding site 2 out of 5 in 9ayu

Go back to Manganese Binding Sites List in 9ayu
Manganese 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 Manganese with other atoms in the Mn 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:Mn702

b:38.7
occ:1.00
 OD1 B:ASP198 2.2 37.7 1.0
O B:ASP195 2.3 24.5 1.0
O B:GLY200 2.4 29.4 1.0
OE1 B:GLU245 2.4 22.6 1.0
O B:HOH974 2.5 29.6 1.0
O B:HOH825 2.5 37.0 1.0
OE2 B:GLU245 2.6 20.0 1.0
CD B:GLU245 2.8 21.4 1.0
CG B:ASP198 3.3 34.0 1.0
C B:GLY200 3.4 32.9 1.0
C B:ASP195 3.5 23.9 1.0
OD2 B:ASP198 3.8 38.8 1.0
O B:HOH1144 4.0 34.0 1.0
N B:GLY200 4.1 37.1 1.0
O B:ASP198 4.2 40.0 1.0
N B:LYS201 4.3 30.7 1.0
CA B:GLY200 4.3 36.2 1.0
CA B:LEU196 4.3 24.9 1.0
CG B:GLU245 4.3 21.4 1.0
N B:LEU196 4.4 23.5 1.0
CA B:LYS201 4.4 28.2 1.0
C B:ASP198 4.4 38.2 1.0
CA B:ASP195 4.5 22.0 1.0
N B:ASP198 4.5 30.8 1.0
CB B:ASP198 4.6 33.3 1.0
N B:ASP195 4.6 20.1 1.0
C B:SER199 4.6 41.0 1.0
CB B:ASP195 4.7 23.7 1.0
C B:LEU196 4.7 26.0 1.0
CA B:ASP198 4.7 34.1 1.0
N B:PHE202 4.8 22.3 1.0
O B:HOH969 4.9 27.2 1.0
N B:SER199 4.9 41.3 1.0
O B:HOH1406 4.9 36.2 1.0
O B:SER199 5.0 40.1 1.0
CD B:LYS201 5.0 34.9 1.0

Manganese binding site 3 out of 5 in 9ayu

Go back to Manganese Binding Sites List in 9ayu
Manganese 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 Manganese with other atoms in the Mn 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:Mn702

b:32.9
occ:1.00
 O C:ASP195 2.2 23.9 1.0
O C:GLY200 2.3 24.6 1.0
OD1 C:ASP198 2.3 22.9 1.0
O1 C:EDO705 2.4 27.9 1.0
O C:HOH1012 2.4 22.3 1.0
OE1 C:GLU245 2.4 23.0 1.0
OE2 C:GLU245 2.6 21.7 1.0
CD C:GLU245 2.8 22.3 1.0
C C:GLY200 3.4 25.7 1.0
CG C:ASP198 3.4 23.2 1.0
C C:ASP195 3.5 23.4 1.0
C1 C:EDO705 3.5 31.9 1.0
OD2 C:ASP198 3.8 21.8 1.0
N C:GLY200 4.2 26.2 1.0
N C:LYS201 4.3 25.8 1.0
CA C:GLY200 4.3 25.8 1.0
CA C:LEU196 4.3 24.1 1.0
N C:LEU196 4.3 23.2 1.0
CA C:LYS201 4.3 26.9 1.0
O C:ASP198 4.4 26.0 1.0
CG C:GLU245 4.4 22.2 1.0
CA C:ASP195 4.4 23.2 1.0
N C:ASP195 4.5 21.3 1.0
C C:ASP198 4.5 26.2 1.0
N C:ASP198 4.5 24.6 1.0
O2 C:EDO705 4.5 30.9 1.0
C2 C:EDO705 4.6 31.3 1.0
CB C:ASP198 4.7 24.0 1.0
C C:SER199 4.7 27.4 1.0
CB C:ASP195 4.7 23.7 1.0
C C:LEU196 4.7 24.6 1.0
O C:HOH873 4.8 20.9 1.0
CD C:LYS201 4.8 39.1 1.0
CA C:ASP198 4.8 25.2 1.0
N C:PHE202 4.8 22.8 1.0
O C:SER199 5.0 28.2 1.0

Manganese binding site 4 out of 5 in 9ayu

Go back to Manganese Binding Sites List in 9ayu
Manganese 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 Manganese with other atoms in the Mn 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:Mn702

b:32.7
occ:1.00
 O D:ASP195 2.3 26.0 1.0
O D:GLY200 2.3 26.3 1.0
OD1 D:ASP198 2.4 25.9 1.0
O1 D:EDO706 2.4 28.3 1.0
O D:HOH1097 2.4 19.9 1.0
OE1 D:GLU245 2.4 25.9 1.0
OE2 D:GLU245 2.6 24.9 1.0
CD D:GLU245 2.8 25.6 1.0
C D:GLY200 3.4 26.0 1.0
CG D:ASP198 3.4 25.2 1.0
C D:ASP195 3.5 25.5 1.0
C1 D:EDO706 3.8 33.7 1.0
OD2 D:ASP198 3.8 24.4 1.0
N D:GLY200 4.2 26.7 1.0
N D:LYS201 4.2 26.3 1.0
CA D:GLY200 4.2 26.2 1.0
CA D:LYS201 4.3 27.2 1.0
CA D:LEU196 4.3 27.1 1.0
N D:LEU196 4.3 26.2 1.0
CG D:GLU245 4.3 25.4 1.0
C2 D:EDO706 4.4 35.6 1.0
O D:ASP198 4.4 27.0 1.0
CA D:ASP195 4.5 25.5 1.0
N D:ASP195 4.5 24.6 1.0
N D:ASP198 4.6 26.6 1.0
C D:ASP198 4.6 26.9 1.0
CB D:ASP198 4.7 25.6 1.0
C D:LEU196 4.7 27.5 1.0
O2 D:EDO706 4.7 36.3 1.0
C D:SER199 4.7 27.4 1.0
CB D:ASP195 4.8 26.1 1.0
CD D:LYS201 4.8 37.6 1.0
N D:PHE202 4.8 24.1 1.0
O D:HOH890 4.8 23.2 1.0
CA D:ASP198 4.9 26.3 1.0

Manganese binding site 5 out of 5 in 9ayu

Go back to Manganese Binding Sites List in 9ayu
Manganese 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 Manganese with other atoms in the Mn 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:Mn702

b:31.6
occ:1.00
 O E:GLY200 2.3 24.8 1.0
O E:ASP195 2.3 22.2 1.0
O2 E:EDO705 2.4 32.7 1.0
OD1 E:ASP198 2.4 22.8 1.0
OE1 E:GLU245 2.4 21.8 1.0
O E:HOH1102 2.4 18.1 1.0
OE2 E:GLU245 2.5 20.5 1.0
CD E:GLU245 2.8 21.4 1.0
C E:GLY200 3.4 25.7 1.0
CG E:ASP198 3.4 22.5 1.0
C E:ASP195 3.5 22.0 1.0
C2 E:EDO705 3.7 30.7 1.0
OD2 E:ASP198 3.9 21.1 1.0
N E:GLY200 4.2 25.9 1.0
N E:LYS201 4.2 26.5 1.0
CA E:GLY200 4.3 25.9 1.0
CG E:GLU245 4.3 22.1 1.0
CA E:LYS201 4.3 27.0 1.0
CA E:LEU196 4.3 23.9 1.0
O E:ASP198 4.4 27.9 1.0
N E:LEU196 4.4 22.5 1.0
CA E:ASP195 4.5 21.1 1.0
C E:ASP198 4.6 27.0 1.0
N E:ASP195 4.6 20.1 1.0
N E:ASP198 4.6 25.1 1.0
O1 E:EDO705 4.6 26.5 1.0
CB E:ASP198 4.7 23.5 1.0
C E:SER199 4.7 27.9 1.0
C1 E:EDO705 4.7 31.1 1.0
C E:LEU196 4.8 25.0 1.0
CB E:ASP195 4.8 22.0 1.0
CD E:LYS201 4.8 40.0 1.0
N E:PHE202 4.8 22.9 1.0
CA E:ASP198 4.9 25.2 1.0
O E:HOH879 4.9 22.7 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 22:55:43 2025

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