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Manganese 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:

Cobalt (Co) 5 atoms
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 From Flavonifractor Plautii (pdb code 9ay8). 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 From Flavonifractor Plautii, PDB code: 9ay8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 9ay8

Go back to Manganese Binding Sites List in 9ay8
Manganese 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 Manganese with other atoms in the Mn 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:Mn704

b:36.9
occ:1.00
 O A:GLY200 2.3 30.5 1.0
O A:ASP195 2.3 25.9 1.0
OD1 A:ASP198 2.3 26.9 1.0
OE1 A:GLU245 2.4 31.3 1.0
OE2 A:GLU245 2.5 27.2 1.0
O A:HOH1184 2.6 24.4 1.0
O A:HOH916 2.6 27.8 1.0
CD A:GLU245 2.8 27.2 1.0
C A:GLY200 3.3 31.3 1.0
CG A:ASP198 3.3 27.7 1.0
C A:ASP195 3.5 26.8 1.0
OD2 A:ASP198 3.7 27.5 1.0
N A:LYS201 4.2 30.1 1.0
N A:GLY200 4.2 29.3 1.0
CA A:GLY200 4.2 28.8 1.0
CA A:LYS201 4.3 30.7 1.0
CA A:LEU196 4.3 29.0 1.0
CG A:GLU245 4.3 26.8 1.0
N A:LEU196 4.4 26.8 1.0
O A:ASP198 4.5 31.7 1.0
CA A:ASP195 4.5 26.3 1.0
N A:ASP198 4.6 28.6 1.0
O A:HOH1404 4.6 32.8 1.0
N A:ASP195 4.6 26.2 1.0
C A:ASP198 4.6 31.3 1.0
CB A:ASP198 4.6 27.3 1.0
O A:HOH1386 4.7 46.7 1.0
N A:PHE202 4.7 27.7 1.0
CB A:ASP195 4.7 29.3 1.0
C A:SER199 4.7 30.9 1.0
C A:LEU196 4.7 29.1 1.0
O A:HOH974 4.8 31.9 1.0
CA A:ASP198 4.8 29.1 1.0
CD A:LYS201 4.9 43.5 1.0

Manganese binding site 2 out of 5 in 9ay8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn704

b:41.9
occ:1.00
 O B:ASP195 2.3 32.9 1.0
O B:GLY200 2.3 40.4 1.0
OD1 B:ASP198 2.3 40.3 1.0
OE1 B:GLU245 2.4 32.2 1.0
OE2 B:GLU245 2.4 32.3 1.0
O B:HOH895 2.5 28.3 1.0
O B:HOH1187 2.5 32.7 1.0
CD B:GLU245 2.7 32.5 1.0
C B:GLY200 3.4 43.0 1.0
CG B:ASP198 3.4 38.1 1.0
C B:ASP195 3.5 32.1 1.0
OD2 B:ASP198 3.8 38.0 1.0
N B:LYS201 4.2 41.0 1.0
CA B:LYS201 4.2 39.7 1.0
CG B:GLU245 4.2 32.4 1.0
N B:GLY200 4.3 46.7 1.0
CA B:LEU196 4.3 34.2 1.0
N B:LEU196 4.3 32.7 1.0
O B:HOH1225 4.3 39.3 1.0
CA B:GLY200 4.4 47.6 1.0
CA B:ASP195 4.5 30.9 1.0
O B:ASP198 4.5 45.2 1.0
N B:ASP195 4.6 29.4 1.0
N B:PHE202 4.6 33.6 1.0
O B:HOH1424 4.6 42.0 1.0
N B:ASP198 4.6 39.6 1.0
C B:ASP198 4.7 43.8 1.0
CB B:ASP195 4.7 34.5 1.0
CB B:ASP198 4.7 39.0 1.0
C B:LEU196 4.7 36.1 1.0
O B:HOH864 4.8 32.8 1.0
C B:SER199 4.9 47.9 1.0
CA B:ASP198 4.9 40.4 1.0
C B:LYS201 4.9 36.1 1.0

Manganese binding site 3 out of 5 in 9ay8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn704

b:45.5
occ:1.00
 O C:ASP195 2.3 37.4 1.0
O C:GLY200 2.3 38.4 1.0
OD1 C:ASP198 2.3 35.5 1.0
O C:HOH1029 2.4 34.8 1.0
OE1 C:GLU245 2.4 38.4 1.0
OE2 C:GLU245 2.6 36.0 1.0
O C:HOH977 2.6 33.6 1.0
CD C:GLU245 2.8 36.3 1.0
C C:GLY200 3.3 38.2 1.0
CG C:ASP198 3.4 35.9 1.0
C C:ASP195 3.5 36.8 1.0
OD2 C:ASP198 3.7 34.2 1.0
N C:LYS201 4.2 37.5 1.0
N C:GLY200 4.2 39.5 1.0
O C:HOH1203 4.3 48.5 1.0
CA C:GLY200 4.3 39.3 1.0
CA C:LYS201 4.3 37.5 1.0
CA C:LEU196 4.3 38.4 1.0
N C:LEU196 4.3 37.7 1.0
CG C:GLU245 4.4 36.3 1.0
O C:HOH1224 4.4 38.4 1.0
O C:ASP198 4.4 40.2 1.0
CA C:ASP195 4.4 36.9 1.0
N C:ASP195 4.5 35.6 1.0
N C:ASP198 4.6 38.4 1.0
C C:ASP198 4.6 39.7 1.0
CB C:ASP198 4.7 37.3 1.0
CB C:ASP195 4.7 36.8 1.0
O C:HOH861 4.7 37.2 1.0
N C:PHE202 4.7 35.1 1.0
C C:SER199 4.7 41.5 1.0
C C:LEU196 4.8 39.3 1.0
CA C:ASP198 4.8 38.2 1.0
CD C:LYS201 5.0 48.0 1.0

Manganese binding site 4 out of 5 in 9ay8

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Manganese 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 Manganese with other atoms in the Mn 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:Mn704

b:43.2
occ:1.00
 O D:GLY200 2.3 40.2 1.0
O D:ASP195 2.3 36.8 1.0
OD1 D:ASP198 2.3 36.5 1.0
OE1 D:GLU245 2.4 36.0 1.0
O D:HOH1092 2.5 34.3 1.0
OE2 D:GLU245 2.6 34.0 1.0
O D:HOH1140 2.7 33.5 1.0
CD D:GLU245 2.8 37.8 1.0
C D:GLY200 3.3 41.0 1.0
CG D:ASP198 3.4 36.1 1.0
C D:ASP195 3.5 37.4 1.0
OD2 D:ASP198 3.8 36.8 1.0
N D:LYS201 4.2 39.6 1.0
N D:GLY200 4.2 41.8 1.0
CA D:LYS201 4.3 39.2 1.0
CA D:GLY200 4.3 40.5 1.0
CA D:LEU196 4.3 37.9 1.0
N D:LEU196 4.3 35.9 1.0
CG D:GLU245 4.4 37.1 1.0
O D:ASP198 4.4 38.8 1.0
CA D:ASP195 4.5 36.5 1.0
O D:HOH1308 4.5 42.5 1.0
N D:ASP195 4.5 35.3 1.0
N D:ASP198 4.6 36.9 1.0
C D:ASP198 4.6 38.6 1.0
CB D:ASP198 4.7 36.3 1.0
N D:PHE202 4.7 33.8 1.0
C D:SER199 4.7 40.8 1.0
C D:LEU196 4.7 38.8 1.0
CB D:ASP195 4.8 37.7 1.0
CA D:ASP198 4.8 37.0 1.0
O D:HOH901 4.8 34.2 1.0
CD D:LYS201 4.9 52.5 1.0

Manganese binding site 5 out of 5 in 9ay8

Go back to Manganese Binding Sites List in 9ay8
Manganese 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 Manganese with other atoms in the Mn 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:Mn704

b:44.0
occ:1.00
 O E:GLY200 2.3 37.3 1.0
O E:ASP195 2.3 36.0 1.0
OE1 E:GLU245 2.4 34.0 1.0
OD1 E:ASP198 2.4 34.1 1.0
OE2 E:GLU245 2.5 33.6 1.0
O E:HOH1061 2.6 29.4 1.0
O E:HOH1138 2.7 34.5 1.0
CD E:GLU245 2.8 33.8 1.0
C E:GLY200 3.3 37.1 1.0
CG E:ASP198 3.4 34.2 1.0
C E:ASP195 3.5 35.9 1.0
OD2 E:ASP198 3.8 31.2 1.0
N E:LYS201 4.2 38.3 1.0
N E:GLY200 4.2 39.1 1.0
CA E:LYS201 4.3 36.6 1.0
CA E:GLY200 4.3 38.3 1.0
CG E:GLU245 4.3 34.8 1.0
CA E:LEU196 4.3 39.4 1.0
N E:LEU196 4.4 36.5 1.0
O E:ASP198 4.5 38.0 1.0
CA E:ASP195 4.5 34.4 1.0
N E:ASP195 4.6 34.2 1.0
O E:HOH871 4.6 39.1 1.0
C E:ASP198 4.6 40.1 1.0
N E:ASP198 4.6 38.0 1.0
O E:HOH1296 4.6 35.1 1.0
O E:HOH1256 4.7 52.8 1.0
C E:SER199 4.7 41.0 1.0
CB E:ASP198 4.7 35.3 1.0
N E:PHE202 4.7 33.3 1.0
C E:LEU196 4.8 39.3 1.0
CB E:ASP195 4.8 35.4 1.0
CA E:ASP198 4.9 38.2 1.0
CD E:LYS201 4.9 49.8 1.0
O E:SER199 5.0 44.5 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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