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

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 5 in 9ay8

Go back to Cobalt Binding Sites List in 9ay8
Cobalt 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 Cobalt with other atoms in the Co 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:Co703

b:55.7
occ:1.00
 SG A:CYS513 1.7 44.8 1.0
SG A:CYS511 2.1 31.9 1.0
OD1 A:ASP463 2.3 33.0 1.0
O A:HOH1338 2.8 49.9 1.0
CB A:CYS511 2.9 28.9 1.0
CB A:CYS513 2.9 32.2 1.0
CA A:CYS513 3.5 28.0 1.0
CG A:ASP463 3.5 34.5 1.0
O A:CYS511 3.5 26.5 1.0
O A:HOH858 3.7 47.3 1.0
N A:CYS513 3.8 24.1 1.0
OD2 A:ASP532 3.8 31.2 1.0
O A:HOH1181 3.8 35.1 1.0
C A:CYS511 3.9 26.6 1.0
CA A:CYS511 4.0 27.7 1.0
OD2 A:ASP463 4.1 35.3 1.0
N A:TYR464 4.1 26.8 1.0
CG A:ASP532 4.1 29.1 1.0
OD1 A:ASP532 4.3 30.6 1.0
CB A:ASP463 4.6 31.4 1.0
CA A:ASP463 4.6 27.9 1.0
N A:ASN512 4.8 25.7 1.0
C A:ASN512 4.8 26.8 1.0
C A:CYS513 4.9 24.8 1.0
C A:ASP463 4.9 28.6 1.0
CA A:TYR464 4.9 29.3 1.0

Cobalt binding site 2 out of 5 in 9ay8

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Cobalt 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 Cobalt with other atoms in the Co 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:Co703

b:52.5
occ:1.00
 SG B:CYS513 1.9 39.9 1.0
SG B:CYS511 2.1 30.8 1.0
OD1 B:ASP463 2.2 33.6 1.0
O B:HOH1351 2.6 40.8 1.0
CB B:CYS511 2.9 24.1 1.0
CB B:CYS513 2.9 29.1 1.0
CG B:ASP463 3.4 32.9 1.0
O B:CYS511 3.5 22.2 1.0
CA B:CYS513 3.5 26.1 1.0
N B:CYS513 3.8 24.8 1.0
O B:HOH861 3.8 51.5 1.0
OD2 B:ASP532 3.8 38.0 1.0
C B:CYS511 3.9 24.7 1.0
CA B:CYS511 4.0 23.2 1.0
OD2 B:ASP463 4.0 35.5 1.0
O B:HOH1047 4.0 30.7 1.0
N B:TYR464 4.1 25.7 1.0
CG B:ASP532 4.2 29.5 1.0
OD1 B:ASP532 4.4 31.4 1.0
CB B:ASP463 4.5 29.4 1.0
CA B:ASP463 4.5 26.4 1.0
N B:ASN512 4.8 22.2 1.0
C B:ASN512 4.9 26.3 1.0
C B:ASP463 4.9 27.2 1.0
CA B:TYR464 4.9 27.2 1.0
C B:CYS513 5.0 24.4 1.0
O B:HOH1274 5.0 43.2 1.0

Cobalt binding site 3 out of 5 in 9ay8

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Cobalt 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 Cobalt with other atoms in the Co 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:Co703

b:58.1
occ:1.00
 SG C:CYS513 1.9 48.0 1.0
SG C:CYS511 2.1 37.4 1.0
OD1 C:ASP463 2.2 38.0 1.0
O C:HOH1208 2.7 49.7 1.0
CB C:CYS511 2.9 29.4 1.0
CB C:CYS513 3.0 39.2 1.0
CG C:ASP463 3.4 35.0 1.0
O C:CYS511 3.5 28.7 1.0
CA C:CYS513 3.6 32.8 1.0
O C:HOH855 3.7 54.5 1.0
OD2 C:ASP532 3.8 33.4 1.0
N C:CYS513 3.9 30.3 1.0
O C:HOH1020 3.9 32.7 1.0
C C:CYS511 4.0 28.9 1.0
OD2 C:ASP463 4.0 34.5 1.0
CA C:CYS511 4.0 29.4 1.0
CG C:ASP532 4.1 33.7 1.0
N C:TYR464 4.2 30.4 1.0
OD1 C:ASP532 4.3 35.3 1.0
CB C:ASP463 4.5 31.5 1.0
CA C:ASP463 4.6 31.0 1.0
O C:HOH1082 4.7 51.7 1.0
N C:ASN512 4.9 27.9 1.0
C C:ASN512 4.9 28.2 1.0
C C:ASP463 5.0 33.4 1.0
O C:HOH1114 5.0 45.5 1.0
C C:CYS513 5.0 31.1 1.0

Cobalt binding site 4 out of 5 in 9ay8

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Cobalt 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 Cobalt with other atoms in the Co 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:Co703

b:59.3
occ:1.00
 SG D:CYS513 2.1 58.2 1.0
SG D:CYS511 2.1 35.2 1.0
OD1 D:ASP463 2.3 40.2 1.0
O D:HOH1204 2.8 54.3 1.0
CB D:CYS513 2.9 41.8 1.0
CB D:CYS511 2.9 29.8 1.0
CA D:CYS513 3.4 30.7 1.0
O D:CYS511 3.5 29.2 1.0
CG D:ASP463 3.5 34.5 1.0
N D:CYS513 3.7 30.2 1.0
O D:HOH1033 3.7 49.2 1.0
OD2 D:ASP532 3.8 37.1 1.0
C D:CYS511 3.9 27.8 1.0
CA D:CYS511 4.0 28.8 1.0
O D:HOH1029 4.0 34.7 1.0
OD2 D:ASP463 4.1 34.7 1.0
N D:TYR464 4.1 30.4 1.0
CG D:ASP532 4.1 33.2 1.0
OD1 D:ASP532 4.3 32.5 1.0
CB D:ASP463 4.6 32.7 1.0
CA D:ASP463 4.6 29.8 1.0
C D:ASN512 4.7 30.5 1.0
N D:ASN512 4.8 26.5 1.0
C D:CYS513 4.8 29.8 1.0
CA D:TYR464 4.9 33.5 1.0
C D:ASP463 4.9 31.1 1.0
O D:HOH1181 4.9 48.5 1.0

Cobalt binding site 5 out of 5 in 9ay8

Go back to Cobalt Binding Sites List in 9ay8
Cobalt 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 Cobalt with other atoms in the Co 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:Co703

b:52.2
occ:1.00
 SG E:CYS513 1.9 49.2 1.0
SG E:CYS511 2.1 30.3 1.0
OD1 E:ASP463 2.4 34.7 1.0
O E:HOH1194 2.6 49.9 1.0
CB E:CYS513 2.9 35.7 1.0
CB E:CYS511 2.9 26.0 1.0
CA E:CYS513 3.4 30.0 1.0
O E:CYS511 3.4 24.1 1.0
CG E:ASP463 3.5 33.7 1.0
N E:CYS513 3.7 26.5 1.0
O E:HOH967 3.7 50.6 1.0
OD2 E:ASP532 3.8 36.4 1.0
C E:CYS511 3.8 25.5 1.0
O E:HOH1123 3.9 29.2 1.0
CA E:CYS511 4.0 24.9 1.0
N E:TYR464 4.1 30.2 1.0
OD2 E:ASP463 4.1 32.9 1.0
CG E:ASP532 4.2 30.5 1.0
OD1 E:ASP532 4.3 29.2 1.0
CB E:ASP463 4.6 29.6 1.0
CA E:ASP463 4.6 28.6 1.0
N E:ASN512 4.8 26.2 1.0
C E:ASN512 4.8 26.1 1.0
C E:CYS513 4.8 29.8 1.0
CA E:TYR464 4.9 32.9 1.0
C E:ASP463 4.9 29.1 1.0
O E:HOH1167 5.0 49.9 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 22:09:46 2025

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