Atomistry » Cobalt » PDB 8xhj-9icb » 9ay8
Atomistry »
  Cobalt »
    PDB 8xhj-9icb »
      9ay8 »

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

Go back to Cobalt Binding Sites List in 9ay8
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

Go back to Cobalt Binding Sites List in 9ay8
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

Go back to Cobalt Binding Sites List in 9ay8
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: Sat Feb 8 17:38:15 2025

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy