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Zinc 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
Manganese (Mn) 5 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 5 in 9ayu

Go back to Zinc Binding Sites List in 9ayu
Zinc 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 Zinc with other atoms in the Zn 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:Zn701

b:21.7
occ:1.00
 NE2 A:HIS478 2.0 23.6 1.0
ND1 A:HIS476 2.1 34.3 1.0
SG A:CYS471 2.3 22.4 1.0
SG A:CYS434 2.3 21.9 1.0
CE1 A:HIS478 2.9 23.9 1.0
CD2 A:HIS478 3.0 25.2 1.0
CE1 A:HIS476 3.0 34.9 1.0
CG A:HIS476 3.1 35.2 1.0
CB A:CYS471 3.1 22.5 1.0
CB A:CYS434 3.3 21.0 1.0
CB A:HIS476 3.4 34.9 1.0
ND1 A:HIS478 4.1 24.3 1.0
CG A:HIS478 4.1 26.3 1.0
NE2 A:HIS476 4.2 35.3 1.0
CD2 A:HIS476 4.2 35.9 1.0
CA A:CYS471 4.5 23.4 1.0
CA A:CYS434 4.6 19.6 1.0
CB A:ASN473 4.6 30.7 1.0
O A:PHE407 4.8 19.1 1.0
C A:CYS471 4.9 24.9 1.0
CB A:SER484 4.9 19.2 1.0
CA A:VAL408 4.9 18.8 1.0
CA A:HIS476 5.0 35.3 1.0

Zinc binding site 2 out of 5 in 9ayu

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Zinc 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 Zinc with other atoms in the Zn 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:Zn701

b:18.1
occ:1.00
 NE2 B:HIS478 2.0 20.9 1.0
ND1 B:HIS476 2.0 27.2 1.0
SG B:CYS434 2.3 19.6 1.0
SG B:CYS471 2.4 19.5 1.0
CE1 B:HIS478 3.0 21.2 1.0
CE1 B:HIS476 3.0 27.4 1.0
CG B:HIS476 3.1 31.1 1.0
CD2 B:HIS478 3.1 22.4 1.0
CB B:CYS471 3.2 19.7 1.0
CB B:CYS434 3.2 18.8 1.0
CB B:HIS476 3.5 32.3 1.0
NE2 B:HIS476 4.1 29.8 1.0
ND1 B:HIS478 4.1 21.6 1.0
CD2 B:HIS476 4.2 32.0 1.0
CG B:HIS478 4.2 23.2 1.0
CA B:CYS434 4.6 17.4 1.0
CA B:CYS471 4.6 20.4 1.0
CB B:ASN473 4.7 31.3 1.0
O B:PHE407 4.8 17.4 1.0
CB B:SER484 4.9 16.5 1.0
CA B:VAL408 4.9 17.0 1.0

Zinc binding site 3 out of 5 in 9ayu

Go back to Zinc Binding Sites List in 9ayu
Zinc 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 Zinc with other atoms in the Zn 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:Zn701

b:21.0
occ:1.00
 NE2 C:HIS478 2.0 25.6 1.0
ND1 C:HIS476 2.1 30.5 1.0
SG C:CYS434 2.3 19.8 1.0
SG C:CYS471 2.3 22.6 1.0
CE1 C:HIS478 2.9 24.9 1.0
CD2 C:HIS478 3.0 26.2 1.0
CE1 C:HIS476 3.0 31.2 1.0
CB C:CYS471 3.1 22.8 1.0
CG C:HIS476 3.1 31.5 1.0
CB C:CYS434 3.2 20.4 1.0
CB C:HIS476 3.5 31.3 1.0
ND1 C:HIS478 4.1 24.5 1.0
CG C:HIS478 4.1 26.3 1.0
NE2 C:HIS476 4.2 30.4 1.0
CD2 C:HIS476 4.2 32.1 1.0
CA C:CYS471 4.5 23.9 1.0
CA C:CYS434 4.6 19.5 1.0
CB C:ASN473 4.6 34.7 1.0
O C:PHE407 4.8 21.4 1.0
CB C:SER484 4.8 19.5 1.0
C C:CYS471 4.9 25.6 1.0
CA C:VAL408 5.0 20.5 1.0

Zinc binding site 4 out of 5 in 9ayu

Go back to Zinc Binding Sites List in 9ayu
Zinc 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 Zinc with other atoms in the Zn 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:Zn701

b:21.2
occ:1.00
 NE2 D:HIS478 2.0 25.2 1.0
ND1 D:HIS476 2.0 31.0 1.0
SG D:CYS434 2.3 21.9 1.0
SG D:CYS471 2.4 21.6 1.0
CE1 D:HIS478 2.9 25.4 1.0
CE1 D:HIS476 3.0 32.2 1.0
CD2 D:HIS478 3.0 26.4 1.0
CG D:HIS476 3.0 33.9 1.0
CB D:CYS471 3.2 21.7 1.0
CB D:CYS434 3.2 21.4 1.0
CB D:HIS476 3.4 33.0 1.0
ND1 D:HIS478 4.1 25.5 1.0
NE2 D:HIS476 4.1 33.9 1.0
CD2 D:HIS476 4.1 35.0 1.0
CG D:HIS478 4.1 27.2 1.0
CA D:CYS471 4.6 23.0 1.0
CA D:CYS434 4.6 20.4 1.0
CB D:ASN473 4.6 33.9 1.0
O D:PHE407 4.8 21.9 1.0
CB D:SER484 4.8 20.5 1.0
C D:CYS471 5.0 24.8 1.0
CA D:HIS476 5.0 33.7 1.0
CA D:VAL408 5.0 22.0 1.0

Zinc binding site 5 out of 5 in 9ayu

Go back to Zinc Binding Sites List in 9ayu
Zinc 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 Zinc with other atoms in the Zn 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:Zn701

b:21.6
occ:1.00
 NE2 E:HIS478 2.0 22.6 1.0
ND1 E:HIS476 2.1 30.9 1.0
SG E:CYS434 2.3 21.1 1.0
SG E:CYS471 2.3 22.8 1.0
CE1 E:HIS478 2.9 22.7 1.0
CE1 E:HIS476 3.0 31.3 1.0
CD2 E:HIS478 3.0 24.8 1.0
CG E:HIS476 3.1 34.0 1.0
CB E:CYS471 3.1 23.0 1.0
CB E:CYS434 3.3 20.6 1.0
CB E:HIS476 3.4 34.1 1.0
ND1 E:HIS478 4.0 23.7 1.0
NE2 E:HIS476 4.1 33.8 1.0
CG E:HIS478 4.1 25.4 1.0
CD2 E:HIS476 4.2 34.6 1.0
CA E:CYS471 4.5 24.8 1.0
CB E:ASN473 4.6 32.8 1.0
CA E:CYS434 4.6 19.7 1.0
O E:PHE407 4.7 21.9 1.0
CB E:SER484 4.8 20.7 1.0
CA E:VAL408 4.9 22.3 1.0
C E:CYS471 4.9 26.3 1.0
CA E:HIS476 5.0 34.8 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 Feb 9 01:00:26 2025

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