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Cadmium in PDB 5oxd: Complex of A C. Perfringens O-Glcnacase with A Fragment Hit

Enzymatic activity of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit

All present enzymatic activity of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit:
3.2.1.169; 3.2.1.52;

Protein crystallography data

The structure of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit, PDB code: 5oxd was solved by K.Rafie, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.60
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 117.794, 117.794, 147.233, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 22.1

Other elements in 5oxd:

The structure of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Cadmium atom in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit (pdb code 5oxd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 22 binding sites of Cadmium where determined in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit, PDB code: 5oxd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 1 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd701

b:0.6
occ:1.00
OE1 A:GLU51 2.4 99.1 1.0
O A:HOH823 2.4 71.8 1.0
OD1 A:ASN450 3.1 56.8 1.0
CD A:GLU51 3.1 99.9 1.0
OE2 A:GLU51 3.1 99.9 1.0
CG A:ASP452 3.6 92.5 1.0
O A:HOH832 3.7 44.4 1.0
OD2 A:ASP452 3.7 0.7 1.0
CB A:ASP452 3.7 70.6 1.0
CG A:ASN450 3.8 47.5 1.0
OD1 A:ASP452 3.9 0.6 1.0
ND2 A:ASN450 4.1 47.6 1.0
N A:ASP452 4.4 65.8 1.0
CG A:GLU51 4.5 87.4 1.0
CA A:ASP452 4.6 69.5 1.0
N A:ASN453 4.6 59.3 1.0
CA A:ASN450 4.8 50.9 1.0
CB A:ASN450 4.8 51.2 1.0
C A:ASN450 4.9 49.6 1.0
CB A:ASN453 5.0 63.0 1.0

Cadmium binding site 2 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 2 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:93.8
occ:1.00
OD2 A:ASP58 2.6 98.6 1.0
OD1 A:ASP58 2.9 80.6 1.0
CG A:ASP58 3.0 83.0 1.0
CB A:ASP58 4.4 78.1 1.0

Cadmium binding site 3 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 3 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:0.3
occ:1.00
OE1 A:GLU71 2.5 0.5 1.0
O A:LEU68 2.8 75.3 1.0
CD A:GLU71 3.7 0.7 1.0
C A:LEU68 3.8 64.3 1.0
CA A:VAL69 4.0 52.7 1.0
N A:VAL69 4.3 58.4 1.0
OE2 A:GLU71 4.4 0.9 1.0
N A:GLY70 4.4 54.5 1.0
OE2 A:GLU72 4.6 0.2 1.0
CG A:GLU71 4.7 96.5 1.0
C A:VAL69 4.7 54.8 1.0
N A:GLU71 4.8 63.6 1.0
CB A:GLU71 5.0 78.3 1.0
CA A:LEU68 5.0 62.8 1.0

Cadmium binding site 4 out of 22 in 5oxd

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Cadmium binding site 4 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd704

b:75.4
occ:1.00
OE1 A:GLU108 2.2 89.7 1.0
O A:GLU73 2.3 48.9 1.0
O A:HOH811 2.4 49.7 1.0
O A:HOH838 2.6 42.9 1.0
OD2 A:ASP111 2.6 79.5 1.0
OD1 A:ASP111 2.7 70.4 1.0
CG A:ASP111 3.0 74.2 1.0
CD A:GLU108 3.4 74.6 1.0
C A:GLU73 3.5 61.6 1.0
CA A:ALA74 4.1 66.0 1.0
OD1 A:ASP110 4.2 71.7 1.0
N A:ALA74 4.2 65.3 1.0
CG A:GLU108 4.3 66.0 1.0
OE2 A:GLU108 4.3 59.2 1.0
C A:ALA74 4.3 64.3 1.0
CB A:GLU108 4.5 62.1 1.0
N A:ASP75 4.5 62.2 1.0
CB A:ASP111 4.5 61.7 1.0
CA A:GLU73 4.6 71.9 1.0
CB A:GLU73 4.8 90.9 1.0
N A:GLU108 4.9 52.6 1.0
O A:ALA74 4.9 61.0 1.0

Cadmium binding site 5 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 5 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd705

b:0.6
occ:1.00
OD2 A:ASP112 3.3 61.3 1.0
CG A:ASP112 4.0 62.7 1.0
OD1 A:ASP112 4.0 52.6 1.0

Cadmium binding site 6 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 6 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd706

b:63.8
occ:1.00
OD1 A:ASP117 2.3 51.9 1.0
OE2 A:GLU145 2.6 57.7 1.0
OD2 A:ASP117 2.9 76.9 1.0
CG A:ASP117 3.0 62.5 1.0
OE1 A:GLU145 3.3 53.8 1.0
CD A:GLU145 3.3 54.9 1.0
OG1 A:THR124 3.5 60.8 1.0
CD A:CD719 4.0 0.1 1.0
CB A:ASP117 4.4 63.0 1.0
CB A:THR124 4.7 59.3 1.0
CD1 A:LEU120 4.8 68.7 1.0
CG A:GLU145 4.8 57.8 1.0
CD A:CD717 4.8 0.7 1.0
CA A:ASP117 5.0 65.5 1.0

Cadmium binding site 7 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 7 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd707

b:0.6
occ:1.00
O A:HOH808 2.7 58.9 1.0
O A:HOH843 2.8 61.9 1.0
OD2 A:ASP139 3.8 0.9 1.0
CB A:ASP139 4.0 92.0 1.0
OD1 A:ASN138 4.2 68.4 1.0
ND2 A:ASN138 4.4 69.4 1.0
CG A:ASP139 4.4 0.8 1.0
O A:HOH801 4.4 67.1 1.0
CG A:ASN138 4.7 68.4 1.0

Cadmium binding site 8 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 8 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd708

b:1.0
occ:1.00
OD2 A:ASP150 2.9 68.3 1.0
CG A:ASP150 3.5 63.3 1.0
OD1 A:ASP252 3.6 49.9 1.0
OD1 A:ASP150 3.9 65.6 1.0
O A:LYS250 4.0 47.9 1.0
OE2 A:GLU131 4.4 59.9 1.0
CG A:ASP252 4.5 59.2 1.0
CB A:ASP150 4.5 55.0 1.0
C A:LYS250 4.6 44.4 1.0
OD2 A:ASP252 4.6 63.9 1.0
CB A:ASN211 4.7 44.3 1.0
CB A:LYS250 4.8 50.0 1.0
CA A:LYS250 4.9 46.7 1.0

Cadmium binding site 9 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 9 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd709

b:75.0
occ:1.00
O A:HOH801 1.9 67.1 1.0
OE2 A:GLU170 1.9 79.1 1.0
O A:HOH831 2.0 40.9 1.0
CD A:GLU170 2.6 76.1 1.0
OE1 A:GLU170 2.6 93.0 1.0
O A:HOH851 3.0 36.4 1.0
CG A:GLU170 4.1 68.5 1.0
N A:ASP58 4.2 66.7 1.0
CA A:GLY57 4.3 57.2 1.0
O A:GLY59 4.6 66.6 1.0
N A:ASP139 4.8 75.4 1.0
C A:GLY57 4.8 62.8 1.0
OD1 A:ASN138 4.8 68.4 1.0
N A:GLY59 4.8 63.0 1.0
CB A:GLU170 4.9 60.8 1.0
CA A:ASP139 5.0 82.6 1.0

Cadmium binding site 10 out of 22 in 5oxd

Go back to Cadmium Binding Sites List in 5oxd
Cadmium binding site 10 out of 22 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd710

b:0.2
occ:1.00
OE1 A:GLU272 3.1 89.9 1.0
NE2 A:HIS276 3.5 83.6 1.0
NH2 A:ARG264 3.6 71.4 1.0
CD A:GLU272 3.7 88.0 1.0
CD2 A:HIS276 4.0 73.4 1.0
OE2 A:GLU272 4.0 0.5 1.0
CE1 A:HIS276 4.5 81.4 1.0
NE A:ARG228 4.6 59.1 1.0
CZ A:ARG264 4.6 67.8 1.0
CG A:GLU272 4.6 73.6 1.0
OD1 A:ASP273 4.7 62.9 1.0
CD A:ARG228 4.7 63.9 1.0
NH1 A:ARG264 4.9 71.0 1.0

Reference:

V.S.Borodkin, K.Rafie, N.Selvan, T.Aristotelous, I.Navratilova, A.T.Ferenbach, D.M.F.Van Aalten. O-Glcnacase Fragment Discovery with Fluorescence Polarimetry. Acs Chem. Biol. V. 13 1353 2018.
ISSN: ESSN 1554-8937
PubMed: 29641181
DOI: 10.1021/ACSCHEMBIO.8B00183
Page generated: Sat Dec 12 08:27:16 2020

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