Cadmium in PDB 5oxd: 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;

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

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

Fluorine

(F)

3 atoms

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 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 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 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 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 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 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 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 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 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 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

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