Cadmium in PDB 8ds5: X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex

The structure of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex, PDB code: 8ds5 was solved by T.O.Fischmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.00 / 1.93
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	114.246, 126.105, 131.602, 90, 90, 90
R / Rfree (%)	20.9 / 22.5

The binding sites of Cadmium atom in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex (pdb code 8ds5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex, PDB code: 8ds5:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:63.1 occ:0.50 NE2 A:HIS75 2.3 41.6 1.0 OE1 A:GLU44 2.4 61.2 1.0 OE2 A:GLU44 2.6 62.6 1.0 CD A:GLU44 2.8 58.6 1.0 CE1 A:HIS75 2.9 41.6 1.0 NH1 A:ARG30 3.5 71.2 1.0 CD2 A:HIS75 3.6 40.2 1.0 CZ A:ARG30 4.2 72.0 1.0 ND1 A:HIS75 4.2 41.1 1.0 CG A:GLU44 4.3 48.2 1.0 CG A:HIS75 4.5 39.2 1.0 O A:HOH316 4.7 61.4 1.0 CD A:PRO45 4.7 35.9 1.0 NE A:ARG30 4.7 69.6 1.0 CD A:ARG30 4.7 66.1 1.0 NH2 A:ARG30 4.8 72.2 1.0 CB A:GLU44 5.0 41.0 1.0

Cadmium binding site 2 out of 6 in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:39.5 occ:1.00 OE1 A:GLU82 2.2 39.7 1.0 NE2 A:HIS80 2.4 39.6 1.0 CD A:GLU82 3.0 39.6 1.0 OE2 A:GLU82 3.2 38.9 1.0 CD2 A:HIS80 3.3 38.9 1.0 CE1 A:HIS80 3.4 40.1 1.0 O A:HOH314 4.3 34.1 1.0 CG A:HIS80 4.5 38.3 1.0 CG A:GLU82 4.5 38.1 1.0 ND1 A:HIS80 4.5 40.0 1.0 NE A:ARG78 4.9 47.1 1.0 CG A:ARG78 4.9 40.9 1.0 CA A:GLU82 5.0 36.6 1.0

Cadmium binding site 3 out of 6 in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd9901 b:124.0 occ:1.00 OD1 B:ASN137 2.6 53.6 1.0 NE2 C:HIS167 2.6 47.6 1.0 CE1 C:HIS167 2.9 47.1 1.0 CG B:ASN137 3.2 53.0 1.0 ND2 B:ASN137 3.4 53.4 1.0 O C:HOH19 3.4 38.5 1.0 O B:HOH16 3.8 43.8 1.0 OD2 B:ASP169 3.8 64.9 1.0 CD2 C:HIS167 3.9 46.4 1.0 ND1 C:HIS167 4.2 46.7 1.0 OD1 B:ASP166 4.6 61.3 1.0 CB B:ASN137 4.6 50.2 1.0 CG C:HIS167 4.7 45.0 1.0 OG1 B:THR171 4.7 52.7 1.0 CG B:ASP169 4.7 63.0 1.0 CG B:ASP166 4.7 60.3 1.0 OD1 B:ASP169 4.8 63.7 1.0 CA C:GLY165 4.9 47.4 1.0 OD2 B:ASP166 4.9 61.8 1.0 ND2 B:ASN136 4.9 50.5 1.0

Cadmium binding site 4 out of 6 in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd9902 b:96.8 occ:1.00 NE2 B:HIS188 2.3 66.5 1.0 CE1 B:HIS188 3.1 66.7 1.0 CD2 B:HIS188 3.5 65.3 1.0 ND1 B:HIS188 4.3 66.3 1.0 CG B:HIS188 4.5 64.2 1.0

Cadmium binding site 5 out of 6 in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd9901 b:76.5 occ:0.70 O C:HOH137 2.4 35.4 1.0 ND1 C:HIS167 2.5 46.7 1.0 O C:VAL166 2.8 43.1 1.0 CE1 C:HIS167 3.2 47.1 1.0 CG C:HIS167 3.6 45.0 1.0 CA C:HIS167 3.7 41.2 1.0 C C:VAL166 3.8 42.9 1.0 O C:HOH75 3.8 52.3 1.0 OD1 B:ASP166 3.8 61.3 1.0 CB C:HIS167 4.1 42.3 1.0 N C:HIS167 4.2 41.7 1.0 NE2 C:HIS167 4.3 47.6 1.0 CD2 C:HIS167 4.6 46.4 1.0 O B:HOH15 4.7 45.8 1.0 C C:HIS167 4.9 40.3 1.0

Cadmium binding site 6 out of 6 in the X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of the MK5890 Fab - CD27 Antibody-Antigen Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd9902 b:69.6 occ:0.70 OE2 C:HOH10 2.3 50.2 1.0 O C:HOH117 2.7 42.2 1.0 CD C:HOH10 3.2 47.2 1.0 OE1 C:HOH10 3.4 47.2 1.0 O C:HOH3 4.5 32.9 1.0 CG C:HOH10 4.5 41.7 1.0 N C:HOH19 5.0 43.7 1.0 CG2 C:HOH18 5.0 45.9 1.0 C C:HOH19 5.0 42.4 1.0 NZ C:HOH12 5.0 53.6 1.0

L.Guelen, T.O.Fischmann, J.Wong, S.Mauze, M.Guadagnoli, N.Babala, J.Wagenaars, V.Juan, D.Rosen, W.Prosise, M.Habraken, I.Lodewijks, D.Gu, J.Stammen-Vogelzangs, Y.Yu, J.Baker, D.Lutje Hulsik, L.Driessen-Engels, D.Malashock, J.Kreijtz, A.Bertens, E.De Vries, A.Bovens, A.Bramer, Y.Zhang, R.Wnek, S.Troth, E.Chartash, K.Dobrenkov, S.Sadekova, A.Van Elsas, J.K.Cheung, L.Fayadat-Dilman, J.Borst, A.M.Beebe, H.Van Eenennaam. Preclinical Characterization and Clinical Translation of Pharmacodynamic Markers For Mk-5890: A Human CD27 Activating Antibody For Cancer Immunotherapy. J Immunother Cancer V. 10 2022.
ISSN: ESSN 2051-1426
PubMed: 36100308
DOI: 10.1136/JITC-2022-005049