Cobalt in PDB 6q3k: Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide

The structure of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide, PDB code: 6q3k was solved by R.Meijers, R.Anjanappa, S.Springer, M.Garcia-Alai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.94 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.158, 80.575, 109.693, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20

The binding sites of Cobalt atom in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide (pdb code 6q3k). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide, PDB code: 6q3k:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:18.9 occ:1.00 O A:HOH465 2.0 19.3 1.0 NE2 A:HIS197 2.1 20.9 1.0 O A:HOH443 2.2 19.3 1.0 CE1 A:HIS197 3.1 17.8 1.0 CD2 A:HIS197 3.1 15.3 1.0 OE2 A:GLU198 4.0 22.8 1.0 OE1 A:GLU198 4.0 29.9 1.0 ND1 A:HIS197 4.2 19.8 1.0 CG A:HIS197 4.2 16.8 1.0 CD A:GLU198 4.4 28.1 1.0

Cobalt binding site 2 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co303 b:24.9 occ:1.00 O A:HOH570 1.8 35.6 1.0 NE2 A:HIS151 2.0 22.0 1.0 O A:HOH620 2.0 37.9 1.0 CE1 A:HIS151 2.8 35.6 1.0 CD2 A:HIS151 3.1 24.6 1.0 O A:HOH768 4.0 42.7 1.0 ND1 A:HIS151 4.0 36.0 1.0 CG A:HIS151 4.2 21.5 1.0 O A:ALA149 4.3 20.8 1.0 O A:HOH731 4.3 57.8 1.0 O A:GLU148 4.6 17.4 1.0

Cobalt binding site 3 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co304 b:26.7 occ:1.00 OE1 A:GLN218 2.0 15.0 0.5 NE2 A:HIS260 2.0 22.5 1.0 O A:HOH510 2.1 28.4 1.0 O A:HOH596 2.1 25.4 1.0 O A:HOH553 2.2 32.1 1.0 CD2 A:HIS260 3.0 24.1 1.0 CD A:GLN218 3.0 13.8 0.5 CE1 A:HIS260 3.0 29.5 1.0 NE2 A:GLN218 3.3 17.7 0.5 CG A:GLN218 4.0 31.3 0.5 CG A:HIS260 4.1 24.7 1.0 ND1 A:HIS260 4.1 25.8 1.0 O A:GLY221 4.2 29.9 1.0 CD A:GLN218 4.3 42.4 0.5 CG A:GLN218 4.3 13.9 0.5 OG1 A:THR258 4.4 18.8 1.0 CA A:GLY221 4.5 24.2 1.0 NE2 A:GLN218 4.5 55.2 0.5 CB A:GLN218 4.6 26.0 0.5 C A:GLY221 4.7 25.0 1.0 CB A:GLN218 4.7 15.4 0.5 OE1 A:GLN218 4.7 52.3 0.5

Cobalt binding site 4 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co305 b:28.1 occ:1.00 O A:HOH591 2.0 34.5 1.0 NE2 A:HIS192 2.1 14.4 0.5 O A:HOH616 2.1 30.7 1.0 CD2 A:HIS192 3.0 16.1 0.5 CE1 A:HIS192 3.1 17.7 0.5 O B:HOH244 4.1 46.8 1.0 ND1 A:HIS192 4.2 17.8 0.5 CG A:HIS192 4.2 16.8 0.5 O A:ALA193 4.3 15.6 1.0 O A:HOH545 4.7 42.1 1.0

Cobalt binding site 5 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co306 b:13.6 occ:1.00 OE2 A:GLU154 2.2 19.5 1.0 OE1 A:GLU154 2.2 20.0 1.0 CD A:GLU154 2.5 21.7 1.0 O A:HOH737 2.7 10.3 1.0 O A:HOH715 2.7 17.4 1.0 O A:HOH701 2.8 31.8 1.0 CG A:GLU154 4.1 21.9 1.0 ND1 A:HIS151 4.1 36.0 1.0 O A:HOH475 4.4 34.6 1.0 O A:HOH422 4.6 44.5 1.0 CE1 A:HIS151 4.8 35.6 1.0 CB A:GLU154 5.0 21.6 1.0

Cobalt binding site 6 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Co307 b:22.1 occ:1.00 O A:HOH676 1.7 29.2 1.0 ND1 A:HIS191 2.2 16.9 1.0 O A:HIS191 2.8 16.1 1.0 CE1 A:HIS191 3.0 19.2 1.0 CG A:HIS191 3.2 16.2 1.0 C A:HIS191 3.6 14.6 1.0 CB A:HIS191 3.6 13.2 1.0 NE2 A:HIS191 4.2 18.8 1.0 CA A:HIS191 4.2 14.9 1.0 CD2 A:HIS191 4.3 17.4 1.0 N A:HIS192 4.4 14.2 1.0 CA A:HIS192 4.7 17.4 0.5 CZ2 A:TRP274 4.7 20.6 1.0 O A:HOH642 4.8 19.5 1.0 CA A:HIS192 4.8 15.5 0.5 N A:ALA193 4.9 14.4 1.0

Cobalt binding site 7 out of 7 in the Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Engineered Human HLA_A2 Mhc Class I Molecule in Complex with NV9 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:52.7 occ:1.00 O B:HOH207 1.4 29.8 1.0 O B:HOH216 1.5 23.4 1.0 O B:HOH266 1.9 41.1 1.0 NE2 B:HIS51 2.1 29.8 1.0 CE1 B:HIS51 3.0 34.5 1.0 CD2 B:HIS51 3.1 30.1 1.0 O A:HOH645 4.0 42.8 1.0 ND1 B:HIS51 4.2 25.4 1.0 CG B:HIS51 4.2 23.6 1.0 O B:HOH325 4.6 47.8 1.0 NH2 A:ARG21 4.9 28.9 1.0 O B:HOH297 5.0 29.3 1.0

R.Meijers, R.Anjanappa, S.Springer, M.Garcia-Alai. Engineered Human HLA_A2MHC Class I Molecule in Complex with NV9 Peptide Sci Immunol 2019.
ISSN: ESSN 2470-9468