Nickel in PDB 8p43: Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide

The structure of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide, PDB code: 8p43 was solved by B.M.Sala, A.Achour, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.69 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.56, 72.797, 96.515, 90, 90, 90
R / Rfree (%)	19.1 / 24.7

The binding sites of Nickel atom in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide (pdb code 8p43). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide, PDB code: 8p43:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:80.3 occ:1.00 O A:SER38 4.5 73.6 1.0 O A:ALA40 4.5 89.7 1.0 CD A:PRO43 4.8 78.2 1.0 CG A:PRO43 4.8 72.8 1.0

Nickel binding site 2 out of 6 in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:88.2 occ:1.00 O A:HOH483 2.4 41.8 1.0 OH A:TYR85 3.5 34.6 1.0 O A:ASP122 3.6 37.6 1.0 O A:TYR118 4.0 34.2 1.0 O A:GLN121 4.0 35.8 1.0 OD2 A:ASP137 4.0 42.4 1.0 CB A:GLN121 4.1 42.7 1.0 CB A:TYR118 4.4 38.3 1.0 CD1 A:TYR123 4.4 28.8 1.0 OE1 A:GLN121 4.4 60.4 1.0 C A:ASP122 4.5 36.3 1.0 C A:GLN121 4.5 36.5 1.0 CZ A:TYR85 4.5 34.3 1.0 CA A:TYR123 4.7 33.2 1.0 CG A:ASP137 4.7 38.8 1.0 C A:TYR118 4.9 33.1 1.0 CD2 A:TYR118 4.9 40.9 1.0 CA A:GLN121 4.9 36.3 1.0 N A:TYR123 4.9 33.0 1.0 N A:TYR118 4.9 37.0 1.0 CB A:TYR123 5.0 32.1 1.0 CA A:TYR118 5.0 36.4 1.0

Nickel binding site 3 out of 6 in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:38.6 occ:1.00 O A:HOH441 1.9 35.2 1.0 O A:HOH415 2.0 29.4 1.0 O A:HOH418 2.2 42.9 1.0 OE2 A:GLU177 2.2 49.0 1.0 CD A:GLU177 2.9 46.6 1.0 OE1 A:GLU177 3.0 45.3 1.0 O A:HOH486 3.8 46.8 1.0 O A:HOH424 4.2 50.2 1.0 CG A:GLU177 4.4 36.6 1.0

Nickel binding site 4 out of 6 in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:61.3 occ:1.00 NE2 A:HIS154 2.1 55.6 1.0 CE1 A:HIS154 2.9 51.6 1.0 CD2 A:HIS154 3.3 46.7 1.0 ND1 A:HIS154 4.1 51.7 1.0 CG A:HIS154 4.3 47.9 1.0 O A:HOH456 4.5 42.6 1.0 CG A:GLN155 5.0 58.3 1.0

Nickel binding site 5 out of 6 in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni100 b:59.7 occ:0.00 NE2 B:HIS34 2.7 67.6 1.0 CE1 B:HIS34 3.4 67.0 1.0 CD2 B:HIS34 3.9 63.0 1.0 CG B:GLU36 4.4 66.6 1.0 ND1 B:HIS34 4.6 66.3 1.0 CB B:GLU36 4.7 52.9 1.0 CG B:HIS34 4.9 65.1 1.0

Nickel binding site 6 out of 6 in the Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of the Mhc Class Ib Molecule Qa-1B in Complex with Q001 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:57.3 occ:0.00 CE1 B:HIS67 3.0 61.4 1.0 OE1 B:GLU50 3.5 74.1 1.0 ND1 B:HIS67 3.6 52.8 1.0 CG B:GLU50 4.0 65.4 1.0 NE2 B:HIS67 4.1 62.3 1.0 CD B:GLU50 4.1 76.2 1.0 CB B:GLU50 4.7 58.1 1.0 CG B:HIS67 4.9 49.2 1.0 O B:HOH219 4.9 44.8 1.0

J.Middelburg, S.Ghaffari, T.Schoufour, M.Sluijter, G.Schaap, B.Goynuk, B.M.Sala, L.Al-Tamimi, F.Scheeren, K.L.M.C.Franken, S.Joosten, I.Derksen, J.Neefjes, S.Van Der Burg, A.Achour, R.H.M.Wijdeven, J.Weidanz, T.Van Hall. Mhc-E Is A Convergent Checkpoint Ligand For LILRB1 on Macrophages and During Inflammation For NKG2A on Lymphocytes To Be Published.