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Nickel in PDB 3vj6: Structure of the Mhc Class Ib Molecule Qa-1B

Protein crystallography data

The structure of Structure of the Mhc Class Ib Molecule Qa-1B, PDB code: 3vj6 was solved by L.Zeng, C.S.Clements, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.45 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.268, 72.833, 95.844, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of the Mhc Class Ib Molecule Qa-1B (pdb code 3vj6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of the Mhc Class Ib Molecule Qa-1B, PDB code: 3vj6:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3vj6

Go back to Nickel Binding Sites List in 3vj6
Nickel binding site 1 out of 4 in the Structure of the Mhc Class Ib Molecule Qa-1B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni278

b:19.9
occ:1.00
O A:HOH384 2.1 20.0 1.0
O A:HOH457 2.1 18.7 1.0
NE2 A:HIS260 2.2 20.5 1.0
O A:HOH383 2.4 20.8 1.0
CD2 A:HIS260 3.1 17.7 1.0
CE1 A:HIS260 3.2 18.1 1.0
O A:HOH379 4.0 37.4 1.0
OG1 A:THR271 4.1 24.8 1.0
CG A:HIS260 4.3 17.9 1.0
ND1 A:HIS260 4.3 14.5 1.0
CG2 A:THR271 4.5 24.4 1.0
O A:HOH304 4.6 19.3 1.0
CB A:THR271 5.0 22.5 1.0

Nickel binding site 2 out of 4 in 3vj6

Go back to Nickel Binding Sites List in 3vj6
Nickel binding site 2 out of 4 in the Structure of the Mhc Class Ib Molecule Qa-1B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni279

b:71.4
occ:1.00
O B:HOH178 2.5 49.8 1.0
CE1 A:HIS192 2.6 52.7 1.0
O A:HOH397 2.7 51.8 1.0
NE2 A:HIS192 3.2 55.5 1.0
ND1 A:HIS192 3.7 44.8 1.0
CD2 A:HIS192 4.5 47.3 1.0
CG A:HIS192 4.7 46.5 1.0
OD2 B:ASP98 4.9 58.3 1.0

Nickel binding site 3 out of 4 in 3vj6

Go back to Nickel Binding Sites List in 3vj6
Nickel binding site 3 out of 4 in the Structure of the Mhc Class Ib Molecule Qa-1B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni100

b:56.9
occ:1.00
O B:HOH134 2.0 21.1 1.0
NE2 B:HIS34 2.3 40.6 1.0
O B:HOH245 2.4 49.3 1.0
CE1 B:HIS34 2.7 39.6 1.0
O B:HOH184 2.8 40.0 1.0
CD2 B:HIS34 3.6 39.5 1.0
ND1 B:HIS34 4.0 34.2 1.0
CG B:HIS34 4.4 33.6 1.0
OE1 B:GLU36 4.4 62.9 1.0
CB B:GLU36 5.0 37.2 1.0

Nickel binding site 4 out of 4 in 3vj6

Go back to Nickel Binding Sites List in 3vj6
Nickel binding site 4 out of 4 in the Structure of the Mhc Class Ib Molecule Qa-1B


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni101

b:43.7
occ:1.00
O B:HOH239 2.3 41.8 1.0
NE2 B:HIS67 2.3 33.2 1.0
O B:HOH135 2.4 41.2 1.0
O B:HOH255 2.7 48.0 1.0
CE1 B:HIS67 3.3 39.7 1.0
CD2 B:HIS67 3.3 31.0 1.0
O A:HOH451 4.0 42.5 1.0
O B:HOH207 4.4 48.0 1.0
ND1 B:HIS67 4.4 23.6 1.0
CG B:HIS67 4.5 26.8 1.0
NH2 B:ARG12 4.6 25.1 1.0
CG B:GLU50 4.8 49.0 1.0
CB B:GLU50 5.0 36.5 1.0

Reference:

L.Zeng, L.C.Sullivan, J.P.Vivian, N.G.Walpole, C.M.Harpur, J.Rossjohn, C.S.Clements, A.G.Brooks. A Structural Basis For Antigen Presentation By the Mhc Class Ib Molecule, Qa-1B J.Immunol. V. 188 302 2012.
ISSN: ISSN 0022-1767
PubMed: 22131332
DOI: 10.4049/JIMMUNOL.1102379
Page generated: Fri Sep 25 08:36:20 2020
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