Atomistry » Nickel » PDB 3u4s-446d » 3vj6
Atomistry »
  Nickel »
    PDB 3u4s-446d »
      3vj6 »

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: Wed Dec 16 01:28:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy