Zinc in PDB 5vge: Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide

The structure of Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide, PDB code: 5vge was solved by J.I.Mobbs, J.P.Vivian, S.Gras, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.16 / 2.60
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	99.670, 99.670, 77.914, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 22.1

The binding sites of Zinc atom in the Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide (pdb code 5vge). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide, PDB code: 5vge:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:54.4 occ:1.00 NE2 A:HIS3 2.0 55.0 1.0 NE2 A:GLN180 2.3 51.5 1.0 CD2 A:HIS3 2.9 52.1 1.0 CD A:GLN180 3.1 54.5 1.0 CG A:GLN180 3.1 54.9 1.0 CE1 A:HIS3 3.1 54.5 1.0 CB A:GLN180 4.0 54.2 1.0 CG A:HIS3 4.1 52.8 1.0 ND1 A:HIS3 4.2 54.5 1.0 OE1 A:GLN180 4.3 54.6 1.0 CA A:GLN180 4.8 54.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:40.2 occ:1.00 NE2 A:HIS197 2.1 32.0 1.0 OE2 A:GLU198 2.3 43.6 1.0 OE1 A:GLU198 2.6 51.1 1.0 CD A:GLU198 2.7 49.2 1.0 CD2 A:HIS197 3.1 32.6 1.0 CE1 A:HIS197 3.1 34.3 1.0 CG A:GLU198 4.2 45.5 1.0 ND1 A:HIS197 4.2 33.8 1.0 CG A:HIS197 4.2 35.8 1.0 O A:HOH409 4.6 40.9 1.0 OG A:SER195 4.6 45.3 1.0 CB A:GLU198 4.7 41.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hla-C*07:02 in Complex with Ryr Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:38.9 occ:1.00 OD1 A:ASP196 1.8 39.8 1.0 ND1 A:HIS197 2.0 33.8 1.0 CG A:ASP196 2.8 44.9 1.0 CE1 A:HIS197 2.9 34.3 1.0 OD2 A:ASP196 3.2 50.3 1.0 CG A:HIS197 3.2 35.8 1.0 CB A:HIS197 3.6 38.2 1.0 N A:HIS197 3.9 41.1 1.0 NE2 A:HIS197 4.1 32.0 1.0 CB A:ASP196 4.2 44.6 1.0 CD2 A:HIS197 4.2 32.6 1.0 CB A:SER195 4.2 43.3 1.0 N A:ASP196 4.3 42.3 1.0 CA A:HIS197 4.4 39.2 1.0 OG A:SER195 4.4 45.3 1.0 CA A:ASP196 4.5 44.4 1.0 C A:ASP196 4.5 43.1 1.0

G.Kaur, S.Gras, J.I.Mobbs, J.P.Vivian, A.Cortes, T.Barber, S.B.Kuttikkatte, L.T.Jensen, K.E.Attfield, C.A.Dendrou, M.Carrington, G.Mcvean, A.W.Purcell, J.Rossjohn, L.Fugger. Structural and Regulatory Diversity Shape Hla-C Protein Expression Levels. Nat Commun V. 8 15924 2017.
ISSN: ESSN 2041-1723
PubMed: 28649982
DOI: 10.1038/NCOMMS15924