Zinc in PDB 3ws6: Crystal Structure of H-2D in Complex with A Mimotopic Peptide

The structure of Crystal Structure of H-2D in Complex with A Mimotopic Peptide, PDB code: 3ws6 was solved by P.R.Kumar, G.Mukherjee, D.Samanta, T.P.Dilorenzo, S.C.Almo, Immunefunction Network, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.50 / 1.98
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	162.723, 69.265, 73.753, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 22.4

The binding sites of Zinc atom in the Crystal Structure of H-2D in Complex with A Mimotopic Peptide (pdb code 3ws6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of H-2D in Complex with A Mimotopic Peptide, PDB code: 3ws6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of H-2D in Complex with A Mimotopic 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 H-2D in Complex with A Mimotopic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:23.4 occ:1.00 N3 A:IMD402 1.8 13.7 1.0 OE1 A:GLU292 2.1 29.6 1.0 N1 A:IMD403 2.3 37.2 1.0 C5 A:IMD403 2.6 34.0 1.0 CD A:GLU292 2.8 33.3 1.0 OE2 A:GLU292 2.8 34.4 1.0 C2 A:IMD402 2.8 25.7 1.0 C4 A:IMD402 2.9 25.9 1.0 O A:HOH669 3.4 45.0 1.0 C2 A:IMD403 3.6 44.8 1.0 N1 A:IMD402 4.0 30.6 1.0 C4 A:IMD403 4.0 37.1 1.0 C5 A:IMD402 4.0 23.5 1.0 CG A:GLU292 4.3 27.9 1.0 CD A:PRO293 4.4 36.7 1.0 N3 A:IMD403 4.4 42.8 1.0 CB A:GLU292 4.8 30.5 1.0 CA A:GLU292 5.0 26.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of H-2D in Complex with A Mimotopic 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 H-2D in Complex with A Mimotopic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:30.3 occ:1.00 O1 D:SO4202 2.0 35.5 1.0 N3 D:IMD203 2.1 24.7 1.0 O1 C:SO4202 2.1 37.9 1.0 NE2 D:HIS33 2.2 25.7 1.0 S D:SO4202 2.9 37.7 1.0 C4 D:IMD203 3.0 23.4 1.0 CD2 D:HIS33 3.1 20.9 1.0 O3 D:SO4202 3.1 38.6 1.0 C2 D:IMD203 3.2 24.1 1.0 S C:SO4202 3.2 38.5 1.0 O2 C:SO4202 3.2 42.7 1.0 CE1 D:HIS33 3.2 28.6 1.0 O4 D:SO4202 3.5 30.9 1.0 O C:HOH315 3.7 26.3 1.0 ZN C:ZN201 3.8 30.6 1.0 O3 C:SO4202 3.9 32.7 1.0 CD D:ARG32 4.0 27.0 1.0 N3 C:IMD204 4.1 24.6 1.0 C5 D:IMD203 4.2 24.6 1.0 O2 D:SO4202 4.2 39.0 1.0 CG D:HIS33 4.2 22.6 1.0 N1 D:IMD203 4.2 23.2 1.0 ND1 D:HIS33 4.3 23.9 1.0 O4 C:SO4202 4.3 46.2 1.0 NH1 D:ARG32 4.3 20.4 1.0 C4 C:IMD204 4.5 29.0 1.0 CG D:ARG32 4.9 20.8 1.0 C2 C:IMD204 4.9 22.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of H-2D in Complex with A Mimotopic 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 H-2D in Complex with A Mimotopic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:24.5 occ:1.00 OE1 B:GLU292 2.0 38.4 1.0 C4 B:IMD402 2.1 8.7 1.0 N3 B:IMD403 2.1 31.0 1.0 OE2 B:GLU292 2.6 37.4 1.0 CD B:GLU292 2.6 36.0 1.0 N3 B:IMD402 2.7 25.1 1.0 C4 B:IMD403 2.8 37.7 1.0 C2 B:IMD403 3.3 41.2 1.0 C5 B:IMD402 3.3 29.4 1.0 C2 B:IMD402 4.0 26.4 1.0 C5 B:IMD403 4.0 39.1 1.0 CG B:GLU292 4.1 33.5 1.0 N1 B:IMD403 4.3 40.9 1.0 N1 B:IMD402 4.3 29.1 1.0 CD B:PRO293 4.4 35.7 1.0 CB B:GLU292 4.7 36.9 1.0 CA B:GLU292 5.0 35.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of H-2D in Complex with A Mimotopic Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of H-2D in Complex with A Mimotopic Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:30.6 occ:1.00 O3 C:SO4202 2.0 32.7 1.0 NE2 C:HIS33 2.0 22.4 1.0 N3 C:IMD204 2.2 24.6 1.0 O3 D:SO4202 2.2 38.6 1.0 CE1 C:HIS33 3.0 21.7 1.0 S C:SO4202 3.0 38.5 1.0 C2 C:IMD204 3.0 22.9 1.0 CD2 C:HIS33 3.0 18.4 1.0 O1 C:SO4202 3.0 37.9 1.0 C4 C:IMD204 3.2 29.0 1.0 O4 D:SO4202 3.2 30.9 1.0 S D:SO4202 3.2 37.7 1.0 O D:HOH334 3.7 30.6 1.0 O2 C:SO4202 3.7 42.7 1.0 ZN D:ZN201 3.8 30.3 1.0 CD C:ARG32 4.0 20.7 1.0 O1 D:SO4202 4.0 35.5 1.0 N3 D:IMD203 4.0 24.7 1.0 ND1 C:HIS33 4.1 24.4 1.0 CG C:HIS33 4.1 25.4 1.0 NH1 C:ARG32 4.2 20.9 1.0 O4 C:SO4202 4.2 46.2 1.0 N1 C:IMD204 4.2 26.7 1.0 C5 C:IMD204 4.3 23.4 1.0 C2 D:IMD203 4.4 24.1 1.0 O2 D:SO4202 4.4 39.0 1.0 C4 D:IMD203 4.7 23.4 1.0 CG C:ARG32 4.9 18.4 1.0 NE C:ARG32 5.0 25.9 1.0

D.Lamont, G.Mukherjee, P.R.Kumar, D.Samanta, C.G.Mcphee, T.W.H.Kay, S.C.Almo, T.P.Dilorenzo, D.V.Serreze. Unusual Antigen Recognition Characteristics To Be Published.