Zinc in PDB 6trk: Phl P 6 Fold Stabilized Mutant - S46Y

The structure of Phl P 6 Fold Stabilized Mutant - S46Y, PDB code: 6trk was solved by W.T.Soh, H.Brandstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.80 / 1.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.825, 73.515, 76.124, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.8

The binding sites of Zinc atom in the Phl P 6 Fold Stabilized Mutant - S46Y (pdb code 6trk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Phl P 6 Fold Stabilized Mutant - S46Y, PDB code: 6trk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phl P 6 Fold Stabilized Mutant - S46Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phl P 6 Fold Stabilized Mutant - S46Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:15.4 occ:1.00 OE1 A:GLU93 2.0 14.4 1.0 O A:HOH417 2.0 16.9 1.0 ND1 A:HIS105 2.0 16.7 1.0 NE2 B:HIS90 2.0 13.3 1.0 CD A:GLU93 2.8 15.5 1.0 CE1 A:HIS105 2.9 23.7 1.0 CE1 B:HIS90 2.9 14.5 1.0 OE2 A:GLU93 3.0 15.8 1.0 HE1 A:HIS105 3.0 28.4 1.0 CG A:HIS105 3.1 21.5 1.0 HE1 B:HIS90 3.1 17.4 1.0 HB2 A:HIS105 3.1 21.1 1.0 CD2 B:HIS90 3.1 16.9 1.0 HD2 B:HIS90 3.3 20.3 1.0 HA A:HIS105 3.3 14.6 1.0 HD11 A:LEU89 3.4 21.2 1.0 CB A:HIS105 3.5 17.6 1.0 O A:HOH418 3.6 18.9 0.5 CA A:HIS105 3.9 12.1 1.0 O A:HOH365 4.0 15.5 1.0 NE2 A:HIS105 4.0 24.6 1.0 ND1 B:HIS90 4.1 14.9 1.0 CD2 A:HIS105 4.1 26.3 1.0 CG B:HIS90 4.2 13.7 1.0 CG A:GLU93 4.2 11.8 1.0 O A:HOH418 4.2 16.9 0.5 HB3 A:HIS105 4.4 21.1 1.0 HG2 A:GLU93 4.4 14.2 1.0 CD1 A:LEU89 4.4 17.6 1.0 HG3 A:GLU93 4.5 14.2 1.0 HD21 A:LEU89 4.6 24.5 1.0 HD12 A:LEU89 4.6 21.2 1.0 N A:HIS105 4.6 13.3 1.0 HD23 B:LEU89 4.7 26.8 1.0 O B:HOH441 4.8 35.7 1.0 HE2 A:HIS105 4.8 29.6 1.0 H A:HIS105 4.8 16.0 1.0 HG12 A:VAL104 4.8 14.8 1.0 HD1 B:HIS90 4.8 17.9 1.0 H A:ALA106 4.8 18.2 1.0 HD13 A:LEU89 4.9 21.2 1.0 O A:HOH432 5.0 27.8 1.0

Zinc binding site 2 out of 4 in the Phl P 6 Fold Stabilized Mutant - S46Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phl P 6 Fold Stabilized Mutant - S46Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:14.9 occ:1.00 OE2 B:GLU103 1.9 15.7 1.0 NE2 A:HIS77 2.0 13.4 1.0 O A:HOH312 2.1 14.7 1.0 CD B:GLU103 2.8 14.6 1.0 OE1 B:GLU103 2.9 13.6 1.0 CE1 A:HIS77 3.0 17.8 1.0 CD2 A:HIS77 3.0 13.8 1.0 HD2 A:HIS77 3.2 16.5 1.0 HE1 A:HIS77 3.2 21.4 1.0 O B:HOH309 4.0 33.0 1.0 HB3 A:ASN73 4.0 15.5 1.0 OD2 A:ASP76 4.0 15.3 1.0 ND1 A:HIS77 4.1 16.2 1.0 CG A:HIS77 4.1 13.4 1.0 OD1 A:ASN73 4.1 13.2 1.0 CG B:GLU103 4.2 15.8 1.0 O B:HOH400 4.4 28.6 1.0 HG3 B:GLU103 4.4 19.0 1.0 HB3 A:ASP76 4.4 13.4 1.0 CG A:ASN73 4.5 12.9 1.0 HG2 B:GLU103 4.5 19.0 1.0 HA A:ASN73 4.7 15.0 1.0 CB A:ASN73 4.7 12.9 1.0 HD1 A:HIS77 4.9 19.4 1.0 O A:ASN73 5.0 12.7 1.0

Zinc binding site 3 out of 4 in the Phl P 6 Fold Stabilized Mutant - S46Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phl P 6 Fold Stabilized Mutant - S46Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:20.5 occ:1.00 NE2 B:HIS77 1.9 22.5 1.0 OE2 A:GLU103 2.0 20.3 1.0 O B:HOH317 2.1 19.0 1.0 CD A:GLU103 2.8 19.4 1.0 CE1 B:HIS77 2.9 30.0 1.0 CD2 B:HIS77 3.0 18.8 1.0 OE1 A:GLU103 3.0 18.2 1.0 HE1 B:HIS77 3.1 36.0 1.0 HD2 B:HIS77 3.2 22.6 1.0 O A:HOH304 3.6 43.4 1.0 HG21 A:VAL107 3.6 38.4 1.0 ND1 B:HIS77 4.0 26.4 1.0 OD2 B:ASP76 4.1 22.8 1.0 CG B:HIS77 4.1 17.8 1.0 O B:HOH363 4.2 50.1 1.0 CG A:GLU103 4.2 16.8 1.0 HB3 B:ASN73 4.3 16.0 1.0 OD1 B:ASN73 4.3 18.7 1.0 HG3 A:GLU103 4.3 20.2 1.0 HG11 A:VAL107 4.4 41.9 1.0 CG2 A:VAL107 4.5 32.0 1.0 HG22 A:VAL107 4.5 38.4 1.0 HG2 A:GLU103 4.6 20.2 1.0 HB3 B:ASP76 4.7 24.9 1.0 HD1 B:HIS77 4.8 31.7 1.0 CG B:ASN73 4.8 15.5 1.0 HA B:ASN73 4.9 17.0 1.0 CB B:ASN73 5.0 13.3 1.0

Zinc binding site 4 out of 4 in the Phl P 6 Fold Stabilized Mutant - S46Y


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phl P 6 Fold Stabilized Mutant - S46Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:14.3 occ:1.00 OE2 B:GLU93 1.9 12.8 1.0 O A:HOH420 2.0 16.9 1.0 NE2 A:HIS90 2.0 13.2 1.0 ND1 B:HIS105 2.1 14.6 1.0 CD B:GLU93 2.8 11.5 1.0 CE1 A:HIS90 3.0 14.0 1.0 CE1 B:HIS105 3.0 20.6 1.0 OE1 B:GLU93 3.0 16.8 1.0 HB2 B:HIS105 3.1 16.0 1.0 CD2 A:HIS90 3.1 12.1 1.0 CG B:HIS105 3.1 18.3 1.0 HE1 A:HIS90 3.1 16.8 1.0 HE1 B:HIS105 3.1 24.7 1.0 HD2 A:HIS90 3.3 14.5 1.0 HA B:HIS105 3.3 11.3 1.0 CB B:HIS105 3.5 13.4 1.0 HD11 B:LEU89 3.5 25.8 1.0 O A:HOH418 3.7 18.9 0.5 O B:HOH326 3.9 15.0 1.0 CA B:HIS105 3.9 9.4 1.0 O A:HOH418 4.0 16.9 0.5 ND1 A:HIS90 4.1 12.9 1.0 NE2 B:HIS105 4.1 26.6 1.0 CG A:HIS90 4.2 12.5 1.0 CD2 B:HIS105 4.2 27.1 1.0 CG B:GLU93 4.2 11.2 1.0 HB3 B:HIS105 4.4 16.0 1.0 HG2 B:GLU93 4.4 13.5 1.0 CD1 B:LEU89 4.5 21.5 1.0 O B:HOH446 4.5 47.1 1.0 HG3 B:GLU93 4.5 13.5 1.0 HD12 B:LEU89 4.6 25.8 1.0 HD21 B:LEU89 4.7 26.8 1.0 HD23 A:LEU89 4.7 24.5 1.0 N B:HIS105 4.7 14.6 1.0 H B:ALA106 4.8 20.3 1.0 O B:HOH348 4.9 33.1 1.0 HD1 A:HIS90 4.9 15.5 1.0 O B:HOH409 4.9 40.7 1.0 HE2 B:HIS105 4.9 31.9 1.0 HG12 B:VAL104 4.9 16.2 1.0 H B:HIS105 5.0 17.5 1.0 HG B:LEU89 5.0 24.0 1.0 HD21 A:LEU89 5.0 24.5 1.0

P.Winter, S.Stubenvoll, S.Scheiblhofer, I.A.Joubert, L.Strasser, C.Briganser, W.T.Soh, F.Hofer, A.S.Kamenik, V.Dietrich, S.Michelini, J.Laimer, P.Lackner, J.Horejs-Hoeck, M.Tollinger, K.R.Liedl, J.Brandstetter, C.G.Huber, R.Weiss. In Silico Design of Phl P 6 Variants with Altered Fold-Stability Significantly Impacts Antigen Processing, Immunogenicity and Immune Polarization. Front Immunol V. 11 1824 2020.
ISSN: ESSN 1664-3224
PubMed: 33013833
DOI: 10.3389/FIMMU.2020.01824