Zinc in PDB 5lyn: Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment

The structure of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment, PDB code: 5lyn was solved by E.M.Krysztofinska, N.J.Evans, A.Thapaliya, J.W.Murray, R.M.L.Morgan, S.Martinez-Lumbreras, R.L.Isaacson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.59 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.490, 61.090, 55.250, 90.00, 108.81, 90.00
R / Rfree (%)	15.8 / 20.3

The binding sites of Zinc atom in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment (pdb code 5lyn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment, PDB code: 5lyn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:38.7 occ:1.00 OD2 A:ASP117 2.3 34.4 1.0 CG A:ASP117 3.2 37.0 1.0 OD1 A:ASP117 3.3 33.1 1.0 CB A:LEU120 4.2 21.8 1.0 CD2 A:LEU120 4.6 25.6 1.0 CB A:ASP117 4.6 30.9 1.0 CG A:LEU120 4.9 21.9 1.0

Zinc binding site 2 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.3 occ:1.00 OE2 A:GLU200 2.0 35.4 1.0 OE2 B:GLU200 2.1 28.7 1.0 O A:HOH461 2.1 31.5 1.0 O A:HOH462 2.1 27.9 1.0 OE1 B:GLU200 2.6 32.8 1.0 CD B:GLU200 2.7 26.7 1.0 CD A:GLU200 2.7 29.6 1.0 OE1 A:GLU200 2.7 23.9 1.0 CG B:GLU200 4.1 19.8 1.0 CG A:GLU200 4.1 26.4 1.0 ND2 B:ASN203 4.3 25.0 1.0 CE2 B:PHE170 4.5 23.2 1.0 CA B:GLU200 4.5 21.6 1.0 CA A:GLU200 4.5 22.5 1.0 ND2 A:ASN203 4.7 24.8 1.0 O A:ILE199 4.7 31.0 1.0 CD2 B:PHE170 4.7 23.6 1.0 O B:ILE199 4.7 23.7 1.0 CE2 A:PHE170 4.7 25.2 1.0 CB B:ASN203 4.8 19.8 1.0 CB B:GLU200 4.8 21.8 1.0 CG2 A:ILE199 4.8 23.1 1.0 CB A:GLU200 4.9 18.4 1.0 CD2 A:PHE170 4.9 23.1 1.0 CG2 B:ILE199 4.9 21.0 1.0 O B:HOH410 5.0 37.7 1.0

Zinc binding site 3 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:30.3 occ:1.00 O A:HOH463 2.0 21.7 1.0 OE1 A:GLU127 2.1 27.8 1.0 NZ A:LYS124 2.1 30.8 1.0 CD A:GLU127 2.8 32.4 1.0 CE A:LYS124 2.8 26.6 1.0 OE2 A:GLU127 2.9 34.4 1.0 CG A:GLU127 4.3 27.0 1.0 CD A:LYS124 4.3 21.8 1.0 CB A:ASN123 4.4 21.8 1.0 O A:HOH417 4.5 28.0 1.0 ND2 A:ASN123 4.9 20.4 1.0

Zinc binding site 4 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:0.2 occ:1.00 O A:HOH401 2.0 35.3 1.0 OXT A:LEU225 3.7 75.2 1.0 C A:LEU225 4.8 69.2 1.0

Zinc binding site 5 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:50.0 occ:1.00 OD2 A:ASP166 1.9 47.8 1.0 OD2 B:ASP202 2.2 36.2 1.0 O A:HOH438 2.3 43.4 1.0 CG A:ASP166 2.7 31.3 1.0 O B:HOH438 2.7 29.9 1.0 OD1 A:ASP166 2.9 26.9 1.0 O B:HOH463 2.9 46.9 1.0 CG B:ASP202 3.2 45.4 1.0 CB B:ASP202 3.5 36.5 1.0 CB A:ASP166 4.1 28.6 1.0 OG A:SER168 4.2 41.9 1.0 OD1 B:ASP202 4.3 49.0 1.0 O A:HOH452 4.3 36.2 1.0 N B:ASP202 4.5 31.6 1.0 CA B:ASP202 4.7 33.5 1.0 CB A:TYR169 4.7 23.1 1.0 N A:TYR169 5.0 28.3 1.0

Zinc binding site 6 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:44.4 occ:1.00 O B:HOH408 1.9 32.6 1.0 O B:HOH433 2.1 36.4 1.0 OD2 B:ASP117 2.2 37.5 1.0 CG B:ASP117 3.0 29.9 1.0 OD1 B:ASP117 3.1 24.7 1.0 CB B:ASP117 4.4 23.7 1.0 OE2 B:GLU119 4.4 32.4 1.0 CB B:LEU120 4.4 24.0 1.0

Zinc binding site 7 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:25.9 occ:1.00 O B:HOH441 2.1 20.9 1.0 OE1 B:GLU127 2.1 33.5 1.0 NZ B:LYS124 2.1 25.0 1.0 OE2 B:GLU127 2.6 24.6 1.0 CD B:GLU127 2.7 22.6 1.0 CE B:LYS124 2.8 26.4 1.0 CG B:GLU127 4.1 16.4 1.0 CD B:LYS124 4.2 24.9 1.0 CB B:ASN123 4.3 19.2 1.0 O B:HOH429 4.3 28.2 1.0 ND2 B:ASN123 4.5 21.1 1.0 CG B:ASN123 4.9 18.6 1.0 O B:HOH466 4.9 43.0 1.0 O B:ASN123 5.0 18.0 1.0

Zinc binding site 8 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:68.5 occ:1.00 N B:GLY93 2.5 78.5 1.0 C B:GLY93 3.2 73.5 1.0 O B:GLY93 3.3 89.3 1.0 CA B:GLY93 3.4 77.0 1.0 N B:SER94 3.8 51.6 1.0 OE1 B:GLU97 4.3 69.5 1.0 CA B:SER94 4.5 41.1 1.0 CB B:SER94 4.7 40.2 1.0

Zinc binding site 9 out of 9 in the Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Tpr Domain of SGT2 in Complex with Yeast SSA1 Peptide Fragment within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:51.5 occ:1.00 O D:PRO1 2.2 41.0 0.9 N D:PRO1 2.3 50.2 0.9 CD D:PRO1 3.0 42.1 0.9 C D:PRO1 3.0 41.7 0.9 CA D:PRO1 3.1 50.2 0.9 CB D:PRO1 4.0 49.3 0.9 CG D:PRO1 4.2 43.2 0.9 N D:THR2 4.3 41.9 0.9 CE1 A:TYR181 4.8 23.0 1.0 CA D:THR2 4.9 54.5 0.9

E.M.Krysztofinska, N.J.Evans, A.Thapaliya, J.W.Murray, R.M.L.Morgan, S.Martinez-Lumbreras, R.L.Isaacson. Structure and Interactions of the Tpr Domain of SGT2 with Yeast Chaperones and YBR137WP. Front Mol Biosci V. 4 68 2017.
ISSN: ISSN 2296-889X
PubMed: 29075633
DOI: 10.3389/FMOLB.2017.00068