Zinc in PDB 1xki: Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein

The structure of Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein, PDB code: 1xki was solved by D.A.Breustedt, I.P.Korndoerfer, B.Redl, A.Skerra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.20 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.397, 61.415, 50.798, 90.00, 129.71, 90.00
R / Rfree (%)	18.9 / 25.4

The structure of Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein (pdb code 1xki). 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 Human Tear Lipocalin/Von Ebners Gland Protein, PDB code: 1xki:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein


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 Human Tear Lipocalin/Von Ebners Gland Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:24.1 occ:1.00 NZ A:LYS76 1.9 26.5 1.0 OE1 A:GLU73 2.0 20.1 1.0 O A:HOH1060 2.2 16.4 1.0 CD A:GLU73 2.8 21.3 1.0 CE A:LYS76 2.8 19.6 1.0 OE2 A:GLU73 2.9 23.2 1.0 CD A:LYS76 3.1 17.2 1.0 CG A:GLU73 4.3 22.7 1.0 OH A:TYR87 4.3 20.2 1.0 CG A:LYS76 4.6 19.4 1.0 O A:HOH1043 4.6 41.9 1.0 CB A:GLU73 4.9 20.6 1.0 CE2 A:TYR87 4.9 18.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein


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 Human Tear Lipocalin/Von Ebners Gland Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:24.1 occ:1.00 OE2 A:GLU125 2.0 29.1 1.0 NE2 A:HIS96 2.1 24.2 1.0 CL A:CL1004 2.2 24.9 1.0 CL A:CL1005 2.3 29.1 1.0 CD A:GLU125 3.0 30.1 1.0 CD2 A:HIS96 3.0 21.5 1.0 CE1 A:HIS96 3.1 24.2 1.0 OE1 A:GLU125 3.3 30.0 1.0 N A:GLU125 4.0 21.8 1.0 N A:ALA126 4.1 21.7 1.0 CG A:HIS96 4.2 22.1 1.0 ND1 A:HIS96 4.2 22.1 1.0 N A:LEU124 4.3 25.2 1.0 O A:HOH1089 4.3 31.6 1.0 CG A:GLU125 4.3 30.8 1.0 CD A:LYS20 4.4 18.7 1.0 CE A:LYS20 4.4 19.8 1.0 CG A:LYS20 4.5 16.2 1.0 CB A:ALA126 4.5 23.4 1.0 N A:ASN123 4.5 23.6 1.0 CB A:ASN123 4.6 30.7 1.0 C A:ASN123 4.7 28.7 1.0 CA A:GLU125 4.7 24.5 1.0 CA A:LEU124 4.7 27.1 1.0 CB A:GLU125 4.8 27.8 1.0 C A:GLU125 4.8 24.0 1.0 CA A:ASN123 4.8 26.9 1.0 C A:LEU124 4.9 29.0 1.0 CA A:ALA126 5.0 18.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human Tear Lipocalin/Von Ebners Gland Protein


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 Human Tear Lipocalin/Von Ebners Gland Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:35.2 occ:1.00 O A:HOH1061 1.8 29.3 1.0 OD1 A:ASP129 2.1 26.4 1.0 ND1 A:HIS92 2.2 32.4 1.0 O A:HOH1059 2.4 35.5 1.0 CG A:ASP129 3.0 29.5 1.0 CE1 A:HIS92 3.1 36.6 1.0 OD2 A:ASP129 3.1 28.9 1.0 CG A:HIS92 3.3 27.9 1.0 CB A:HIS92 3.6 24.4 1.0 O A:HOH1041 4.0 28.9 1.0 O A:HOH1138 4.0 49.8 1.0 NE2 A:HIS92 4.3 32.8 1.0 CB A:ASP129 4.3 24.3 1.0 CD2 A:HIS92 4.4 32.2 1.0 N A:HIS92 4.6 22.8 1.0 CA A:ASP129 4.6 23.7 1.0 N A:ASP129 4.6 19.9 1.0 CA A:HIS92 4.7 27.7 1.0 CD A:GLU128 4.9 40.8 1.0 CG A:GLU128 5.0 36.1 1.0

D.A.Breustedt, I.P.Korndoerfer, B.Redl, A.Skerra. The 1.8-A Crystal Structure of Human Tear Lipocalin Reveals An Extended Branched Cavity with Capacity For Multiple Ligands J.Biol.Chem. V. 280 484 2005.
ISSN: ISSN 0021-9258
PubMed: 15489503
DOI: 10.1074/JBC.M410466200