Zinc in PDB 1dy0: Murine Endostatin, Crystal Form II

The structure of Murine Endostatin, Crystal Form II, PDB code: 1dy0 was solved by E.Hohenester, T.Sasaki, R.Timpl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.810, 62.810, 88.070, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 27.2

The binding sites of Zinc atom in the Murine Endostatin, Crystal Form II (pdb code 1dy0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Murine Endostatin, Crystal Form II, PDB code: 1dy0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Murine Endostatin, Crystal Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Murine Endostatin, Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.2 occ:1.00 OD1 A:ASP207 1.8 23.9 1.0 NE2 A:HIS134 1.9 11.6 1.0 OD2 A:ASP136 2.0 27.1 1.0 NE2 A:HIS142 2.1 15.7 1.0 CE1 A:HIS134 2.7 16.2 1.0 CG A:ASP207 2.7 18.0 1.0 CG A:ASP136 2.8 26.0 1.0 CE1 A:HIS142 2.8 19.3 1.0 OD1 A:ASP136 2.9 24.7 1.0 OD2 A:ASP207 3.0 24.3 1.0 CD2 A:HIS134 3.0 19.3 1.0 CD2 A:HIS142 3.3 18.9 1.0 ND1 A:HIS134 3.9 20.9 1.0 ND1 A:HIS142 4.0 19.0 1.0 CG A:HIS134 4.0 14.5 1.0 CB A:ASP207 4.1 12.6 1.0 CB A:ASP136 4.2 20.1 1.0 CG A:HIS142 4.3 22.5 1.0 O A:HOH2002 4.3 31.4 1.0 CG2 A:VAL140 4.5 6.5 1.0 O A:LEU205 4.6 17.0 1.0 CA A:ASP207 4.7 14.8 1.0 CG2 A:VAL203 4.8 10.5 1.0 N A:ASP207 4.9 16.4 1.0 O A:GLN135 4.9 24.6 1.0 CA A:ASP136 4.9 23.5 1.0

Zinc binding site 2 out of 2 in the Murine Endostatin, Crystal Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Murine Endostatin, Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:36.3 occ:1.00 ND1 A:HIS132 2.2 35.1 1.0 N A:HIS132 2.5 43.8 1.0 CG A:HIS132 3.0 35.9 1.0 CB A:ALA131 3.1 47.3 1.0 CB A:HIS132 3.2 39.9 1.0 CA A:HIS132 3.2 42.4 1.0 CE1 A:HIS132 3.3 34.9 1.0 C A:ALA131 3.4 44.9 1.0 CA A:ALA131 3.6 46.6 1.0 N A:ALA131 3.8 49.7 1.0 N A:THR133 3.8 35.1 1.0 C A:HIS132 3.9 41.2 1.0 CD2 A:HIS132 4.2 39.5 1.0 NE2 A:HIS132 4.4 35.5 1.0 O A:ALA131 4.5 45.0 1.0 CG2 A:THR133 4.5 28.5 1.0 O A:HIS132 4.9 43.8 1.0

E.Hohenester, T.Sasaki, K.Mann, R.Timpl. Variable Zinc Coordination in Endostatin J.Mol.Biol. V. 297 1 2000.
ISSN: ISSN 0022-2836
PubMed: 10704302
DOI: 10.1006/JMBI.2000.3553