Zinc in PDB 2ero: Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form), PDB code: 2ero was solved by S.Takeda, T.Igarashi, S.Araki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.710, 93.270, 137.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.8

The structure of Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) (pdb code 2ero). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form), PDB code: 2ero:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)


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 Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:41.3 occ:1.00 NE2 A:HIS345 1.9 46.0 1.0 NE2 A:HIS339 2.3 27.9 1.0 NE2 A:HIS335 2.3 32.5 1.0 O A:HOH814 2.6 34.2 1.0 CE1 A:HIS345 2.8 45.6 1.0 CD2 A:HIS345 3.0 47.1 1.0 CD2 A:HIS335 3.0 28.1 1.0 CD2 A:HIS339 3.1 22.7 1.0 CE1 A:HIS339 3.4 26.6 1.0 CE1 A:HIS335 3.5 30.8 1.0 ND1 A:HIS345 3.9 44.3 1.0 O A:HOH752 4.0 43.3 1.0 CG A:HIS345 4.1 45.1 1.0 CG A:HIS335 4.3 30.8 1.0 CG A:HIS339 4.3 26.7 1.0 ND1 A:HIS339 4.4 26.2 1.0 ND1 A:HIS335 4.5 30.4 1.0 OE1 A:GLU336 4.5 43.0 1.0 OE2 A:GLU336 4.7 39.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form)


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 Vascular Apoptosis-Inducing Protein- 1(Orthorhombic Crystal Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:40.4 occ:1.00 NE2 B:HIS345 1.9 48.6 1.0 NE2 B:HIS339 2.2 25.9 1.0 NE2 B:HIS335 2.3 31.2 1.0 O B:HOH787 2.7 40.2 1.0 CE1 B:HIS345 2.7 50.2 1.0 CD2 B:HIS345 3.1 48.0 1.0 CE1 B:HIS339 3.1 29.0 1.0 CD2 B:HIS339 3.2 25.4 1.0 CD2 B:HIS335 3.2 34.2 1.0 CE1 B:HIS335 3.3 32.1 1.0 ND1 B:HIS345 3.9 45.2 1.0 O B:HOH762 4.0 43.5 1.0 CG B:HIS345 4.1 46.6 1.0 ND1 B:HIS339 4.2 28.8 1.0 CG B:HIS339 4.3 24.4 1.0 CG B:HIS335 4.4 33.6 1.0 ND1 B:HIS335 4.4 33.5 1.0 OE2 B:GLU336 4.4 44.3 1.0 OE1 B:GLU336 4.9 41.9 1.0

S.Takeda, T.Igarashi, H.Mori, S.Araki. Crystal Structures of VAP1 Reveal Adams' Mdc Domain Architecture and Its Unique C-Shaped Scaffold Embo J. V. 25 2388 2006.
ISSN: ISSN 0261-4189
PubMed: 16688218
DOI: 10.1038/SJ.EMBOJ.7601131