Calcium in PDB 2zah: X-Ray Structure of Melon Necrotic Spot Virus

The structure of X-Ray Structure of Melon Necrotic Spot Virus, PDB code: 2zah was solved by Y.Wada, T.Tsukihara, T.Omura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	187.50 / 2.81
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	375.004, 375.004, 375.004, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 22.4

The binding sites of Calcium atom in the X-Ray Structure of Melon Necrotic Spot Virus (pdb code 2zah). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the X-Ray Structure of Melon Necrotic Spot Virus, PDB code: 2zah:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the X-Ray Structure of Melon Necrotic Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Melon Necrotic Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:43.2 occ:0.70 OD1 C:ASP179 2.3 37.1 1.0 OD1 A:ASP146 2.5 40.9 1.0 OD2 C:ASP174 2.5 28.1 1.0 OE1 A:GLN260 2.6 28.6 1.0 OD1 C:ASP174 2.8 30.8 1.0 CG C:ASP174 2.9 29.1 1.0 CG A:ASP146 3.2 36.0 1.0 OD2 A:ASP146 3.2 40.5 1.0 CB A:GLN260 3.4 30.1 1.0 CG C:ASP179 3.5 34.8 1.0 CD A:GLN260 3.5 29.2 1.0 ND2 A:ASN217 4.0 42.1 1.0 CG A:GLN260 4.1 29.7 1.0 CB C:ASP179 4.1 32.7 1.0 CB C:ASP174 4.3 28.4 1.0 OD2 C:ASP179 4.5 36.7 1.0 CE1 C:TYR191 4.5 28.6 1.0 CB A:ASP146 4.6 31.5 1.0 NE2 A:GLN260 4.6 28.1 1.0 CD A:PRO261 4.7 30.3 1.0 CA A:GLN260 4.7 30.6 1.0 CA C:ASP174 4.9 28.2 1.0 CB C:ASP176 4.9 30.4 1.0 CD1 C:TYR191 4.9 28.6 1.0 CG A:ASN217 5.0 43.7 1.0

Calcium binding site 2 out of 4 in the X-Ray Structure of Melon Necrotic Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Melon Necrotic Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:42.6 occ:0.70 OD2 B:ASP146 2.4 40.5 1.0 OD1 A:ASP179 2.5 36.0 1.0 OD1 A:ASP174 2.5 30.8 1.0 OD2 A:ASP174 2.6 31.9 1.0 CG A:ASP174 2.7 30.1 1.0 OE1 B:GLN260 2.8 33.0 1.0 OD1 B:ASP146 3.0 39.6 1.0 CG B:ASP146 3.1 35.5 1.0 CB B:GLN260 3.3 29.7 1.0 CD B:GLN260 3.7 32.6 1.0 CG A:ASP179 3.7 34.0 1.0 CB A:ASP174 4.1 28.4 1.0 CG B:GLN260 4.1 30.8 1.0 CB A:ASP179 4.3 31.6 1.0 CE1 A:TYR191 4.4 29.1 1.0 CB B:ASP146 4.5 30.7 1.0 CA A:ASP174 4.5 28.2 1.0 CA B:GLN260 4.6 29.9 1.0 CD B:PRO261 4.7 28.9 1.0 OD2 A:ASP179 4.7 36.5 1.0 CD1 A:TYR191 4.7 29.0 1.0 NE2 B:GLN260 4.8 33.0 1.0 N A:ARG175 4.8 29.4 1.0 O B:HOH393 4.8 9.7 1.0 CB A:ASP176 4.8 29.7 1.0 N A:ASP176 4.9 29.6 1.0 C A:ASP174 5.0 28.9 1.0

Calcium binding site 3 out of 4 in the X-Ray Structure of Melon Necrotic Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Melon Necrotic Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:49.1 occ:1.00 OD1 B:ASP176 2.5 34.4 1.0 OD1 C:ASP146 2.5 35.6 1.0 OD2 C:ASP218 2.6 50.3 1.0 OD1 C:ASP218 2.7 50.2 1.0 OD2 B:ASP179 2.8 36.5 1.0 OD1 B:ASP179 2.9 37.3 1.0 CG C:ASP218 3.0 49.4 1.0 CG B:ASP179 3.2 35.4 1.0 OE1 C:GLN260 3.4 32.1 1.0 CG B:ASP176 3.4 32.8 1.0 CB B:ASP176 3.7 31.8 1.0 CG C:ASP146 3.8 34.0 1.0 CA B:CA3 4.1 47.9 1.0 CD C:GLN260 4.2 32.8 1.0 NE2 C:GLN260 4.2 33.5 1.0 O C:MET216 4.4 40.5 1.0 CB C:ASP218 4.5 48.0 1.0 CA C:ASP146 4.5 30.0 1.0 OD2 B:ASP176 4.5 33.7 1.0 O C:ASP146 4.6 29.8 1.0 OD2 C:ASP146 4.6 38.1 1.0 CB C:ASP146 4.7 30.8 1.0 CB B:ASP179 4.7 34.1 1.0 NZ B:LYS225 4.8 34.2 1.0

Calcium binding site 4 out of 4 in the X-Ray Structure of Melon Necrotic Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Melon Necrotic Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:47.9 occ:1.00 OD2 B:ASP179 2.2 36.5 1.0 OE1 C:GLN260 2.5 32.1 1.0 OD1 B:ASP174 2.6 29.0 1.0 OD2 C:ASP146 2.7 38.1 1.0 OD2 B:ASP174 2.9 30.2 1.0 OD1 C:ASP146 3.0 35.6 1.0 CG B:ASP174 3.1 29.8 1.0 CG C:ASP146 3.2 34.0 1.0 CG B:ASP179 3.4 35.4 1.0 CD C:GLN260 3.6 32.8 1.0 CB C:GLN260 3.7 32.4 1.0 CB B:ASP179 4.0 34.1 1.0 CA B:CA2 4.1 49.1 1.0 CG C:GLN260 4.2 32.1 1.0 CE1 B:TYR191 4.3 38.8 1.0 CB B:ASP176 4.3 31.8 1.0 OD1 B:ASP179 4.4 37.3 1.0 CB B:ASP174 4.5 29.7 1.0 CB C:ASP146 4.6 30.8 1.0 NE2 C:GLN260 4.7 33.5 1.0 CD1 B:TYR191 4.9 38.0 1.0 CA C:GLN260 4.9 32.5 1.0 CD C:PRO261 5.0 31.8 1.0

Y.Wada, H.Tanaka, E.Yamashita, C.Kubo, T.Ichiki-Uehara, E.Nakazono-Nagaoka, T.Omura, T.Tsukihara. X-Ray Structure of Melon Necrotic Spot Virus Acta Crystallogr.,Sect.F V. 64 8 2008.
ISSN: ESSN 1744-3091
PubMed: 18097092
DOI: 10.1107/S1744309107066481