Calcium in PDB 2xf2: Pvc-at

All present enzymatic activity of Pvc-at:
1.11.1.6;

The structure of Pvc-at, PDB code: 2xf2 was solved by A.Borovik, W.R.Melik-Adamyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.63 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.300, 144.300, 133.800, 90.00, 90.00, 120.00
R / Rfree (%)	14.9 / 17.3

The structure of Pvc-at also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Pvc-at (pdb code 2xf2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Pvc-at, PDB code: 2xf2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Pvc-at


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pvc-at within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1690 b:29.8 occ:1.00 O A:SER653 2.3 18.7 1.0 O A:ARG655 2.4 17.3 1.0 O A:VAL658 2.4 15.0 1.0 O A:HOH2451 2.5 25.8 1.0 C A:ARG655 3.4 17.9 1.0 C A:SER653 3.5 19.2 1.0 C A:VAL658 3.5 15.2 1.0 C A:GLU654 3.6 18.3 1.0 O A:GLU654 3.7 18.4 1.0 N A:VAL658 3.9 14.7 1.0 N A:ARG655 3.9 17.8 1.0 CA A:GLU654 4.0 18.6 1.0 CA A:VAL658 4.1 14.6 1.0 CB A:VAL658 4.1 14.3 1.0 N A:GLU654 4.2 18.5 1.0 N A:GLN656 4.3 17.4 1.0 CA A:ARG655 4.3 17.9 1.0 CA A:GLN656 4.4 17.9 1.0 N A:GLY657 4.5 16.0 1.0 CA A:SER653 4.6 20.0 1.0 C A:GLN656 4.6 16.8 1.0 N A:TYR659 4.7 15.2 1.0 O A:HOH2450 4.8 32.1 1.0

Calcium binding site 2 out of 6 in the Pvc-at


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pvc-at within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1691 b:16.6 occ:1.00 O A:HOH2194 2.1 13.3 1.0 O A:HOH2440 2.1 2.0 0.3 O E:HOH2400 2.1 2.0 0.3 O E:HOH2182 2.2 14.1 1.0 O A:HOH2443 2.2 4.9 0.7 O A:HOH2441 2.3 21.6 1.0 O E:HOH2181 2.3 29.4 1.0 O E:HOH2402 2.3 6.0 0.7 OE1 A:GLN245 3.8 12.9 1.0 OE1 E:GLN245 3.9 12.7 1.0 OD2 A:ASP628 4.0 14.5 1.0 ND2 E:ASN624 4.0 19.2 1.0 OD2 E:ASP628 4.1 15.7 1.0 O A:HOH2411 4.1 17.4 1.0 OD1 A:ASN624 4.1 21.2 1.0 OD1 A:ASP628 4.1 15.5 1.0 ND2 A:ASN624 4.1 20.3 1.0 O E:HOH2375 4.2 15.5 1.0 OD1 E:ASP628 4.2 16.5 1.0 OD1 E:ASN624 4.2 21.6 1.0 CG A:ASP628 4.5 13.4 1.0 O A:HOH2439 4.5 39.3 1.0 CG A:ASN624 4.6 19.0 1.0 NH2 A:ARG631 4.6 29.3 1.0 CG E:ASN624 4.6 18.6 1.0 CG E:ASP628 4.6 15.1 1.0 NH2 E:ARG631 4.6 30.3 1.0 CD A:GLN245 4.7 12.2 1.0 CD E:GLN245 4.7 12.6 1.0 O A:HOH2193 4.8 23.1 1.0 O A:HOH2078 4.8 35.2 1.0 O E:HOH2184 4.8 19.6 1.0 NE2 A:GLN245 4.9 11.6 1.0

Calcium binding site 3 out of 6 in the Pvc-at


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pvc-at within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1692 b:11.7 occ:1.00 O A:THR432 2.3 11.6 1.0 O A:HOH2128 2.4 10.8 1.0 O E:HOH2029 2.4 9.0 1.0 O A:HOH2127 2.4 12.6 1.0 O E:HOH2034 2.4 11.9 1.0 O E:HOH2031 2.5 15.4 1.0 O A:HOH2342 2.5 13.3 1.0 C A:THR432 3.5 12.5 1.0 OG E:SER32 4.1 11.8 1.0 N A:THR432 4.2 11.2 1.0 O A:HOH2126 4.3 16.0 1.0 O E:GLN35 4.3 14.4 1.0 OD2 A:ASP146 4.4 10.9 1.0 O E:SER30 4.4 10.8 1.0 OG1 A:THR432 4.4 13.6 1.0 O E:HOH2033 4.4 26.1 1.0 N A:SER434 4.4 13.9 1.0 CA A:LEU433 4.4 14.1 1.0 N A:LEU433 4.4 12.6 1.0 CA A:THR432 4.5 12.1 1.0 OD1 E:ASN29 4.6 13.1 1.0 CB E:SER32 4.7 12.3 1.0 O E:HOH2038 4.7 16.1 1.0 CG A:PRO342 4.8 11.3 1.0 C A:LEU433 4.8 14.4 1.0

Calcium binding site 4 out of 6 in the Pvc-at


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pvc-at within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1690 b:43.9 occ:0.50 O E:ARG655 2.5 26.9 1.0 O E:VAL658 2.6 24.4 1.0 O E:SER653 2.7 31.6 1.0 C E:ARG655 3.6 27.0 1.0 C E:VAL658 3.8 24.3 1.0 C E:SER653 3.8 31.3 1.0 C E:GLU654 3.9 30.1 1.0 O E:GLU654 4.0 30.4 1.0 N E:VAL658 4.1 23.3 1.0 N E:ARG655 4.1 28.9 1.0 CA E:VAL658 4.3 23.6 1.0 N E:GLN656 4.4 26.8 1.0 CA E:GLU654 4.4 30.7 1.0 CB E:VAL658 4.4 23.4 1.0 CA E:GLN656 4.4 26.5 1.0 CA E:ARG655 4.5 27.8 1.0 N E:GLU654 4.5 30.9 1.0 N E:GLY657 4.6 24.5 1.0 O E:HOH2408 4.6 38.3 1.0 C E:GLN656 4.7 25.3 1.0 CA E:SER653 4.8 31.5 1.0 N E:TYR659 4.9 24.6 1.0

Calcium binding site 5 out of 6 in the Pvc-at


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pvc-at within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1691 b:12.5 occ:1.00 O E:THR432 2.4 11.8 1.0 O A:HOH2040 2.4 14.4 1.0 O A:HOH2035 2.4 10.9 1.0 O E:HOH2122 2.4 12.5 1.0 O E:HOH2123 2.4 13.6 1.0 O A:HOH2038 2.5 17.6 1.0 O E:HOH2319 2.5 11.7 1.0 C E:THR432 3.6 13.4 1.0 OG A:SER32 4.1 12.1 1.0 N E:THR432 4.3 12.9 1.0 O A:GLN35 4.3 14.7 1.0 O A:SER30 4.3 11.9 1.0 O E:HOH2119 4.3 15.4 1.0 OD2 E:ASP146 4.4 11.1 1.0 O A:HOH2039 4.4 28.6 1.0 OG1 E:THR432 4.4 13.2 1.0 CA E:LEU433 4.4 15.2 1.0 N E:SER434 4.4 15.7 1.0 N E:LEU433 4.5 13.8 1.0 CA E:THR432 4.5 13.0 1.0 OD1 A:ASN29 4.5 14.6 1.0 CB A:SER32 4.7 12.2 1.0 O A:HOH2045 4.8 14.7 1.0 CG E:PRO342 4.8 12.7 1.0 C E:LEU433 4.9 15.7 1.0 CB A:ASN29 5.0 11.3 1.0

Calcium binding site 6 out of 6 in the Pvc-at


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pvc-at within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1692 b:26.9 occ:0.50 O A:HOH2109 2.0 43.1 1.0 O E:HOH2257 2.1 18.3 0.5 O A:HOH2276 2.2 22.8 0.5 O A:HOH2274 2.2 21.1 1.0 O E:GLY360 4.1 12.3 1.0 O E:HOH2258 4.1 30.0 1.0 O E:HOH2256 4.2 40.1 1.0 O A:HOH2275 4.2 29.6 1.0 O A:GLY360 4.2 12.1 1.0 C E:GLY360 4.9 11.4 1.0 CA E:GLY360 4.9 10.8 1.0

A.Borovik, A.I.Grebenko, W.R.Melik-Adamyan. X-Ray Investigation of Penicillium Vitale Catalase Inhibited By Aminotriazole Crystallography Reports V. 56 590 2011.
ISSN: ISSN 1063-7745
DOI: 10.1134/S1063774511030060