Calcium in PDB 7w9q: Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14

The structure of Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14, PDB code: 7w9q was solved by W.Katayama, A.Shimane, Y.Nabeshima, T.Yokoyama, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.51 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.378, 85.38, 63.957, 90, 90, 90
R / Rfree (%)	18.7 / 20.1

The structure of Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14 (pdb code 7w9q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14, PDB code: 7w9q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:62.5 occ:1.00 O A:ASP99 2.4 35.4 1.0 OD1 A:ASP99 2.4 52.7 1.0 OE1 A:GLU66 2.7 40.0 1.0 O A:HOH359 3.0 46.0 1.0 C A:ASP99 3.4 37.6 1.0 CD A:GLU66 3.5 41.7 1.0 CG A:ASP99 3.6 52.6 1.0 OE2 A:GLU66 3.8 33.5 1.0 CA A:ASP99 3.9 30.7 1.0 O A:HOH356 3.9 42.3 1.0 CB A:ASP99 4.4 35.6 1.0 O A:HOH341 4.5 44.0 1.0 OD2 A:ASP99 4.5 55.9 1.0 N A:SER100 4.6 34.0 1.0 O A:HOH355 4.6 46.1 1.0 CG A:GLU66 4.7 37.1 1.0 O A:ASN98 5.0 30.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of V30M-Ttr in Complex with Naringenin Derivative-14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:58.3 occ:1.00 OE1 B:GLU66 2.9 41.0 1.0 O B:HOH313 3.2 43.3 1.0 OD1 B:ASN98 3.3 61.3 1.0 O B:ASP99 3.6 55.3 1.0 CD B:GLU66 3.8 40.9 1.0 OE2 B:GLU66 3.8 33.7 1.0 CG B:ASN98 4.4 55.1 1.0 N B:ASP99 4.6 45.7 1.0 C B:ASP99 4.6 51.0 1.0 CB B:ASP99 4.7 42.9 1.0 CA B:ASP99 4.9 50.3 1.0 ND2 B:ASN98 4.9 59.6 1.0

W.Katayama, K.Imui, Y.Nakagawa, Y.Sawai, A.Shimane, R.Kitakami, T.Okada, Y.Nabeshima, T.Yokoyama, K.Kanamitsu, S.Nakagawa, N.Toyooka, M.Mizuguchi. Inhibitory Activities of Naringenin Derivatives Against Transthyretin Amyloidogenesis To Be Published.