Calcium in PDB 4mn0: Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State

The structure of Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State, PDB code: 4mn0 was solved by Z.J.Liu, G.A.Stepanyuk, E.S.Vysotski, J.Lee, J.P.Rose, B.C.Wang, Southeastcollaboratory For Structural Genomics (Secsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.78 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.770, 33.899, 77.406, 90.00, 126.74, 90.00
R / Rfree (%)	19.3 / 25.6

The structure of Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State (pdb code 4mn0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State, PDB code: 4mn0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:16.8 occ:1.00 O A:HOH401 2.1 25.1 1.0 O A:LYS52 2.3 20.3 1.0 OD1 A:ASP46 2.3 19.5 1.0 OE2 A:GLU57 2.3 15.9 1.0 OD1 A:ASP50 2.4 18.6 1.0 OD1 A:ASP48 2.4 20.1 1.0 OE1 A:GLU57 2.7 15.7 1.0 CD A:GLU57 2.8 15.8 1.0 CG A:ASP50 3.2 21.3 1.0 CG A:ASP46 3.5 18.2 1.0 C A:LYS52 3.5 19.6 1.0 CG A:ASP48 3.5 20.9 1.0 OD2 A:ASP50 3.6 21.4 1.0 OD2 A:ASP48 3.9 20.6 1.0 CA A:ASP46 4.1 18.5 1.0 N A:LYS52 4.2 20.9 1.0 N A:ASP48 4.3 19.2 1.0 OD2 A:ASP46 4.3 21.2 1.0 CA A:LYS52 4.3 21.5 1.0 N A:ASP50 4.3 22.0 1.0 C A:ASP46 4.3 20.8 1.0 CB A:ASP46 4.3 19.4 1.0 CG A:GLU57 4.4 13.5 1.0 N A:LEU47 4.4 17.8 1.0 CB A:ASP50 4.4 20.7 1.0 N A:MSE53 4.5 17.5 1.0 O A:HOH428 4.5 17.5 1.0 CA A:MSE53 4.5 19.6 1.0 CB A:LYS52 4.6 20.6 1.0 CB A:ASP48 4.7 19.7 1.0 N A:SER49 4.7 19.1 1.0 O A:HOH419 4.8 21.1 1.0 OE1 A:GLU54 4.8 21.3 1.0 O A:HOH422 4.8 19.1 1.0 N A:GLU54 4.8 18.7 1.0 CA A:ASP50 4.8 21.4 1.0 CA A:ASP48 4.9 19.2 1.0 N A:GLY51 5.0 19.5 1.0 O A:ASP46 5.0 20.6 1.0 C A:ASP48 5.0 20.0 1.0

Calcium binding site 2 out of 3 in the Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:23.0 occ:1.00 O A:HOH554 2.3 40.1 1.0 OD1 A:ASP138 2.3 19.7 1.0 O A:THR144 2.3 21.6 1.0 OD1 A:ASP142 2.4 31.1 1.0 OE1 A:GLU149 2.4 21.7 1.0 OD1 A:ASP140 2.4 26.3 1.0 OE2 A:GLU149 2.5 20.0 1.0 CD A:GLU149 2.8 19.4 1.0 CG A:ASP142 3.3 36.2 1.0 CG A:ASP138 3.3 24.6 1.0 CG A:ASP140 3.4 30.1 1.0 C A:THR144 3.5 24.0 1.0 OD2 A:ASP142 3.6 38.8 1.0 OD2 A:ASP140 3.7 28.8 1.0 CA A:ASP138 3.9 21.4 1.0 CB A:ASP138 4.1 21.8 1.0 OD2 A:ASP138 4.2 24.3 1.0 N A:THR144 4.3 26.5 1.0 CG A:GLU149 4.3 17.2 1.0 N A:ASP142 4.3 35.3 1.0 CA A:VAL145 4.4 19.8 1.0 C A:ASP138 4.4 21.7 1.0 N A:VAL145 4.4 21.9 1.0 N A:ASP140 4.4 27.1 1.0 CB A:ASP142 4.5 34.2 1.0 CA A:THR144 4.5 25.8 1.0 N A:ASP146 4.5 20.6 1.0 N A:ASP139 4.6 22.6 1.0 CB A:ASP140 4.7 29.2 1.0 OD2 A:ASP146 4.7 31.4 1.0 N A:GLY141 4.7 30.6 1.0 CG2 A:THR144 4.8 27.4 1.0 N A:GLY143 4.8 31.6 1.0 CA A:ASP142 4.8 34.4 1.0 CA A:ASP140 4.9 29.1 1.0 C A:VAL145 4.9 21.0 1.0 CG A:ASP146 4.9 27.1 1.0 C A:ASP140 5.0 30.9 1.0

Calcium binding site 3 out of 3 in the Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the CA2+-Loaded Apoprotein Conformation State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:29.8 occ:1.00 OE1 A:GLU180 2.2 36.5 1.0 OD1 A:ASP172 2.3 34.5 1.0 OD1 A:ASP174 2.3 46.7 1.0 O A:LYS178 2.3 26.1 1.0 OG A:SER176 2.4 31.9 1.0 OE1 A:GLU183 2.5 29.0 1.0 OE2 A:GLU183 2.6 32.3 1.0 CD A:GLU183 2.9 29.0 1.0 CD A:GLU180 3.3 35.8 1.0 CG A:ASP174 3.4 45.9 1.0 CG A:ASP172 3.5 31.8 1.0 C A:LYS178 3.6 30.7 1.0 CB A:SER176 3.6 39.2 1.0 OE2 A:GLU180 3.7 46.8 1.0 OD2 A:ASP174 3.8 40.2 1.0 N A:SER176 4.0 36.1 1.0 OD2 A:ASP172 4.3 29.6 1.0 CA A:ASP172 4.3 34.1 1.0 N A:GLU180 4.3 25.3 1.0 CA A:SER176 4.3 35.5 1.0 CA A:LEU179 4.3 29.7 1.0 N A:LYS178 4.3 33.7 1.0 CG A:GLU183 4.4 27.8 1.0 CB A:ASP172 4.4 30.8 1.0 N A:LEU179 4.4 28.0 1.0 N A:ASP174 4.5 40.0 1.0 CA A:LYS178 4.5 29.7 1.0 CG A:GLU180 4.6 32.5 1.0 C A:ASP172 4.6 34.7 1.0 CB A:ASP174 4.6 41.5 1.0 N A:GLY177 4.7 33.9 1.0 O A:HOH485 4.7 31.4 1.0 C A:LEU179 4.8 27.9 1.0 N A:LYS175 4.8 39.2 1.0 CA A:ASP174 4.8 41.6 1.0 C A:SER176 4.8 37.4 1.0 N A:THR173 4.8 40.1 1.0 C A:ASP174 4.8 39.1 1.0 CB A:GLU180 4.9 28.5 1.0 CD2 A:LEU179 5.0 26.4 1.0

G.A.Stepanyuk, Z.J.Liu, L.P.Burakova, J.Lee, J.Rose, E.S.Vysotski, B.C.Wang. Spatial Structure of the Novel Light-Sensitive Photoprotein Berovin From the Ctenophore Beroe Abyssicola in the Ca(2+)-Loaded Apoprotein Conformation State. Biochim.Biophys.Acta V.1834 2139 2013.
ISSN: ISSN 0006-3002
PubMed: 23891746
DOI: 10.1016/J.BBAPAP.2013.07.006