Calcium in PDB 5a2h: Crystal Structure of Arabidopsis Thaliana Calmodulin-7

The structure of Crystal Structure of Arabidopsis Thaliana Calmodulin-7, PDB code: 5a2h was solved by S.Kumar, S.Gourinath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.96 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.455, 67.901, 111.290, 90.00, 90.00, 90.00
R / Rfree (%)	19.079 / 23.822

The binding sites of Calcium atom in the Crystal Structure of Arabidopsis Thaliana Calmodulin-7 (pdb code 5a2h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Arabidopsis Thaliana Calmodulin-7, PDB code: 5a2h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana Calmodulin-7


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 Arabidopsis Thaliana Calmodulin-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1150 b:44.4 occ:1.00 OD1 A:ASP25 2.3 43.0 1.0 OD1 A:ASP21 2.4 43.2 1.0 OE2 A:GLU32 2.4 46.1 1.0 O A:HOH2003 2.4 48.4 1.0 OE1 A:GLU32 2.4 51.9 1.0 OD1 A:ASP23 2.5 55.9 1.0 O A:CYS27 2.6 46.8 1.0 CD A:GLU32 2.7 50.1 1.0 CG A:ASP23 3.0 54.8 1.0 OD2 A:ASP23 3.1 62.9 1.0 CG A:ASP25 3.2 47.1 1.0 CG A:ASP21 3.6 43.1 1.0 OD2 A:ASP25 3.7 50.6 1.0 C A:CYS27 3.8 45.3 1.0 N A:ASP25 4.1 46.6 1.0 N A:ASP23 4.1 49.3 1.0 CG A:GLU32 4.2 47.5 1.0 CB A:ASP25 4.2 43.8 1.0 CA A:ASP21 4.3 42.8 1.0 CB A:ASP23 4.3 52.0 1.0 C A:ASP21 4.4 45.9 1.0 OD2 A:ASP21 4.4 41.7 1.0 N A:LYS22 4.4 47.6 1.0 N A:CYS27 4.4 41.5 1.0 N A:GLY24 4.5 51.4 1.0 CB A:ASP21 4.5 44.2 1.0 CA A:ILE28 4.6 45.1 1.0 CA A:ASP23 4.6 51.2 1.0 N A:ILE28 4.6 44.2 1.0 CA A:ASP25 4.7 46.7 1.0 C A:ASP23 4.7 49.7 1.0 SG A:CYS27 4.7 63.8 1.0 CA A:CYS27 4.7 45.1 1.0 N A:THR29 4.8 47.5 1.0 O A:ASP21 4.9 47.0 1.0 CG2 A:THR29 4.9 42.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana Calmodulin-7


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 Arabidopsis Thaliana Calmodulin-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1151 b:37.2 occ:1.00 OE1 A:GLU68 2.2 32.6 1.0 OD1 A:ASP59 2.3 36.9 1.0 O A:THR63 2.3 35.4 1.0 OD1 A:ASP57 2.4 34.2 1.0 O A:HOH2008 2.4 35.5 1.0 OE2 A:GLU68 2.5 34.1 1.0 OD1 A:ASN61 2.6 37.5 1.0 CD A:GLU68 2.7 34.0 1.0 O A:HOH2013 2.9 43.7 1.0 CG A:ASP59 3.1 36.3 1.0 OD2 A:ASP59 3.3 40.5 1.0 CG A:ASP57 3.5 35.5 1.0 CG A:ASN61 3.5 37.8 1.0 C A:THR63 3.5 37.9 1.0 ND2 A:ASN61 3.9 36.1 1.0 N A:ASP65 4.1 31.2 1.0 CA A:ILE64 4.2 34.0 1.0 CG A:GLU68 4.2 32.1 1.0 OD2 A:ASP57 4.3 39.0 1.0 N A:ILE64 4.3 35.2 1.0 CB A:ASP59 4.3 36.0 1.0 CA A:ASP57 4.4 36.0 1.0 OD2 A:ASP65 4.4 32.2 1.0 CG A:ASP65 4.4 33.5 1.0 N A:ASP59 4.4 39.7 1.0 CB A:ASP57 4.5 35.4 1.0 N A:THR63 4.5 39.5 1.0 C A:ILE64 4.5 32.7 1.0 OD1 A:ASP65 4.6 31.3 1.0 OG1 A:THR63 4.6 34.0 1.0 CA A:THR63 4.6 37.2 1.0 N A:ASN61 4.6 40.8 1.0 C A:ASP57 4.7 35.5 1.0 CB A:ASN61 4.8 36.8 1.0 CA A:ASP59 4.8 38.0 1.0 N A:ALA58 4.8 35.7 1.0 C A:ASP59 4.9 40.1 1.0 CB A:ASP65 4.9 31.9 1.0 O A:HOH2017 4.9 33.9 1.0 O A:HOH2014 5.0 49.5 1.0 CB A:GLU68 5.0 31.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana Calmodulin-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Arabidopsis Thaliana Calmodulin-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1152 b:27.0 occ:1.00 OD1 A:ASP96 2.2 29.9 1.0 OD1 A:ASP94 2.3 32.7 1.0 O A:PHE100 2.3 27.8 1.0 OD1 A:ASN98 2.3 30.7 1.0 OE1 A:GLU105 2.3 30.2 1.0 OE2 A:GLU105 2.4 28.0 1.0 O A:HOH2025 2.4 37.6 1.0 CD A:GLU105 2.7 30.4 1.0 CG A:ASN98 3.0 32.7 1.0 CG A:ASP96 3.2 32.4 1.0 CG A:ASP94 3.4 31.5 1.0 C A:PHE100 3.5 27.4 1.0 OD2 A:ASP96 3.6 34.4 1.0 ND2 A:ASN98 3.6 35.1 1.0 CB A:ASN98 4.0 33.1 1.0 N A:ASP96 4.0 33.1 1.0 N A:ASN98 4.1 33.5 1.0 CA A:ASP94 4.2 30.6 1.0 CG A:GLU105 4.2 31.3 1.0 N A:LYS95 4.3 37.0 1.0 OD2 A:ASP94 4.3 32.5 1.0 C A:ASP94 4.3 35.0 1.0 CB A:ASP94 4.3 30.7 1.0 N A:PHE100 4.3 28.6 1.0 CB A:ASP96 4.4 32.8 1.0 CA A:PHE100 4.4 27.6 1.0 N A:GLN97 4.4 33.1 1.0 N A:ILE101 4.5 26.8 1.0 CA A:ASP96 4.5 33.3 1.0 CA A:ASN98 4.5 33.5 1.0 CA A:ILE101 4.6 26.8 1.0 O A:HOH2027 4.6 33.1 1.0 C A:ASP96 4.6 33.5 1.0 O A:HOH2026 4.7 39.2 1.0 N A:SER102 4.7 27.3 1.0 CB A:PHE100 4.8 27.6 1.0 N A:GLY99 4.9 30.9 1.0 O A:ASP94 4.9 34.8 1.0 CB A:GLU105 5.0 31.7 1.0 C A:ASN98 5.0 32.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana Calmodulin-7


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Arabidopsis Thaliana Calmodulin-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1153 b:26.6 occ:1.00 OD1 A:ASP134 2.3 28.1 1.0 OD1 A:ASP132 2.3 31.6 1.0 OD1 A:ASP130 2.3 28.0 1.0 O A:GLN136 2.4 25.2 1.0 OE1 A:GLU141 2.4 26.1 1.0 O A:HOH2041 2.4 25.4 1.0 OE2 A:GLU141 2.5 27.3 1.0 CD A:GLU141 2.8 28.0 1.0 CG A:ASP134 3.2 28.3 1.0 CG A:ASP132 3.3 33.5 1.0 CG A:ASP130 3.5 29.9 1.0 C A:GLN136 3.6 25.4 1.0 OD2 A:ASP134 3.6 27.7 1.0 OD2 A:ASP132 3.7 37.0 1.0 OD2 A:ASP130 4.2 31.6 1.0 N A:ASP134 4.2 28.3 1.0 N A:ASP132 4.3 31.4 1.0 CG A:GLU141 4.3 28.5 1.0 N A:GLN136 4.3 25.9 1.0 CA A:ASP130 4.4 29.9 1.0 CB A:ASP134 4.4 28.3 1.0 CB A:ASP130 4.4 29.3 1.0 CA A:ILE137 4.4 25.5 1.0 N A:ASN138 4.4 26.0 1.0 N A:ILE137 4.4 25.5 1.0 N A:GLY133 4.5 30.0 1.0 CB A:ASP132 4.6 32.7 1.0 N A:VAL131 4.6 32.2 1.0 C A:ASP130 4.6 32.2 1.0 CG A:GLN136 4.6 25.9 1.0 CA A:GLN136 4.6 25.2 1.0 CA A:ASP134 4.7 27.9 1.0 CA A:ASP132 4.8 32.3 1.0 N A:GLY135 4.8 26.4 1.0 C A:ASP132 4.9 31.7 1.0 O A:HOH2045 4.9 40.5 1.0 C A:ILE137 4.9 26.2 1.0 C A:ASP134 5.0 26.3 1.0 OD1 A:ASN138 5.0 36.7 1.0

S.Kumar, M.Mazumder, N.Gupta, S.Chattopadhyay, S.Gourinath. Crystal Structure of Arabidopsis Thaliana CALMODULIN7 and Insight Into Its Mode of Dna Binding. Febs Lett. V. 590 3029 2016.
ISSN: ISSN 0014-5793
PubMed: 27500568
DOI: 10.1002/1873-3468.12349