Calcium in PDB 5mpy: Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9

The structure of Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9, PDB code: 5mpy was solved by S.Haag, M.Schindler, L.Berndt, A.Brennicke, M.Takenaka, G.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.02 / 2.25
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.875, 73.875, 264.938, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.8

The binding sites of Calcium atom in the Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9 (pdb code 5mpy). 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 Rna Editing Factor MORF9, PDB code: 5mpy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9


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 Rna Editing Factor MORF9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:61.6 occ:1.00 O A:HOH385 3.1 58.7 1.0 N A:GLY176 3.3 40.2 1.0 N A:TYR174 3.4 55.9 1.0 NE2 A:GLN141 3.5 50.4 1.0 NZ A:LYS178 3.6 62.6 1.0 CB A:ASP173 3.8 66.1 1.0 N A:GLY175 3.9 46.0 1.0 CA A:GLY176 3.9 51.1 1.0 CB A:TYR174 3.9 48.8 1.0 O A:GLY176 4.0 57.6 1.0 CA A:TYR174 4.0 54.3 1.0 O A:HOH331 4.0 47.5 1.0 C A:TYR174 4.2 54.5 1.0 C A:GLY176 4.2 51.9 1.0 CD2 A:TYR174 4.3 40.5 1.0 C A:ASP173 4.3 65.1 1.0 OH A:TYR137 4.4 52.5 1.0 C A:GLY175 4.4 52.1 1.0 CA A:ASP173 4.4 59.9 1.0 CE A:LYS178 4.5 70.3 1.0 CG A:ASP173 4.6 58.1 1.0 CG A:TYR174 4.6 42.6 1.0 CB A:ALA131 4.6 44.2 1.0 CA A:GLY175 4.6 46.4 1.0 CD A:GLN141 4.8 55.1 1.0 OD1 A:ASP173 4.8 57.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9


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 Rna Editing Factor MORF9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:48.9 occ:0.53 O B:VAL169 2.2 53.4 1.0 O B:HOH337 2.3 46.0 1.0 O B:LYS172 2.4 61.2 1.0 O B:HOH331 2.4 48.4 1.0 O B:HOH344 2.4 55.7 1.0 O B:TYR166 2.5 44.0 1.0 C B:VAL169 3.4 55.0 1.0 C B:LYS172 3.6 55.7 1.0 N B:VAL169 3.7 52.2 1.0 C B:TYR166 3.7 51.3 1.0 CA B:VAL169 4.0 56.8 1.0 N B:LYS172 4.1 61.6 1.0 O B:HOH319 4.3 48.7 1.0 O B:ILE167 4.3 53.3 1.0 C B:ILE167 4.4 44.4 1.0 CA B:LYS172 4.4 52.8 1.0 O B:HOH350 4.4 62.7 1.0 N B:LYS170 4.4 60.2 1.0 CB B:TYR166 4.5 45.4 1.0 CA B:TYR166 4.5 50.0 1.0 CB B:VAL169 4.5 62.9 1.0 N B:ASP168 4.6 45.6 1.0 N B:ASP173 4.6 45.8 1.0 N B:ASN171 4.6 68.1 1.0 O B:HOH310 4.6 62.5 1.0 O B:HOH354 4.6 46.0 1.0 C B:ASP168 4.7 58.2 1.0 CA B:LYS170 4.7 74.8 1.0 N B:ILE167 4.7 48.3 1.0 C B:LYS170 4.7 63.4 1.0 CA B:ASP173 4.7 44.0 1.0 CB B:ASP173 4.7 55.8 1.0 O B:HOH334 4.8 62.3 1.0 O B:HOH360 4.8 66.8 1.0 CA B:ILE167 4.8 47.9 1.0 CB B:LYS172 4.9 52.8 1.0 CA B:ASP168 5.0 53.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9


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 Rna Editing Factor MORF9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:61.4 occ:1.00 O B:HOH354 3.0 46.0 1.0 N B:GLY176 3.2 50.8 1.0 NZ B:LYS178 3.3 57.5 1.0 N B:TYR174 3.3 49.3 1.0 NE2 B:GLN141 3.5 40.0 1.0 CA B:GLY176 3.6 61.8 1.0 CB B:ASP173 3.7 55.8 1.0 CB B:TYR174 3.9 42.8 1.0 N B:GLY175 3.9 51.8 1.0 CA B:TYR174 3.9 39.5 1.0 C B:TYR174 4.1 63.2 1.0 C B:ASP173 4.2 50.4 1.0 C B:GLY176 4.2 49.8 1.0 O B:HOH309 4.2 42.0 1.0 CA B:ASP173 4.2 44.0 1.0 OH B:TYR137 4.3 47.4 1.0 CD2 B:TYR174 4.3 61.5 1.0 O B:GLY176 4.3 47.6 1.0 C B:GLY175 4.4 54.2 1.0 OD1 B:ASP173 4.4 49.4 1.0 CG B:ASP173 4.5 67.2 1.0 CG B:TYR174 4.6 64.8 1.0 CE B:LYS178 4.6 89.9 1.0 CA B:GLY175 4.7 50.7 1.0 CB B:ALA131 4.7 43.0 1.0 CD B:GLN141 4.8 53.1 1.0 O B:TYR174 4.9 45.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Arabidopsis Thaliana Rna Editing Factor MORF9


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 Rna Editing Factor MORF9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:75.8 occ:1.00 O B:LYS127 2.3 54.4 0.6 O B:LYS127 2.4 54.7 0.4 OD1 B:ASN181 2.5 53.3 1.0 O B:HOH318 2.6 44.9 1.0 O B:HOH313 2.6 50.1 1.0 C B:LYS127 3.3 56.9 0.6 C B:LYS127 3.3 56.9 0.4 CG B:ASN181 3.4 51.7 1.0 O B:HOH314 3.6 47.7 1.0 CA B:LYS127 3.9 62.3 0.6 CA B:LYS127 3.9 62.2 0.4 ND2 B:ASN181 4.0 45.9 1.0 N B:ASN181 4.1 46.8 1.0 N B:ASN128 4.2 54.1 1.0 O B:ASN128 4.4 47.8 1.0 CA B:ASN181 4.5 59.6 1.0 CB B:LYS127 4.6 57.4 0.6 CB B:ASN181 4.6 52.3 1.0 CB B:LYS127 4.6 57.5 0.4 CA B:ASN128 4.6 50.8 1.0 O B:LYS126 4.6 50.1 1.0 O B:MET129 4.7 58.3 1.0 C B:ASN128 4.7 49.4 1.0

S.Haag, M.Schindler, L.Berndt, A.Brennicke, M.Takenaka, G.Weber. Crystal Structures of the Arabidopsis Thaliana Organellar Rna Editing Factors MORF1 and MORF9. Nucleic Acids Res. V. 45 4915 2017.
ISSN: ESSN 1362-4962
PubMed: 28201607
DOI: 10.1093/NAR/GKX099