Calcium in PDB 9k6m: Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)

The structure of Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu), PDB code: 9k6m was solved by M.Jin, J.Yang, J.Park, H.Kim, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.11 / 2.50
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.937, 103.937, 297.505, 90, 90, 90
R / Rfree (%)	22.1 / 26

The binding sites of Calcium atom in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) (pdb code 9k6m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu), PDB code: 9k6m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)


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 the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:35.7 occ:1.00 OD1 A:ASP191 2.2 29.1 1.0 OD1 A:ASP193 2.2 51.7 1.0 O A:LEU197 2.3 32.1 1.0 OE1 A:GLU202 2.4 30.0 1.0 OE2 A:GLU202 2.5 46.6 1.0 OD1 A:ASP195 2.6 48.7 1.0 O A:HOH607 2.7 32.5 1.0 CD A:GLU202 2.8 33.2 1.0 CG A:ASP193 3.0 51.4 1.0 OD2 A:ASP193 3.3 57.5 1.0 CG A:ASP191 3.4 29.7 1.0 CG A:ASP195 3.4 44.7 1.0 C A:LEU197 3.5 30.1 1.0 OD2 A:ASP195 3.7 47.1 1.0 CA A:ASP191 4.2 32.8 1.0 CB A:ASP191 4.2 30.5 1.0 N A:LEU197 4.2 34.7 1.0 OD2 A:ASP191 4.3 26.8 1.0 CG A:GLU202 4.3 30.7 1.0 N A:ASP195 4.3 38.8 1.0 N A:GLY194 4.3 42.5 1.0 N A:ASP193 4.3 45.6 1.0 CB A:ASP193 4.4 47.1 1.0 N A:SER199 4.4 29.4 1.0 CA A:LEU197 4.4 33.1 1.0 N A:ILE198 4.4 27.3 1.0 CA A:ILE198 4.4 26.7 1.0 C A:ASP191 4.5 35.6 1.0 N A:VAL192 4.6 35.4 1.0 CB A:ASP195 4.7 37.4 1.0 CA A:ASP193 4.7 44.9 1.0 CB A:LEU197 4.8 35.3 1.0 N A:GLY196 4.9 34.0 1.0 C A:ILE198 4.9 27.9 1.0 CA A:ASP195 4.9 37.9 1.0 C A:ASP193 4.9 41.4 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)


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 the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:29.2 occ:1.00 O A:HOH623 2.2 35.8 1.0 O A:SER231 2.2 26.6 1.0 OD1 A:ASP229 2.3 31.2 1.0 OD1 A:ASP225 2.4 25.3 1.0 OD1 A:ASN227 2.5 29.8 1.0 OE2 A:GLU236 2.5 41.6 1.0 OE1 A:GLU236 2.6 39.4 1.0 CD A:GLU236 2.9 40.4 1.0 CG A:ASP229 3.2 30.9 1.0 CG A:ASN227 3.4 29.0 1.0 C A:SER231 3.4 26.3 1.0 OD2 A:ASP229 3.5 36.6 1.0 CG A:ASP225 3.6 23.2 1.0 ND2 A:ASN227 3.7 28.0 1.0 N A:SER231 4.1 23.4 1.0 CA A:SER231 4.2 25.8 1.0 N A:ASP229 4.3 21.9 1.0 OD2 A:ASP225 4.3 20.5 1.0 CG A:GLU236 4.4 35.7 1.0 N A:ASN227 4.4 28.3 1.0 N A:ILE232 4.4 27.2 1.0 CA A:ASP225 4.4 29.0 1.0 CB A:ASP229 4.4 23.4 1.0 CB A:ASP225 4.5 25.1 1.0 CA A:ILE232 4.5 29.0 1.0 C A:ASP225 4.5 28.1 1.0 N A:VAL226 4.6 33.1 1.0 CB A:ASN227 4.6 29.5 1.0 CB A:SER231 4.6 29.2 1.0 N A:GLY228 4.7 24.3 1.0 N A:ASP233 4.7 33.9 1.0 N A:GLY230 4.8 22.6 1.0 CA A:ASP229 4.8 22.0 1.0 CA A:ASN227 4.9 27.9 1.0 C A:ASN227 4.9 26.4 1.0 OD2 A:ASP233 5.0 54.8 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)


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 the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:68.1 occ:1.00 OD1 A:ASP416 2.2 81.2 1.0 O A:ASP420 2.2 64.5 1.0 OD1 A:ASP414 2.3 45.9 1.0 OE2 A:GLU425 2.5 68.3 1.0 OD1 A:ASN418 2.7 69.0 1.0 OE1 A:GLU425 2.9 72.6 1.0 O A:HOH615 3.0 54.0 1.0 CD A:GLU425 3.1 64.8 1.0 CG A:ASP416 3.2 75.8 1.0 CG A:ASN418 3.3 66.9 1.0 C A:ASP420 3.3 61.6 1.0 OD2 A:ASP416 3.4 74.8 1.0 CG A:ASP414 3.5 56.2 1.0 ND2 A:ASN418 3.5 67.7 1.0 N A:ASP420 4.0 55.7 1.0 CA A:ASP420 4.2 62.2 1.0 N A:LEU421 4.2 59.4 1.0 N A:ASN418 4.2 69.2 1.0 OD2 A:ASP414 4.3 47.3 1.0 CA A:LEU421 4.3 55.7 1.0 CB A:ASN418 4.4 69.8 1.0 N A:GLY419 4.4 64.5 1.0 CB A:ASP414 4.4 60.6 1.0 N A:ALA422 4.4 51.7 1.0 CA A:ASP414 4.5 63.6 1.0 CB A:ASP416 4.5 75.0 1.0 CG A:GLU425 4.6 58.2 1.0 N A:ASP416 4.6 82.0 1.0 CB A:ASP420 4.7 68.3 1.0 CA A:ASN418 4.7 69.7 1.0 C A:ASP414 4.7 69.1 1.0 C A:ASN418 4.8 69.5 1.0 OD2 A:ASP420 4.8 83.0 1.0 C A:LEU421 4.9 56.2 1.0 N A:LYS417 4.9 62.4 1.0 CA A:ASP416 4.9 73.4 1.0 C A:ASP416 5.0 64.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)


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 the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:26.1 occ:1.00 OD1 B:ASP191 2.3 20.9 1.0 O B:LEU197 2.3 23.1 1.0 OD1 B:ASP193 2.3 34.9 1.0 OE1 B:GLU202 2.4 20.0 1.0 OD1 B:ASP195 2.4 42.2 1.0 O B:HOH624 2.5 43.5 1.0 OE2 B:GLU202 2.6 24.0 1.0 CD B:GLU202 2.8 22.4 1.0 CG B:ASP193 3.1 33.7 1.0 CG B:ASP195 3.1 41.7 1.0 OD2 B:ASP193 3.3 37.1 1.0 CG B:ASP191 3.4 22.3 1.0 C B:LEU197 3.5 23.1 1.0 OD2 B:ASP195 3.6 40.4 1.0 N B:SER199 4.2 21.8 1.0 CA B:ASP191 4.2 23.6 1.0 CA B:ILE198 4.2 20.6 1.0 OD2 B:ASP191 4.2 23.2 1.0 N B:LEU197 4.3 22.8 1.0 CB B:ASP195 4.3 35.1 1.0 N B:ASP195 4.3 31.9 1.0 N B:ILE198 4.3 21.0 1.0 CB B:ASP191 4.3 22.9 1.0 CG B:GLU202 4.4 22.6 1.0 CA B:LEU197 4.4 24.4 1.0 CB B:ASP193 4.4 32.5 1.0 N B:ASP193 4.6 30.6 1.0 N B:GLY194 4.7 30.9 1.0 C B:ILE198 4.7 22.1 1.0 CA B:ASP195 4.7 31.0 1.0 C B:ASP191 4.7 28.0 1.0 N B:GLY196 4.8 23.5 1.0 CB B:LEU197 4.9 27.5 1.0 CA B:ASP193 4.9 31.1 1.0 CB B:SER199 4.9 21.4 1.0 OG B:SER199 4.9 18.3 1.0 N B:VAL192 4.9 28.3 1.0 C B:ASP195 5.0 27.3 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:31.1 occ:1.00 OD1 B:ASN227 2.2 32.4 1.0 OD1 B:ASP225 2.2 28.8 1.0 OE1 B:GLU236 2.3 30.1 1.0 O B:SER231 2.4 26.4 1.0 O B:HOH618 2.5 34.9 1.0 OD1 B:ASP229 2.6 31.7 1.0 OE2 B:GLU236 2.6 28.9 1.0 CD B:GLU236 2.8 30.0 1.0 CG B:ASN227 3.2 32.2 1.0 CG B:ASP229 3.3 29.0 1.0 CG B:ASP225 3.4 28.4 1.0 OD2 B:ASP229 3.5 26.4 1.0 C B:SER231 3.6 27.6 1.0 ND2 B:ASN227 3.7 30.6 1.0 OD2 B:ASP225 4.2 24.3 1.0 CA B:ASP225 4.3 27.6 1.0 CG B:GLU236 4.3 33.2 1.0 OD2 B:ASP233 4.3 41.1 1.0 CB B:ASP225 4.3 26.8 1.0 N B:ASP233 4.3 30.9 1.0 CA B:ILE232 4.4 26.4 1.0 N B:ASN227 4.4 31.5 1.0 N B:ILE232 4.4 28.3 1.0 CB B:ASN227 4.4 32.8 1.0 N B:SER231 4.5 31.1 1.0 N B:ASP229 4.6 27.6 1.0 CB B:ASP229 4.6 28.4 1.0 C B:ASP225 4.6 33.2 1.0 CA B:SER231 4.6 29.5 1.0 O B:HOH644 4.6 25.2 1.0 N B:VAL226 4.8 31.2 1.0 OG B:SER231 4.8 28.6 1.0 CG B:ASP233 4.8 40.3 1.0 N B:GLY228 4.8 29.2 1.0 CA B:ASN227 4.8 32.4 1.0 C B:ILE232 4.8 28.1 1.0 NH2 B:ARG280 5.0 69.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Dictyostelium Discoideum Mitochondrial Calcium Uptake Protein (Ddmicu) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:49.8 occ:1.00 O B:ASP420 2.2 42.0 1.0 OD1 B:ASP414 2.3 43.9 1.0 OE1 B:GLU425 2.3 49.2 1.0 OD1 B:ASN418 2.4 47.3 1.0 OE2 B:GLU425 2.4 39.7 1.0 CD B:GLU425 2.7 45.6 1.0 OD1 B:ASP416 2.7 69.2 1.0 CG B:ASN418 3.3 43.7 1.0 C B:ASP420 3.4 42.3 1.0 CG B:ASP416 3.4 59.7 1.0 CG B:ASP414 3.5 42.4 1.0 OD2 B:ASP416 3.6 54.8 1.0 ND2 B:ASN418 3.7 46.8 1.0 CG B:GLU425 4.2 47.0 1.0 N B:ASP420 4.2 39.8 1.0 CA B:ASP420 4.3 42.5 1.0 OD2 B:ASP414 4.3 38.7 1.0 N B:LEU421 4.3 36.2 1.0 N B:ALA422 4.3 35.6 1.0 CA B:ASP414 4.4 40.2 1.0 N B:ASN418 4.4 37.9 1.0 CA B:LEU421 4.4 32.3 1.0 CB B:ASP414 4.5 41.0 1.0 C B:ASP414 4.5 40.2 1.0 N B:ASP416 4.6 53.3 1.0 CB B:ASN418 4.6 39.8 1.0 CB B:ASP416 4.6 59.5 1.0 N B:LYS417 4.6 44.9 1.0 CB B:ASP420 4.7 49.1 1.0 N B:THR415 4.8 44.2 1.0 N B:GLY419 4.9 39.3 1.0 C B:LEU421 4.9 33.4 1.0 O B:ASP414 4.9 41.7 1.0 CA B:ASN418 4.9 38.5 1.0 CA B:ASP416 4.9 55.3 1.0 C B:ASP416 5.0 50.8 1.0 CB B:ALA422 5.0 45.9 1.0 CB B:GLU425 5.0 52.4 1.0

M.Jin, J.Yang, J.Park, H.Kim, S.H.Eom. Structure of Micu From Non-Metazoan Dictyostelium Discoideum Reveals Unique Characteristics. Commun Biol V. 8 782 2025.
ISSN: ESSN 2399-3642
PubMed: 40399431
DOI: 10.1038/S42003-025-08218-1