Calcium in PDB 6iih: Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2)

All present enzymatic activity of Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2):
3.2.1.17;

The structure of Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2), PDB code: 6iih was solved by Q.Shen, W.Wu, J.Zheng, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.68 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.743, 96.311, 85.488, 90.00, 98.98, 90.00
R / Rfree (%)	18 / 22.7

The binding sites of Calcium atom in the Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2) (pdb code 6iih). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2), PDB code: 6iih:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2)


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 Mitochondrial Calcium Uptake 2(MICU2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:28.3 occ:1.00 O A:HOH630 2.2 43.0 1.0 O A:MET270 2.3 24.0 1.0 OE1 A:GLU275 2.4 30.3 1.0 OE2 A:GLU275 2.4 29.2 1.0 OD1 A:ASN268 2.5 28.8 1.0 OD1 A:ASP266 2.5 33.3 1.0 OD1 A:ASP264 2.5 24.1 1.0 CD A:GLU275 2.8 26.9 1.0 CG A:ASP266 3.2 38.2 1.0 CG A:ASN268 3.3 32.2 1.0 HD21 A:ASN268 3.4 39.2 1.0 HA A:ASP264 3.4 26.1 1.0 H A:ASN268 3.5 30.1 1.0 H A:ASP266 3.5 35.4 1.0 C A:MET270 3.5 20.8 1.0 OD2 A:ASP266 3.5 43.9 1.0 H A:MET270 3.5 20.0 1.0 HA A:ILE271 3.6 23.1 1.0 CG A:ASP264 3.6 21.5 1.0 ND2 A:ASN268 3.7 32.7 1.0 HG3 A:GLU272 3.9 41.2 1.0 H A:GLU272 4.0 25.3 1.0 CA A:ASP264 4.2 21.8 1.0 HB2 A:MET270 4.2 26.3 1.0 N A:MET270 4.2 16.7 1.0 CG A:GLU275 4.3 24.6 1.0 H A:GLY267 4.3 30.8 1.0 N A:ASN268 4.3 25.1 1.0 N A:ASP266 4.3 29.5 1.0 CA A:ILE271 4.3 19.2 1.0 CB A:ASP264 4.4 18.1 1.0 N A:ILE271 4.4 16.4 1.0 CA A:MET270 4.4 20.9 1.0 HD22 A:ASN268 4.4 39.2 1.0 C A:ASP264 4.5 27.6 1.0 H A:THR265 4.5 26.2 1.0 CB A:ASP266 4.5 33.3 1.0 OD2 A:ASP264 4.5 25.9 1.0 HB2 A:ASP264 4.5 21.7 1.0 CB A:ASN268 4.5 27.9 1.0 HG3 A:GLU275 4.6 29.5 1.0 N A:GLU272 4.6 21.1 1.0 OE1 A:GLU272 4.6 40.3 1.0 N A:GLY267 4.6 25.7 1.0 N A:THR265 4.6 21.9 1.0 HG2 A:GLU275 4.7 29.5 1.0 HB3 A:ASN268 4.7 33.5 1.0 CA A:ASP266 4.8 37.5 1.0 H A:GLU269 4.8 27.1 1.0 HB3 A:ASP266 4.8 39.9 1.0 CA A:ASN268 4.8 29.7 1.0 CG A:GLU272 4.8 34.3 1.0 C A:ASP266 4.9 32.4 1.0 CB A:MET270 4.9 21.9 1.0 C A:ILE271 4.9 22.7 1.0 HB2 A:GLU275 4.9 31.0 1.0 N A:GLU269 5.0 22.6 1.0 C A:ASN268 5.0 28.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2)


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 Mitochondrial Calcium Uptake 2(MICU2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:45.5 occ:1.00 O B:MET270 2.3 32.8 1.0 OE2 B:GLU275 2.3 31.8 1.0 OD1 B:ASP266 2.4 38.9 1.0 OD1 B:ASN268 2.5 41.2 1.0 OE1 B:GLU275 2.5 29.6 1.0 OD1 B:ASP264 2.6 28.8 1.0 CD B:GLU275 2.7 30.9 1.0 CG B:ASP266 3.0 46.6 1.0 OD2 B:ASP266 3.3 47.5 1.0 CG B:ASN268 3.4 43.4 1.0 H B:ASP266 3.4 48.2 1.0 OE2 B:GLU272 3.4 49.3 1.0 HA B:ASP264 3.4 26.7 1.0 H B:ASN268 3.5 45.5 1.0 HD21 B:ASN268 3.5 49.6 1.0 H B:MET270 3.5 36.9 1.0 C B:MET270 3.5 34.9 1.0 CG B:ASP264 3.7 28.5 1.0 ND2 B:ASN268 3.8 41.3 1.0 HA B:ILE271 3.8 33.5 1.0 H B:GLY267 4.0 47.9 1.0 N B:ASP266 4.1 40.2 1.0 CA B:ASP264 4.1 22.3 1.0 HB2 B:MET270 4.1 49.6 1.0 CB B:ASP266 4.2 39.9 1.0 H B:GLU272 4.2 30.5 1.0 CG B:GLU275 4.2 32.1 1.0 HD13 B:ILE271 4.3 34.5 1.0 N B:MET270 4.3 30.7 1.0 N B:ASN268 4.3 38.0 1.0 H B:THR265 4.3 33.1 1.0 HG3 B:GLU272 4.3 51.3 1.0 C B:ASP264 4.3 22.8 1.0 CB B:ASP264 4.4 26.0 1.0 N B:GLY267 4.4 39.9 1.0 CA B:MET270 4.4 33.6 1.0 HB3 B:ASP266 4.4 47.9 1.0 N B:THR265 4.4 27.6 1.0 N B:ILE271 4.5 29.6 1.0 CD B:GLU272 4.5 53.6 1.0 CA B:ILE271 4.5 27.9 1.0 CA B:ASP266 4.5 43.1 1.0 OD2 B:ASP264 4.5 27.4 1.0 HB2 B:ASP264 4.5 31.2 1.0 HD22 B:ASN268 4.5 49.6 1.0 HG3 B:GLU275 4.6 38.5 1.0 CB B:ASN268 4.6 43.6 1.0 HG2 B:GLU275 4.6 38.5 1.0 C B:ASP266 4.6 41.5 1.0 H B:GLU269 4.7 50.0 1.0 N B:GLU272 4.8 25.5 1.0 CB B:MET270 4.8 41.3 1.0 CA B:ASN268 4.8 40.4 1.0 HB3 B:ASN268 4.8 52.3 1.0 CG B:GLU272 4.9 42.7 1.0 HB2 B:GLU275 4.9 37.2 1.0 N B:GLU269 4.9 41.7 1.0 O B:ASP264 5.0 29.3 1.0 HB2 B:ASP266 5.0 47.9 1.0 C B:ASN268 5.0 41.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2)


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 Mitochondrial Calcium Uptake 2(MICU2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:15.9 occ:1.00 OD1 B:ASP454 2.3 14.5 1.0 OD1 B:ASP456 2.4 14.7 1.0 OD1 B:ASP458 2.4 14.8 1.0 OE1 B:GLU465 2.4 11.2 1.0 O B:CYS460 2.4 9.8 1.0 OE2 B:GLU465 2.5 15.6 1.0 O B:HOH728 2.5 17.4 1.0 CD B:GLU465 2.8 11.0 1.0 CG B:ASP458 3.3 20.0 1.0 HA B:ASP454 3.4 17.4 1.0 CG B:ASP454 3.4 19.8 1.0 H B:ASP456 3.4 24.3 1.0 CG B:ASP456 3.5 23.5 1.0 C B:CYS460 3.5 10.0 1.0 H B:CYS460 3.5 16.1 1.0 H B:ASP458 3.5 26.3 1.0 H B:LEU455 3.7 23.4 1.0 HA B:LEU461 3.7 12.7 1.0 OD2 B:ASP458 3.7 17.0 1.0 H B:SER462 3.8 16.8 1.0 OD2 B:ASP456 3.9 25.6 1.0 CA B:ASP454 4.1 14.6 1.0 CB B:ASP454 4.1 13.6 1.0 H B:GLY457 4.2 29.3 1.0 HB2 B:CYS460 4.2 19.1 1.0 N B:CYS460 4.2 13.4 1.0 N B:LEU455 4.2 19.5 1.0 N B:ASP456 4.2 20.2 1.0 HB2 B:ASP454 4.2 16.2 1.0 OD2 B:ASP454 4.2 17.2 1.0 O B:HOH631 4.2 27.0 1.0 CG B:GLU465 4.3 12.5 1.0 N B:ASP458 4.3 21.9 1.0 HD23 B:LEU461 4.3 12.5 1.0 CA B:CYS460 4.4 15.0 1.0 N B:LEU461 4.4 11.1 1.0 CA B:LEU461 4.5 10.6 1.0 H B:GLU459 4.5 26.9 1.0 C B:ASP454 4.5 17.6 1.0 N B:SER462 4.5 14.0 1.0 CB B:ASP458 4.6 25.1 1.0 HB3 B:PRO423 4.6 18.2 1.0 N B:GLY457 4.6 24.5 1.0 HB3 B:SER462 4.6 12.5 1.0 CB B:ASP456 4.7 21.5 1.0 HG2 B:GLU465 4.7 15.0 1.0 HG3 B:GLU465 4.7 15.0 1.0 N B:GLU459 4.8 22.4 1.0 HB3 B:ASP458 4.8 30.0 1.0 CA B:ASP456 4.8 24.4 1.0 CB B:CYS460 4.8 16.0 1.0 CA B:ASP458 4.9 17.0 1.0 C B:ASP456 4.9 25.4 1.0 HB2 B:GLU465 4.9 12.5 1.0 C B:LEU461 4.9 11.6 1.0

W.Wu, Q.Shen, Z.Lei, D.Li, Z.Qiu, H.Pei, Q.Wang, J.Zheng, Z.Jia. Crystal Structure of Mitochondrial Calcium Uptake 2(MICU2) Embo Rep. 2019.
ISSN: ESSN 1469-3178
DOI: 10.15252/EMBR.201847488