Calcium in PDB 6agi: Crystal Structure of EFHA2 in Ca-Binding State

The structure of Crystal Structure of EFHA2 in Ca-Binding State, PDB code: 6agi was solved by X.Yangfei, Y.Xue, S.Yuequan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.387, 77.177, 172.669, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 26

The binding sites of Calcium atom in the Crystal Structure of EFHA2 in Ca-Binding State (pdb code 6agi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of EFHA2 in Ca-Binding State, PDB code: 6agi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of EFHA2 in Ca-Binding State


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 EFHA2 in Ca-Binding State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:74.9 occ:1.00 OD1 A:ASN249 2.4 56.2 1.0 OD1 A:ASP245 2.5 56.7 1.0 O A:MET251 2.5 69.5 1.0 OE1 A:GLU256 2.6 56.0 1.0 OE2 A:GLU256 2.6 47.6 1.0 OD1 A:ASP247 2.8 89.6 1.0 CD A:GLU256 2.9 47.6 1.0 CG A:ASN249 3.1 57.5 1.0 OD2 A:ASP247 3.1 91.2 1.0 ND2 A:ASN249 3.1 65.2 1.0 CG A:ASP247 3.3 86.0 1.0 C A:MET251 3.4 61.8 1.0 CG A:ASP245 3.6 54.0 1.0 OD1 A:ASP253 3.6 88.2 1.0 N A:VAL252 4.2 61.9 1.0 CA A:VAL252 4.2 52.8 1.0 CG A:ASP253 4.3 85.8 1.0 N A:ASP253 4.3 62.7 1.0 N A:MET251 4.3 55.5 1.0 OD2 A:ASP245 4.3 42.9 1.0 CA A:MET251 4.4 51.6 1.0 CG A:GLU256 4.4 52.5 1.0 CA A:ASP245 4.4 42.1 1.0 CB A:ASP245 4.5 53.6 1.0 CB A:ASN249 4.5 51.3 1.0 OD2 A:ASP253 4.5 88.5 1.0 N A:ASN249 4.6 49.4 1.0 CB A:ASP247 4.7 73.6 1.0 N A:ASP247 4.7 51.4 1.0 CB A:MET251 4.7 45.6 1.0 C A:VAL252 4.8 56.8 1.0 N A:GLY248 4.8 51.9 1.0 C A:ASP245 4.9 43.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of EFHA2 in Ca-Binding State


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 EFHA2 in Ca-Binding State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:43.3 occ:1.00 OE1 A:GLU494 2.3 46.9 1.0 OD1 A:ASP483 2.6 27.6 1.0 O A:GLN489 2.6 43.8 1.0 OD1 A:ASP487 2.7 62.8 1.0 CB A:ASP485 3.0 59.3 1.0 CD A:GLU494 3.1 44.1 1.0 OD2 A:ASP487 3.1 66.8 1.0 CG A:ASP487 3.1 55.3 1.0 CG A:ASP485 3.2 81.6 1.0 OD2 A:ASP485 3.3 84.9 1.0 OE2 A:GLU494 3.4 58.9 1.0 C A:GLN489 3.7 28.2 1.0 CG A:ASP483 3.7 33.8 1.0 N A:ASP485 3.9 52.2 1.0 CA A:ASP485 3.9 42.0 1.0 OD1 A:ASP485 4.0 90.5 1.0 CG A:GLU494 4.2 32.1 1.0 N A:VAL484 4.3 32.7 1.0 CA A:ASP483 4.4 23.6 1.0 CB A:ASP483 4.4 23.6 1.0 N A:LYS486 4.5 44.0 1.0 CB A:ASP487 4.5 34.9 1.0 N A:ASP487 4.5 39.1 1.0 CA A:LEU490 4.5 21.6 1.0 N A:LEU490 4.5 34.3 1.0 C A:ASP485 4.5 46.9 1.0 N A:SER491 4.6 36.3 1.0 C A:ASP483 4.6 26.0 1.0 N A:GLN489 4.6 40.7 1.0 OD2 A:ASP483 4.7 33.1 1.0 CA A:GLN489 4.7 25.5 1.0 C A:VAL484 5.0 52.0 1.0 C A:LEU490 5.0 32.2 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of EFHA2 in Ca-Binding State


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 EFHA2 in Ca-Binding State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:78.2 occ:1.00 OD2 B:ASP438 3.9 62.3 1.0 OD1 B:ASP438 4.2 63.6 1.0 OD2 A:ASP438 4.2 54.2 1.0 OD1 A:ASP438 4.4 64.6 1.0 CG B:ASP438 4.5 56.8 1.0 CB A:ALA235 4.7 21.8 1.0 CG A:ASP438 4.8 51.6 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of EFHA2 in Ca-Binding State


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 EFHA2 in Ca-Binding State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:65.0 occ:1.00 OD1 B:ASN249 2.5 43.3 1.0 OE1 B:GLU256 2.5 51.8 1.0 O B:MET251 2.5 33.1 1.0 OD1 B:ASP245 2.6 32.6 1.0 OD1 B:ASP247 2.8 68.4 1.0 OE2 B:GLU256 2.8 56.2 1.0 CD B:GLU256 2.9 50.0 1.0 OD2 B:ASP247 3.0 64.7 1.0 CG B:ASN249 3.1 53.6 1.0 ND2 B:ASN249 3.1 56.1 1.0 CG B:ASP247 3.2 63.0 1.0 OD1 B:ASP253 3.5 92.5 1.0 C B:MET251 3.5 40.0 1.0 CG B:ASP245 3.8 39.8 1.0 CG B:ASP253 4.2 88.6 1.0 CA B:VAL252 4.3 30.6 1.0 N B:VAL252 4.3 39.5 1.0 CG B:GLU256 4.3 40.1 1.0 N B:ASP253 4.4 53.3 1.0 N B:MET251 4.4 42.2 1.0 OD2 B:ASP253 4.4 96.8 1.0 CB B:ASN249 4.5 31.2 1.0 CA B:MET251 4.5 42.5 1.0 OD2 B:ASP245 4.6 42.3 1.0 CA B:ASP245 4.6 22.4 1.0 N B:ASN249 4.7 36.9 1.0 CB B:ASP247 4.7 50.8 1.0 CB B:ASP245 4.7 26.4 1.0 N B:ASP247 4.8 23.8 1.0 C B:VAL252 4.8 26.0 1.0 CB B:MET251 5.0 43.0 1.0 N B:GLY248 5.0 25.4 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of EFHA2 in Ca-Binding State


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 EFHA2 in Ca-Binding State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:67.6 occ:1.00 OD2 B:ASP485 1.9 0.2 1.0 OD1 B:ASP485 2.1 0.2 1.0 O B:GLN489 2.1 64.4 1.0 OD1 B:ASP487 2.2 95.3 1.0 CG B:ASP485 2.2 0.0 1.0 OD1 B:ASP483 2.4 59.7 1.0 OE2 B:GLU494 2.6 79.0 1.0 CG B:ASP487 2.7 97.4 1.0 OD2 B:ASP487 2.8 97.5 1.0 C B:GLN489 3.2 63.0 1.0 CG B:ASP483 3.3 58.0 1.0 CD B:GLU494 3.7 76.4 1.0 CB B:ASP485 3.7 81.2 1.0 N B:GLN489 3.8 69.5 1.0 CB B:ASP483 4.0 57.6 1.0 N B:ASP487 4.0 71.0 1.0 CA B:GLN489 4.0 66.8 1.0 CB B:ASP487 4.0 67.8 1.0 OE1 B:GLU494 4.1 71.4 1.0 N B:LEU490 4.1 62.2 1.0 OD2 B:ASP483 4.1 59.5 1.0 CA B:LEU490 4.2 51.3 1.0 CA B:ASP483 4.3 53.5 1.0 N B:LYS486 4.3 86.7 1.0 CB B:GLN489 4.4 65.1 1.0 N B:ASP485 4.4 82.1 1.0 CA B:ASP487 4.5 68.7 1.0 CA B:ASP485 4.5 83.4 1.0 C B:ASP483 4.7 59.2 1.0 N B:ASP488 4.8 72.3 1.0 C B:ASP485 4.8 86.3 1.0 N B:SER491 4.8 52.1 1.0 C B:ASP487 4.9 69.6 1.0 C B:LEU490 4.9 52.1 1.0 CG B:GLU494 4.9 68.3 1.0 N B:VAL484 4.9 60.9 1.0

Y.Xing, M.Wang, J.Wang, Z.Nie, G.Wu, X.Yang, Y.Shen. Dimerization of Micu Proteins Controls CA2+Influx Through the Mitochondrial CA2+Uniporter. Cell Rep V. 26 1203 2019.
ISSN: ESSN 2211-1247
PubMed: 30699349
DOI: 10.1016/J.CELREP.2019.01.022