Calcium in PDB 4nsd: Crystal Structure of CBARA1 in the CA2+ Binding Form

The structure of Crystal Structure of CBARA1 in the CA2+ Binding Form, PDB code: 4nsd was solved by L.Wang, X.Yang, S.Li, Y.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.38 / 2.70
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.283, 105.804, 156.851, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 28.2

The structure of Crystal Structure of CBARA1 in the CA2+ Binding Form also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of CBARA1 in the CA2+ Binding Form (pdb code 4nsd). 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 CBARA1 in the CA2+ Binding Form, PDB code: 4nsd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CBARA1 in the CA2+ Binding Form


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 CBARA1 in the CA2+ Binding Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:59.4 occ:1.00 OD1 A:ASP235 2.5 63.2 1.0 OD1 A:ASP231 2.5 36.8 1.0 OE1 A:GLU242 2.6 60.0 1.0 O A:HOH608 2.6 46.0 1.0 OD1 A:ASN233 2.6 76.0 1.0 O A:GLU237 2.7 65.7 1.0 OE2 A:GLU242 2.8 72.4 1.0 CD A:GLU242 3.0 61.5 1.0 CG A:ASP235 3.2 63.6 1.0 C A:GLU237 3.4 62.9 1.0 CG A:ASN233 3.5 70.2 1.0 CG A:ASP231 3.6 54.5 1.0 OD2 A:ASP235 3.6 54.6 1.0 ND2 A:ASN233 3.9 69.2 1.0 N A:VAL238 4.0 67.9 1.0 CA A:VAL238 4.0 60.5 1.0 CA A:ASP231 4.0 51.6 1.0 N A:ASP235 4.2 59.7 1.0 OD2 A:ASP239 4.2 88.2 1.0 CA A:GLU237 4.2 63.1 1.0 N A:GLU237 4.3 71.1 1.0 N A:LEU232 4.3 61.0 1.0 CB A:ASP231 4.3 53.3 1.0 C A:ASP231 4.4 58.8 1.0 CB A:ASP235 4.4 50.0 1.0 N A:ASN233 4.4 59.3 1.0 CB A:GLU237 4.5 73.6 1.0 CG A:GLU242 4.5 57.1 1.0 OD2 A:ASP231 4.6 54.0 1.0 CA A:ASP235 4.7 61.6 1.0 N A:GLY234 4.8 54.9 1.0 CB A:ASN233 4.8 60.2 1.0 C A:ASP235 4.9 69.8 1.0 N A:ASP239 4.9 59.0 1.0 C A:VAL238 4.9 61.4 1.0 CG2 A:VAL238 4.9 41.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CBARA1 in the CA2+ Binding Form


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 CBARA1 in the CA2+ Binding Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:52.6 occ:1.00 O A:GLU427 2.4 45.2 1.0 OE2 A:GLU432 2.6 56.2 1.0 OD1 A:ASN425 2.7 66.5 1.0 OE1 A:GLU432 2.7 51.5 1.0 OD1 A:ASP421 2.8 75.5 1.0 OD1 A:ASP423 2.9 80.8 1.0 CD A:GLU432 3.0 48.6 1.0 OD2 A:ASP423 3.1 72.1 1.0 CG A:ASP423 3.2 75.2 1.0 CG A:ASN425 3.5 61.3 1.0 CG A:ASP421 3.6 69.9 1.0 C A:GLU427 3.6 42.7 1.0 ND2 A:ASN425 4.0 64.3 1.0 CA A:ASP421 4.1 50.4 1.0 N A:ASP423 4.2 60.2 1.0 OD2 A:ASP421 4.2 73.7 1.0 C A:ASP421 4.2 50.6 1.0 N A:ASN425 4.3 54.0 1.0 N A:GLU427 4.3 49.9 1.0 CB A:ASP421 4.4 56.3 1.0 CB A:ASP423 4.4 68.0 1.0 N A:GLY424 4.4 57.1 1.0 CA A:LEU428 4.5 45.0 1.0 CG A:GLU432 4.5 35.7 1.0 N A:LEU428 4.5 39.6 1.0 CA A:GLU427 4.6 47.8 1.0 O A:ASP421 4.6 46.2 1.0 N A:SER429 4.6 44.1 1.0 N A:CYS422 4.6 42.5 1.0 CB A:ASN425 4.6 55.6 1.0 CA A:ASP423 4.7 56.2 1.0 N A:GLY426 4.8 48.9 1.0 C A:ASP423 4.8 58.7 1.0 CA A:ASN425 4.9 51.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CBARA1 in the CA2+ Binding Form


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 CBARA1 in the CA2+ Binding Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:58.0 occ:1.00 O B:GLU237 2.4 42.4 1.0 OD1 B:ASP231 2.6 61.5 1.0 OE2 B:GLU242 2.6 60.6 1.0 OD1 B:ASN233 2.6 53.5 1.0 OE1 B:GLU242 2.7 61.7 1.0 CD B:GLU242 3.0 59.1 1.0 OD1 B:ASP235 3.0 47.3 1.0 OD2 B:ASP235 3.2 47.1 1.0 CG B:ASP235 3.3 46.3 1.0 CG B:ASN233 3.4 39.8 1.0 CG B:ASP231 3.5 50.1 1.0 C B:GLU237 3.6 45.5 1.0 ND2 B:ASN233 3.6 33.4 1.0 OD2 B:ASP231 4.0 41.3 1.0 N B:GLU237 4.1 49.2 1.0 N B:ASP235 4.1 42.3 1.0 CB B:ASP235 4.3 45.4 1.0 CA B:GLU237 4.4 45.0 1.0 CB B:ASP231 4.4 44.1 1.0 N B:ASN233 4.4 51.3 1.0 CA B:ASP231 4.5 53.1 1.0 CG B:GLU242 4.5 42.5 1.0 N B:VAL238 4.6 42.3 1.0 CB B:ASN233 4.6 31.4 1.0 CA B:ASP235 4.6 45.6 1.0 N B:GLY236 4.6 43.9 1.0 CA B:VAL238 4.6 43.0 1.0 C B:ASP231 4.7 62.2 1.0 CB B:GLU237 4.7 43.7 1.0 OD2 B:ASP239 4.8 58.1 1.0 N B:LEU232 4.8 56.9 1.0 C B:ASP235 4.8 44.6 1.0 N B:GLY234 4.8 48.9 1.0 C B:ASN233 4.8 53.8 1.0 CA B:ASN233 4.8 48.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CBARA1 in the CA2+ Binding Form


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 CBARA1 in the CA2+ Binding Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:66.8 occ:1.00 OE2 B:GLU432 2.5 71.8 1.0 OD1 B:ASP421 2.5 69.8 1.0 OD1 B:ASN425 2.7 80.0 1.0 OD2 B:ASP423 2.8 91.9 1.0 O B:GLU427 2.9 92.4 1.0 ND2 B:ASN425 2.9 76.4 1.0 CG B:ASN425 3.0 74.5 1.0 CD B:GLU432 3.0 60.5 1.0 OE1 B:GLU432 3.1 51.3 1.0 CG B:ASP421 3.4 66.0 1.0 C B:GLU427 3.5 78.5 1.0 CG B:ASP423 3.6 82.1 1.0 OD1 B:ASP423 3.8 71.5 1.0 N B:GLU427 3.9 82.0 1.0 CA B:ASP421 4.0 52.5 1.0 N B:ASN425 4.0 62.8 1.0 N B:LEU428 4.1 65.5 1.0 CB B:ASP421 4.1 58.5 1.0 CA B:LEU428 4.2 59.2 1.0 CB B:ASN425 4.2 72.9 1.0 OD2 B:ASP421 4.2 55.6 1.0 CG B:GLU432 4.3 49.9 1.0 CA B:GLU427 4.3 75.3 1.0 N B:GLY426 4.3 68.4 1.0 C B:ASP421 4.4 57.4 1.0 N B:SER429 4.5 59.4 1.0 CA B:ASN425 4.5 71.5 1.0 N B:GLY424 4.6 62.3 1.0 O B:ASP421 4.7 55.9 1.0 C B:LEU428 4.7 61.0 1.0 C B:ASN425 4.7 74.2 1.0 C B:GLY426 4.9 80.8 1.0 CD2 B:LEU428 4.9 42.4 1.0 N B:CYS422 5.0 65.8 1.0 N B:ASP423 5.0 66.8 1.0

L.Wang, X.Yang, S.Li, Z.Wang, Y.Liu, J.Feng, Y.Zhu, Y.Shen. Structural and Mechanistic Insights Into MICU1 Regulation of Mitochondrial Calcium Uptake. Embo J. V. 33 594 2014.
ISSN: ISSN 0261-4189
PubMed: 24514027
DOI: 10.1002/EMBJ.201386523