Calcium in PDB 1ij6: CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold

The structure of CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold, PDB code: 1ij6 was solved by W.Iwasaki, H.Sasaki, A.Nakamura, K.Kohama, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.400, 64.400, 209.400, 90.00, 90.00, 120.00
R / Rfree (%)	24.9 / 29.3

The binding sites of Calcium atom in the CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold (pdb code 1ij6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold, PDB code: 1ij6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca356 b:43.9 occ:1.00 OD1 A:ASP230 2.4 54.1 1.0 O A:THR236 2.6 38.0 1.0 OE2 A:GLU241 2.7 48.0 1.0 ND2 A:ASN232 2.7 58.7 1.0 OD1 A:ASN234 2.8 62.3 1.0 OE1 A:GLU241 2.8 45.7 1.0 CD A:GLU241 3.1 47.9 1.0 CG A:ASN232 3.2 56.3 1.0 OD1 A:ASN232 3.5 56.2 1.0 CG A:ASP230 3.5 52.1 1.0 C A:THR236 3.7 40.8 1.0 CG A:ASN234 3.8 58.6 1.0 O A:ASN234 4.0 55.5 1.0 CA A:ASP230 4.0 48.8 1.0 CB A:ASP230 4.1 51.4 1.0 CB A:ASN232 4.2 55.7 1.0 CA A:LEU237 4.2 43.7 1.0 ND2 A:ASN234 4.2 60.5 1.0 N A:ASN232 4.2 54.0 1.0 N A:SER238 4.3 47.1 1.0 C A:ASP230 4.3 49.0 1.0 N A:LEU237 4.4 42.7 1.0 N A:THR231 4.5 48.7 1.0 OD2 A:ASP230 4.6 54.4 1.0 CG A:GLU241 4.6 48.7 1.0 C A:LEU237 4.6 46.3 1.0 N A:ASN234 4.7 56.0 1.0 CA A:ASN232 4.7 55.4 1.0 N A:THR236 4.8 39.3 1.0 N A:SER233 4.8 55.6 1.0 CA A:THR236 4.8 40.0 1.0 C A:ASN234 4.9 53.3 1.0 OG1 A:THR236 4.9 36.5 1.0 C A:ASN232 5.0 56.1 1.0 O A:ASP230 5.0 49.8 1.0

Calcium binding site 2 out of 4 in the CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca357 b:35.4 occ:1.00 OD1 A:ASP265 2.5 40.4 1.0 O A:ASP271 2.8 39.4 1.0 OG A:SER269 2.8 33.0 1.0 OE1 A:GLU276 2.9 43.4 1.0 OD1 A:ASP267 2.9 50.1 1.0 OE2 A:GLU276 2.9 41.5 1.0 CD A:GLU276 3.2 41.4 1.0 OD1 A:ASP271 3.3 46.4 1.0 CG A:ASP265 3.5 40.3 1.0 CG A:ASP267 3.5 52.2 1.0 OD2 A:ASP267 3.5 55.9 1.0 O A:SER269 3.9 46.4 1.0 C A:ASP271 3.9 41.6 1.0 CB A:SER269 4.1 37.0 1.0 CB A:ASP265 4.1 38.0 1.0 N A:SER269 4.1 45.0 1.0 CA A:ASP265 4.2 35.9 1.0 OD2 A:ASP265 4.4 44.3 1.0 CA A:VAL272 4.4 39.5 1.0 CG A:ASP271 4.5 47.3 1.0 CA A:SER269 4.5 42.5 1.0 N A:VAL272 4.6 38.4 1.0 CG A:GLU276 4.6 40.5 1.0 C A:ASP265 4.6 37.8 1.0 C A:SER269 4.6 44.8 1.0 N A:GLY273 4.7 40.1 1.0 N A:GLU266 4.7 40.5 1.0 N A:ASP267 4.7 48.0 1.0 N A:GLU268 4.8 47.0 1.0 CB A:ASP267 4.9 50.5 1.0 CA A:ASP271 4.9 42.6 1.0 N A:ASP271 4.9 42.3 1.0

Calcium binding site 3 out of 4 in the CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca358 b:48.5 occ:1.00 OE1 A:GLU306 2.6 40.5 1.0 OG A:SER299 2.7 39.8 1.0 OE2 A:GLU306 2.7 43.6 1.0 OD2 A:ASP297 2.7 58.3 1.0 O A:GLN301 2.8 46.2 1.0 OD1 A:ASP297 2.9 59.0 1.0 CD A:GLU306 3.0 42.4 1.0 CG A:ASP297 3.0 57.5 1.0 OD1 A:ASP295 3.1 50.5 1.0 C A:GLN301 3.7 45.5 1.0 CB A:SER299 3.7 41.1 1.0 CG A:ASP295 3.8 47.9 1.0 N A:SER299 4.2 40.9 1.0 CA A:LEU302 4.2 44.6 1.0 OG A:SER303 4.2 49.7 1.0 N A:LEU302 4.3 45.8 1.0 OD2 A:ASP295 4.3 51.0 1.0 CB A:ASP297 4.4 53.9 1.0 N A:GLN301 4.4 47.5 1.0 CG A:GLU306 4.4 44.5 1.0 CA A:SER299 4.5 41.6 1.0 CA A:ASP295 4.5 45.9 1.0 C A:LEU302 4.5 45.8 1.0 N A:ASP297 4.6 50.5 1.0 N A:SER303 4.6 47.7 1.0 CA A:GLN301 4.7 47.1 1.0 N A:GLY300 4.7 44.8 1.0 CB A:ASP295 4.7 46.2 1.0 C A:ASP295 4.8 47.6 1.0 C A:SER299 4.9 43.9 1.0 CA A:ASP297 4.9 48.4 1.0 N A:LYS298 4.9 41.3 1.0 CB A:SER303 5.0 47.7 1.0

Calcium binding site 4 out of 4 in the CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of CA2+-Bound Structure of Multidomain Ef-Hand Protein, CBP40, From True Slime Mold within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca359 b:42.1 occ:1.00 OG A:SER336 2.8 62.6 1.0 O A:SER338 2.8 46.1 1.0 OD1 A:ASP334 2.8 61.8 1.0 OE2 A:GLU343 2.9 29.7 1.0 OD2 A:ASP334 3.2 57.1 1.0 OD1 A:ASP332 3.2 45.3 1.0 CG A:ASP334 3.3 58.4 1.0 OE1 A:GLU343 3.3 27.3 1.0 CD A:GLU343 3.5 27.4 1.0 CB A:SER336 3.6 58.6 1.0 C A:SER338 3.7 45.0 1.0 OG A:SER338 3.9 45.4 1.0 OE1 A:GLN301 4.2 51.7 1.0 CA A:LEU339 4.2 38.4 1.0 N A:LEU339 4.3 42.5 1.0 N A:SER340 4.3 37.0 1.0 N A:SER336 4.4 57.5 1.0 CG A:ASP332 4.4 43.6 1.0 N A:SER338 4.4 50.4 1.0 CA A:SER336 4.6 58.1 1.0 C A:LEU339 4.6 38.7 1.0 CA A:SER338 4.6 45.9 1.0 CB A:ASP334 4.7 55.3 1.0 N A:ASP334 4.8 51.3 1.0 CB A:SER338 4.8 45.9 1.0 CD A:GLN301 4.9 52.4 1.0 N A:LYS337 4.9 54.9 1.0 CA A:ASP332 4.9 40.5 1.0 CG A:GLU343 4.9 28.3 1.0 NE2 A:GLN301 5.0 56.1 1.0

W.Iwasaki, H.Sasaki, A.Nakamura, K.Kohama, M.Tanokura. Metal-Free and Ca(2+)-Bound Structures of A Multidomain Ef-Hand Protein, CBP40, From the Lower Eukaryote Physarum Polycephalum Structure V. 11 75 2003.
ISSN: ISSN 0969-2126
PubMed: 12517342
DOI: 10.1016/S0969-2126(02)00932-2