Calcium in PDB 3m8d: Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin

The structure of Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin, PDB code: 3m8d was solved by D.M.Freed, P.S.Horanyi, M.C.Wiener, D.S.Cafiso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.04 / 2.44
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.051, 82.051, 224.457, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 27.5

The structure of Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin (pdb code 3m8d). 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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin, PDB code: 3m8d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin


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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:75.5 occ:1.00 OD2 A:ASP230 2.0 31.9 1.0 OD1 A:ASP193 2.2 29.0 1.0 OD1 A:ASP179 2.2 27.4 1.0 O A:ASP193 2.5 32.3 1.0 O A:GLN191 2.5 34.1 1.0 OD2 A:ASP195 2.6 33.9 1.0 CG A:ASP230 2.7 31.8 1.0 OD1 A:ASP230 2.8 30.4 1.0 OD1 A:ASP195 3.2 35.0 1.0 CG A:ASP195 3.2 34.1 1.0 CG A:ASP179 3.2 35.2 1.0 CG A:ASP193 3.4 31.1 1.0 C A:ASP193 3.4 33.0 1.0 C A:GLN191 3.5 34.1 1.0 N A:ASP193 3.6 32.2 1.0 C A:THR192 3.8 32.7 1.0 CA A:ASP193 3.9 32.2 1.0 CB A:ASP179 4.0 34.3 1.0 CA A:ASP179 4.1 34.4 1.0 CA A:CA710 4.1 82.8 1.0 N A:THR192 4.1 33.5 1.0 OD2 A:ASP179 4.1 37.0 1.0 CA A:THR192 4.2 32.9 1.0 N A:VAL180 4.2 34.5 1.0 CB A:ASP230 4.2 31.4 1.0 CB A:GLN191 4.3 34.8 1.0 CB A:ASP193 4.3 32.1 1.0 O A:THR192 4.3 33.2 1.0 OD2 A:ASP193 4.3 26.5 1.0 CA A:GLN191 4.5 34.6 1.0 C A:ASP179 4.5 34.5 1.0 N A:ASN194 4.6 33.5 1.0 CB A:ASP195 4.6 33.8 1.0 N A:VAL181 4.7 34.0 1.0 C A:ASN194 4.9 33.8 1.0 N A:ASP195 5.0 33.8 1.0 CG2 A:VAL180 5.0 32.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin


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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca710 b:82.8 occ:1.00 OD1 A:ASP230 2.2 30.4 1.0 O A:TYR229 2.3 29.6 1.0 OD1 A:ASP195 2.4 35.0 1.0 OD2 A:ASP193 2.5 26.5 1.0 OD1 A:ASP193 2.9 29.0 1.0 CG A:ASP193 3.1 31.1 1.0 C A:TYR229 3.3 29.9 1.0 CG A:ASP230 3.5 31.8 1.0 CG A:ASP195 3.6 34.1 1.0 N A:TYR229 3.9 28.9 1.0 N A:ASP230 4.0 30.9 1.0 CA A:ASP230 4.1 32.0 1.0 CA A:CA709 4.1 75.5 1.0 CA A:TYR229 4.1 29.3 1.0 OD2 A:ASP195 4.3 33.9 1.0 OD2 A:ASP241 4.3 33.4 1.0 O A:ASP241 4.3 37.3 1.0 CB A:ASP241 4.3 36.4 1.0 OD2 A:ASP230 4.3 31.9 1.0 CB A:ASP230 4.4 31.4 1.0 CG A:ASP241 4.5 35.7 1.0 CB A:ASN228 4.5 29.5 1.0 CB A:ASP193 4.6 32.1 1.0 C A:ASN228 4.7 29.3 1.0 CB A:ASP195 4.7 33.8 1.0 CB A:GLN191 4.7 34.8 1.0 OE1 A:GLN191 4.9 29.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin


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 Spin-Labeled Btub V10R1 with Bound Calcium and Cyanocobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca711 b:88.8 occ:1.00 NE2 A:HIS176 2.4 46.2 1.0 NE2 A:HIS174 2.6 42.7 1.0 CE1 A:HIS174 2.8 42.0 1.0 CE1 A:HIS176 3.3 46.6 1.0 CD2 A:HIS176 3.4 44.7 1.0 CD2 A:HIS174 3.9 41.0 1.0 ND1 A:HIS174 4.1 41.9 1.0 ND1 A:HIS176 4.5 45.2 1.0 CG A:HIS176 4.5 41.5 1.0 CG A:HIS174 4.6 39.0 1.0

D.M.Freed, P.S.Horanyi, M.C.Wiener, D.S.Cafiso. Conformational Exchange in A Membrane Transport Protein Is Altered in Protein Crystals. Biophys.J. V. 99 1604 2010.
ISSN: ISSN 0006-3495
PubMed: 20816073
DOI: 10.1016/J.BPJ.2010.06.026