Calcium in PDB 1nqh: Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate

The structure of Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate, PDB code: 1nqh was solved by D.P.Chimento, A.K.Mohanty, R.J.Kadner, M.C.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.687, 81.687, 225.814, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.5

The structure of Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Calcium atom in the Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate (pdb code 1nqh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate, PDB code: 1nqh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca595 b:54.7 occ:1.00 OD2 A:ASP193 1.3 16.7 1.0 OD1 A:ASP179 2.0 18.0 1.0 O A:ASP193 2.3 22.8 1.0 OD2 A:ASP230 2.3 18.7 1.0 OD2 A:ASP195 2.3 22.8 1.0 CG A:ASP179 2.5 22.2 1.0 CB A:GLN191 2.5 25.6 1.0 OD2 A:ASP179 2.5 32.9 1.0 CG A:ASP193 2.5 22.1 1.0 OD1 A:ASP195 2.7 30.7 1.0 NE2 A:GLN191 2.8 23.3 1.0 CG A:ASP195 2.9 20.3 1.0 OD1 A:ASP193 3.3 28.0 1.0 CG A:ASP230 3.3 16.9 1.0 C A:ASP193 3.3 24.0 1.0 OD1 A:ASP230 3.3 14.4 1.0 CG A:GLN191 3.4 25.1 1.0 CD A:GLN191 3.5 35.5 1.0 N A:ASP193 3.5 21.4 1.0 CB A:ASP193 3.6 19.8 1.0 CB A:ASP179 3.6 21.1 1.0 CA A:GLN191 3.6 26.5 1.0 O A:GLN191 3.7 34.9 1.0 CA A:ASP193 3.7 22.1 1.0 C A:GLN191 3.7 31.7 1.0 CA A:CA596 3.8 57.4 1.0 CA A:ASP179 3.8 21.4 1.0 N A:VAL180 4.1 19.5 1.0 N A:THR192 4.2 31.0 1.0 CB A:ASP195 4.4 23.2 1.0 N A:ASN194 4.5 26.1 1.0 C A:ASP179 4.5 19.6 1.0 OE1 A:GLN191 4.6 29.0 1.0 C A:THR192 4.7 23.3 1.0 N A:VAL181 4.7 21.5 1.0 CB A:ASP230 4.7 13.6 1.0 N A:GLN191 4.8 27.8 1.0 C A:ASN194 4.9 26.1 1.0 N A:ASP195 4.9 27.1 1.0 CA A:ASN194 4.9 26.1 1.0 CA A:THR192 4.9 25.2 1.0

Calcium binding site 2 out of 4 in the Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca596 b:57.4 occ:1.00 OD1 A:ASP193 1.9 28.0 1.0 OD1 A:ASP195 2.0 30.7 1.0 OD1 A:ASP230 2.0 14.4 1.0 O A:TYR229 2.5 13.4 1.0 CG A:ASP193 2.9 22.1 1.0 OD2 A:ASP193 3.1 16.7 1.0 OD1 A:ASP241 3.1 37.6 1.0 CG A:ASP195 3.2 20.3 1.0 CG A:ASP230 3.2 16.9 1.0 C A:TYR229 3.6 16.9 1.0 OD2 A:ASP230 3.7 18.7 1.0 CA A:CA595 3.8 54.7 1.0 OD2 A:ASP195 4.0 22.8 1.0 CB A:ASP195 4.1 23.2 1.0 N A:TYR229 4.1 15.2 1.0 CB A:ASP193 4.2 19.8 1.0 CG A:ASP241 4.3 29.6 1.0 CB A:ASP230 4.5 13.6 1.0 N A:ASP230 4.5 18.6 1.0 CA A:TYR229 4.5 16.9 1.0 CA A:ASP230 4.6 18.5 1.0 C A:ASN228 4.7 15.2 1.0 CB A:ASN228 4.7 15.5 1.0 CB A:GLN191 4.7 25.6 1.0 CA A:ASP195 4.9 24.5 1.0 O A:ASP193 4.9 22.8 1.0 OD2 A:ASP241 4.9 36.6 1.0

Calcium binding site 3 out of 4 in the Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca597 b:76.7 occ:1.00 OE1 A:GLU378 2.8 33.0 1.0 OE2 A:GLU378 2.8 19.0 1.0 CD A:GLU378 3.2 22.6 1.0 OE2 A:GLU381 3.3 47.5 1.0 CD A:GLU381 4.4 53.0 1.0 CG A:GLU378 4.7 17.4 1.0 CG A:GLU381 4.9 32.2 1.0

Calcium binding site 4 out of 4 in the Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Outer Membrane Cobalamin Transporter (Btub) From E. Coli, with Bound Calcium and Cyanocobalamin (Vitamin B12) Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca598 b:76.6 occ:1.00 OD1 A:ASP411 3.0 28.2 1.0 O A:PHE365 3.9 24.0 1.0 CG A:ASP411 4.1 28.1 1.0 OD2 A:ASP411 4.7 33.4 1.0 C A:PHE365 4.8 18.1 1.0 O A:ASN409 4.9 13.3 1.0

D.P.Chimento, A.K.Mohanty, R.J.Kadner, M.C.Wiener. Substrate-Induced Transmembrane Signaling in the Cobalamin Transporter Btub Nat.Struct.Biol. V. 10 394 2003.
ISSN: ISSN 1072-8368
PubMed: 12652322
DOI: 10.1038/NSB914