Cadmium in PDB 1n2z: 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli

The structure of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli, PDB code: 1n2z was solved by E.L.Borths, K.P.Locher, A.T.Lee, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	133.066, 133.066, 67.687, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 21

The structure of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Chlorine	(Cl)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Cadmium atom in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli (pdb code 1n2z). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 22 binding sites of Cadmium where determined in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli, PDB code: 1n2z:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:28.2 occ:0.47 OE2 A:GLU245 2.5 33.0 1.0 CL A:CL426 2.5 22.3 0.9 OE1 A:GLU245 2.5 36.0 1.0 O A:HOH443 2.6 33.5 1.0 CL A:CL427 2.7 33.0 0.6 O A:HOH459 2.7 37.0 1.0 CD A:GLU245 2.8 26.8 1.0 CL A:CL429 3.2 32.4 0.2 O A:HOH621 3.7 68.3 1.0 OG1 A:THR215 3.7 29.3 1.0 CD A:CD404 3.9 28.2 0.4 CG A:GLU245 4.4 20.2 1.0 C37 A:CNC400 4.5 20.2 1.0 O A:HOH607 4.7 46.6 1.0 CB A:THR215 4.8 26.5 1.0 OG A:SER241 4.9 30.6 1.0 N22 A:CNC400 5.0 16.3 1.0

Cadmium binding site 2 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:28.2 occ:0.71 OD2 A:ASP242 2.4 30.6 1.0 O A:HOH431 2.5 15.8 1.0 OD2 A:ASP52 2.5 27.5 1.0 OD1 A:ASP242 2.5 17.8 1.0 O A:HOH442 2.6 28.7 1.0 CG A:ASP242 2.8 23.2 1.0 OD1 A:ASP52 3.0 23.2 1.0 CG A:ASP52 3.1 26.5 1.0 NH2 A:ARG246 3.1 16.3 1.0 CZ A:ARG246 3.9 17.5 1.0 O A:HOH517 4.2 40.5 1.0 CB A:ASP242 4.3 21.9 1.0 NH1 A:ARG246 4.4 19.3 1.0 N40 A:CNC400 4.5 17.9 1.0 O A:HOH481 4.5 36.1 1.0 CB A:ASP52 4.6 21.2 1.0 O A:HOH462 4.7 18.8 1.0 NE A:ARG246 4.7 15.2 1.0 O A:TYR50 4.9 18.4 1.0

Cadmium binding site 3 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:28.2 occ:0.42 OG1 A:THR215 2.4 29.3 1.0 O A:THR215 2.6 29.8 1.0 O A:HOH459 2.6 37.0 1.0 O A:HOH443 2.6 33.5 1.0 O A:HOH515 2.7 48.6 1.0 CL A:CL428 2.7 32.6 0.7 C A:THR215 3.4 27.9 1.0 CB A:THR215 3.5 26.5 1.0 CL A:CL429 3.6 32.4 0.2 CA A:THR215 3.8 24.3 1.0 N A:THR215 3.8 20.9 1.0 CD A:CD402 3.9 28.2 0.5 OE1 A:GLN220 4.2 61.8 1.0 OE2 A:GLU245 4.5 33.0 1.0 OG A:SER241 4.6 30.6 1.0 N A:GLY216 4.6 28.2 1.0 CG2 A:THR215 4.7 28.3 1.0 N A:GLY163 4.8 32.5 1.0

Cadmium binding site 4 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:28.2 occ:0.79 OD1 A:ASP266 2.5 31.1 1.0 OD2 A:ASP266 2.6 35.0 1.0 O A:HOH445 2.7 30.7 1.0 CG A:ASP266 2.9 35.1 1.0 CD A:CD413 4.0 28.2 0.2 CB A:ASP266 4.4 34.6 1.0 O A:HOH475 4.4 27.4 1.0

Cadmium binding site 5 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd411 b:28.2 occ:0.29 O B:HOH482 2.9 34.3 1.0 O B:HOH429 3.0 16.8 1.0 NH2 A:ARG86 3.0 28.7 1.0 N B:ASP108 3.3 20.1 1.0 N B:ALA109 3.5 19.3 1.0 O A:HOH524 3.7 34.0 1.0 C B:ASP108 3.8 21.7 1.0 CA B:ALA109 3.9 18.8 1.0 CA B:VAL107 3.9 21.1 1.0 CG1 B:VAL107 4.1 19.3 1.0 C B:VAL107 4.1 20.7 1.0 CZ A:ARG86 4.1 31.5 1.0 CA B:ASP108 4.2 22.7 1.0 CD1 A:TRP106 4.2 19.9 1.0 CB B:ALA109 4.2 18.4 1.0 O B:ASP108 4.3 18.8 1.0 NH1 A:ARG86 4.4 32.7 1.0 O B:TRP106 4.4 20.1 1.0 O B:GLN114 4.4 15.1 1.0 CB B:GLN114 4.5 15.5 1.0 OE1 B:GLN114 4.5 19.8 1.0 CB B:VAL107 4.6 22.3 1.0 NE1 A:TRP106 4.7 19.8 1.0 CG B:GLN114 4.9 17.8 1.0 CB B:ASP108 4.9 27.6 1.0 CG A:TRP106 4.9 19.6 1.0

Cadmium binding site 6 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd412 b:28.2 occ:0.29 O A:HOH436 3.0 17.4 1.0 NH2 B:ARG86 3.0 31.9 1.0 O A:HOH494 3.1 34.3 1.0 O B:HOH539 3.3 34.8 1.0 N A:ASP108 3.4 18.9 1.0 N A:ALA109 3.5 19.0 1.0 C A:ASP108 3.8 19.9 1.0 CA A:ALA109 3.9 20.2 1.0 CA A:VAL107 3.9 20.2 1.0 CG1 A:VAL107 4.1 19.6 1.0 C A:VAL107 4.1 22.3 1.0 CZ B:ARG86 4.1 28.0 1.0 CD1 B:TRP106 4.2 21.4 1.0 CB A:ALA109 4.2 18.2 1.0 CA A:ASP108 4.2 21.6 1.0 O A:ASP108 4.3 21.2 1.0 OE1 A:GLN114 4.4 16.6 1.0 NH1 B:ARG86 4.4 24.6 1.0 CB A:GLN114 4.4 14.3 1.0 O A:GLN114 4.4 15.5 1.0 O A:TRP106 4.5 21.2 1.0 CB A:VAL107 4.6 21.1 1.0 NE1 B:TRP106 4.7 21.8 1.0 CG A:GLN114 4.8 15.7 1.0 CG B:TRP106 4.9 20.1 1.0 CB A:ASP108 4.9 25.6 1.0 CD A:GLN114 5.0 21.3 1.0

Cadmium binding site 7 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd413 b:28.2 occ:0.21 OD2 A:ASP266 2.6 35.0 1.0 O A:HOH445 2.7 30.7 1.0 O A:HOH475 2.8 27.4 1.0 O A:HOH562 2.9 43.0 1.0 CG A:ASP266 3.5 35.1 1.0 CD A:CD405 4.0 28.2 0.8 CG A:PRO235 4.2 34.6 1.0 CB A:ASP266 4.3 34.6 1.0 OD1 A:ASP266 4.3 31.1 1.0 CD A:PRO235 4.5 31.5 1.0 O A:HOH550 4.7 31.0 1.0

Cadmium binding site 8 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd414 b:28.2 occ:0.16 OE1 A:GLU181 2.5 31.6 1.0 NH2 B:ARG92 2.6 69.2 1.0 OE2 A:GLU181 2.6 36.6 1.0 NZ A:LYS190 2.8 55.2 1.0 CD A:GLU181 2.9 34.4 1.0 CE A:LYS190 3.1 51.5 1.0 CZ B:ARG92 3.7 67.2 1.0 NH1 B:ARG92 4.3 67.8 1.0 CG A:GLU181 4.4 30.1 1.0 CD A:LYS190 4.4 45.8 1.0 ND2 A:ASN177 4.6 20.6 1.0 NE B:ARG92 4.6 63.6 1.0

Cadmium binding site 9 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd415 b:28.2 occ:0.17 OD1 A:ASP130 2.8 36.2 1.0 O A:HOH504 2.8 52.8 1.0 OD2 A:ASP130 2.9 40.5 1.0 CG A:ASP130 3.2 31.8 1.0 CB A:ASP130 4.6 23.9 1.0 OE1 A:GLU133 5.0 52.3 1.0

Cadmium binding site 10 out of 22 in the 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of 2.0 Angstrom Structure of Btuf, the Vitamin B12 Binding Protein of E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd417 b:28.2 occ:0.52 OD2 A:ASP219 2.4 43.1 1.0 OD1 A:ASP219 2.5 34.6 1.0 O A:HOH484 2.6 35.1 1.0 O A:HOH528 2.6 39.1 1.0 CG A:ASP219 2.8 38.0 1.0 CB A:ASP219 4.3 37.5 1.0 O A:HOH499 4.3 37.4 1.0

E.L.Borths, K.P.Locher, A.T.Lee, D.C.Rees. The Structure of Escherichia Coli Btuf and Binding to Its Cognate Atp Binding Cassette Transporter Proc.Natl.Acad.Sci.Usa V. 99 16642 2002.
ISSN: ISSN 0027-8424
PubMed: 12475936
DOI: 10.1073/PNAS.262659699