Cadmium in PDB 2zur: Crystal Structure of Rh(Nbd)/Apo-Fr

The structure of Crystal Structure of Rh(Nbd)/Apo-Fr, PDB code: 2zur was solved by S.Abe, K.Hirata, T.Ueno, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.01 / 1.80
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.276, 181.276, 181.276, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.6

The structure of Crystal Structure of Rh(Nbd)/Apo-Fr also contains other interesting chemical elements:

Rhodium

(Rh)

3 atoms

The binding sites of Cadmium atom in the Crystal Structure of Rh(Nbd)/Apo-Fr (pdb code 2zur). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Rh(Nbd)/Apo-Fr, PDB code: 2zur:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd175 b:19.6 occ:0.50 OD1 X:ASP80 2.4 12.8 1.0 OD2 X:ASP80 2.4 18.4 1.0 CG X:ASP80 2.7 15.9 1.0 CB X:ASP80 4.3 14.3 1.0 O X:HOH213 4.4 15.9 1.0 O X:HOH217 4.6 26.4 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd176 b:23.5 occ:0.10 O X:HOH381 2.0 35.8 1.0 OE1 X:GLU60 2.4 25.4 0.7 O X:HOH369 3.1 62.5 1.0 CD X:GLU60 3.1 21.8 0.7 OE2 X:GLU60 3.1 24.7 0.7 CG X:GLU57 4.5 18.8 1.0 CG X:GLU60 4.6 18.7 1.0 CD X:GLU56 4.9 19.3 1.0 OE2 X:GLU56 4.9 21.4 0.5 CG X:GLU56 5.0 18.1 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd177 b:24.2 occ:0.10 OE2 X:GLU11 2.5 26.1 1.0 OE1 X:GLU11 2.7 30.1 1.0 CD X:GLU11 3.0 27.7 1.0 O X:HOH236 3.0 30.0 1.0 OG1 X:THR10 3.9 22.6 1.0 CG X:GLU11 4.5 22.2 1.0 CB X:SER9 4.6 17.5 1.0 N X:THR10 4.7 17.8 1.0 OE1 X:GLN120 4.8 38.9 1.0 NE2 X:GLN120 4.8 38.7 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd178 b:57.5 occ:0.10 OD1 X:ASP127 3.5 34.2 0.5 OG X:SER131 4.5 34.3 0.5 CD X:CD179 4.7 59.0 0.1 CG X:ASP127 4.7 33.3 0.5 CB X:GLU130 4.8 34.6 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Rh(Nbd)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Rh(Nbd)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd179 b:59.0 occ:0.10 RH1 X:RH183 3.2 46.1 0.2 O X:HOH192 4.1 57.9 1.0 CA X:ASP127 4.4 32.7 1.0 N X:ASP127 4.5 32.6 1.0 CD X:CD178 4.7 57.5 0.1 C X:CYS126 4.7 32.2 1.0 O X:CYS126 4.7 32.6 1.0 CB X:CYS126 4.8 32.1 1.0 CB X:GLU130 4.8 34.6 1.0 CB X:ASP127 4.9 32.8 0.5

S.Abe, K.Hirata, T.Ueno, K.Morino, N.Shimizu, M.Yamamoto, M.Takata, E.Yashima, Y.Watanabe. Polymerization of Phenylacetylene By Rhodium Complexes Within A Discrete Space of Apo-Ferritin J.Am.Chem.Soc. V. 131 6958 2009.
ISSN: ISSN 0002-7863
PubMed: 19453195
DOI: 10.1021/JA901234J