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Cadmium in PDB 3iiu: Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L

Protein crystallography data

The structure of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L, PDB code: 3iiu was solved by T.Schulte, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.07 / 1.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.510, 81.730, 75.330, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 17.6

Other elements in 3iiu:

The structure of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L (pdb code 3iiu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L, PDB code: 3iiu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3iiu

Go back to Cadmium Binding Sites List in 3iiu
Cadmium binding site 1 out of 6 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd151

b:8.7
occ:0.50
 CD M:CD151 0.0 8.7 0.5
CD M:CD151 1.8 23.2 0.3
O M:HOH221 2.2 14.4 1.0
OD2 M:ASP5 2.3 8.7 1.0
O M:HOH228 2.4 35.9 1.0
OE1 M:GLU2 2.4 17.7 1.0
O M:HOH220 2.4 21.4 1.0
CL M:CL156 2.5 15.3 0.3
OE2 M:GLU2 2.8 14.1 1.0
CD M:GLU2 3.0 15.7 1.0
CG M:ASP5 3.4 9.8 1.0
O M:HOH235 3.6 28.1 1.0
CB M:ASP5 3.7 8.0 1.0
O M:HOH383 4.2 17.6 1.0
CD M:CD152 4.4 7.2 0.9
OD1 M:ASP5 4.5 7.8 1.0
CG M:GLU2 4.5 12.5 1.0
O M:HOH295 4.5 6.3 1.0
O M:HOH302 4.7 11.7 1.0
O M:HOH351 4.8 15.0 1.0
O M:HOH389 4.9 25.2 1.0
O M:HOH218 5.0 8.0 1.0

Cadmium binding site 2 out of 6 in 3iiu

Go back to Cadmium Binding Sites List in 3iiu
Cadmium binding site 2 out of 6 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd151

b:23.2
occ:0.30
 CD M:CD151 0.0 23.2 0.3
CL M:CL156 1.7 15.3 0.3
CD M:CD151 1.8 8.7 0.5
OE2 M:GLU2 2.1 14.1 1.0
O M:HOH235 2.1 28.1 1.0
O M:HOH221 2.3 14.4 1.0
OE1 M:GLU2 2.4 17.7 1.0
CD M:GLU2 2.5 15.7 1.0
O M:HOH351 3.7 15.0 1.0
O M:HOH228 3.7 35.9 1.0
O M:HOH220 3.7 21.4 1.0
OD2 M:ASP5 3.8 8.7 1.0
CG M:GLU2 3.9 12.5 1.0
O M:HOH302 4.5 11.7 1.0
O M:HOH282 4.6 33.1 1.0
O M:HOH389 4.6 25.2 1.0
O M:HOH383 4.8 17.6 1.0
CG M:ASP5 4.9 9.8 1.0

Cadmium binding site 3 out of 6 in 3iiu

Go back to Cadmium Binding Sites List in 3iiu
Cadmium binding site 3 out of 6 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd152

b:7.2
occ:0.90
 OD1 M:ASP5 2.3 7.8 1.0
O M:HOH218 2.4 8.0 1.0
CL M:CL159 2.5 6.6 0.9
OD2 M:ASP5 2.5 8.7 1.0
O M:HOH295 2.5 6.3 1.0
CG M:ASP5 2.7 9.8 1.0
O M:HOH362 3.9 18.0 1.0
O M:HOH221 4.0 14.4 1.0
O M:HOH228 4.2 35.9 1.0
CB M:ASP5 4.3 8.0 1.0
O M:HOH302 4.4 11.7 1.0
CD M:CD151 4.4 8.7 0.5
CB M:ALA0 4.7 9.6 1.0
O M:ASP1 4.7 6.8 1.0

Cadmium binding site 4 out of 6 in 3iiu

Go back to Cadmium Binding Sites List in 3iiu
Cadmium binding site 4 out of 6 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd153

b:8.6
occ:0.50
 OD1 M:ASP106 2.2 9.9 1.0
O M:HOH358 2.4 16.5 1.0
OD1 M:ASN102 2.4 16.0 1.0
OD2 M:ASP106 2.5 9.1 1.0
O M:HOH250 2.5 16.6 1.0
CG M:ASP106 2.7 10.5 1.0
CG M:ASN102 3.3 14.1 1.0
ND2 M:ASN102 3.6 19.9 1.0
O M:HOH418 4.1 18.4 1.0
O M:HOH231 4.1 19.3 1.0
CB M:ASP106 4.2 7.3 1.0
O M:ASN102 4.4 10.0 1.0
NZ M:LYS46 4.6 22.8 1.0
CB M:ASN102 4.7 12.0 1.0
O M:HOH341 4.9 12.6 1.0
CA M:ASP106 5.0 7.3 1.0

Cadmium binding site 5 out of 6 in 3iiu

Go back to Cadmium Binding Sites List in 3iiu
Cadmium binding site 5 out of 6 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd154

b:7.1
occ:0.80
 O M:HOH217 2.0 9.1 1.0
O M:HOH307 2.3 11.9 1.0
OD2 M:ASP116 2.3 7.8 1.0
CL M:CL157 2.6 13.3 0.8
CL M:CL158 2.6 5.5 0.5
CG M:ASP116 3.2 7.7 1.0
OD1 M:ASP116 3.5 6.9 1.0
CD M:CD155 3.6 6.2 0.4
O M:HOH434 3.8 31.6 1.0
O M:HOH178 4.3 32.3 1.0
O M:HOH385 4.5 15.5 1.0
CE M:LYS118 4.5 17.6 1.0
CD M:LYS118 4.6 15.5 1.0
CB M:ASP116 4.7 6.5 1.0
NZ M:LYS118 4.7 22.4 1.0
O M:HOH209 4.9 16.7 1.0

Cadmium binding site 6 out of 6 in 3iiu

Go back to Cadmium Binding Sites List in 3iiu
Cadmium binding site 6 out of 6 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) Mutant N89L within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd155

b:6.2
occ:0.40
 CL M:CL158 2.5 5.5 0.5
O M:HOH209 2.5 16.7 1.0
O M:HOH249 2.6 7.6 1.0
CL M:CL157 2.8 13.3 0.8
CD M:CD154 3.6 7.1 0.8
NZ M:LYS34 4.3 35.1 1.0
O M:HOH307 4.4 11.9 1.0
O M:HOH178 4.5 32.3 1.0
CE M:LYS34 4.8 29.4 1.0

Reference:

T.Schulte, D.M.Niedzwiedzki, R.R.Birge, R.G.Hiller, T.Polivka, E.Hofmann, H.A.Frank. Identification of A Single Peridinin Sensing Chl-A Excitation in Reconstituted Pcp By Crystallography and Spectroscopy. Proc.Natl.Acad.Sci.Usa V. 106 20764 2009.
ISSN: ISSN 0027-8424
PubMed: 19934052
DOI: 10.1073/PNAS.0908938106
Page generated: Thu Jul 10 12:42:00 2025

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