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

Protein crystallography data

The structure of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp), PDB code: 3iis 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) 35.85 / 1.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.690, 81.623, 75.080, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.7

Other elements in 3iis:

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

Magnesium (Mg) 1 atom
Potassium (K) 4 atoms
Chlorine (Cl) 7 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 5 in 3iis

Go back to Cadmium Binding Sites List in 3iis
Cadmium binding site 1 out of 5 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd151

b:7.0
occ:0.90
 OD1 M:ASP5 2.3 9.0 1.0
O M:HOH434 2.4 8.3 1.0
OD2 M:ASP5 2.5 9.4 1.0
CG M:ASP5 2.7 11.2 1.0
O M:HOH433 3.9 21.7 1.0
O M:HOH436 4.0 14.5 1.0
O M:HOH437 4.1 34.1 1.0
CB M:ASP5 4.2 8.6 1.0
O M:HOH435 4.3 11.4 1.0
CD M:CD152 4.4 9.0 0.5
O M:HOH164 4.5 38.0 1.0
O M:ASP1 4.6 6.2 1.0
CB M:ALA0 4.7 7.4 1.0

Cadmium binding site 2 out of 5 in 3iis

Go back to Cadmium Binding Sites List in 3iis
Cadmium binding site 2 out of 5 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd152

b:9.0
occ:0.50
 CD M:CD152 0.0 9.0 0.5
CD M:CD152 1.7 11.5 0.2
O M:HOH437 2.1 34.1 1.0
OE1 M:GLU2 2.4 19.6 1.0
O M:HOH436 2.4 14.5 1.0
OD2 M:ASP5 2.4 9.4 1.0
O M:HOH438 2.4 24.3 1.0
CL M:CL159 2.5 25.1 0.5
OE2 M:GLU2 2.9 17.2 1.0
CD M:GLU2 3.0 15.9 1.0
CG M:ASP5 3.4 11.2 1.0
O M:HOH264 3.5 22.3 1.0
CB M:ASP5 3.7 8.6 1.0
O M:HOH440 4.2 16.4 1.0
CD M:CD151 4.4 7.0 0.9
OD1 M:ASP5 4.5 9.0 1.0
CG M:GLU2 4.5 11.7 1.0
O M:HOH435 4.7 11.4 1.0
O M:HOH439 5.0 23.5 1.0

Cadmium binding site 3 out of 5 in 3iis

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


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd152

b:11.5
occ:0.20
 CD M:CD152 0.0 11.5 0.2
CL M:CL159 1.6 25.1 0.5
CD M:CD152 1.7 9.0 0.5
O M:HOH264 1.9 22.3 1.0
OE2 M:GLU2 2.2 17.2 1.0
O M:HOH436 2.4 14.5 1.0
OE1 M:GLU2 2.5 19.6 1.0
CD M:GLU2 2.6 15.9 1.0
O M:HOH437 3.4 34.1 1.0
O M:HOH438 3.7 24.3 1.0
OD2 M:ASP5 3.8 9.4 1.0
CG M:GLU2 4.0 11.7 1.0
O M:HOH435 4.5 11.4 1.0
O M:HOH439 4.7 23.5 1.0
O M:HOH440 4.9 16.4 1.0
CG M:ASP5 5.0 11.2 1.0

Cadmium binding site 4 out of 5 in 3iis

Go back to Cadmium Binding Sites List in 3iis
Cadmium binding site 4 out of 5 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd153

b:7.6
occ:0.80
 CL M:CL161 1.5 9.7 0.8
CL M:CL160 2.3 21.0 0.8
OD2 M:ASP116 2.3 8.0 1.0
CL M:CL161 2.5 2.0 0.2
O M:HOH289 2.5 9.9 1.0
CG M:ASP116 3.2 7.0 1.0
OD1 M:ASP116 3.5 5.7 1.0
K M:K157 3.6 8.1 0.8
O M:HOH288 3.8 32.1 1.0
K M:K156 3.8 9.3 0.5
O M:HOH221 4.5 13.3 1.0
CB M:ASP116 4.6 6.5 1.0
CE M:LYS118 4.7 18.2 1.0
CD M:LYS118 4.8 14.8 1.0
K M:K156 4.8 20.9 0.5
NZ M:LYS118 4.9 22.4 1.0
O M:HOH290 4.9 25.6 1.0

Cadmium binding site 5 out of 5 in 3iis

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


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cd154

b:13.7
occ:0.50
 OD1 M:ASP106 2.2 11.0 1.0
O M:HOH377 2.4 25.2 1.0
O M:HOH267 2.4 23.6 1.0
OD2 M:ASP106 2.4 11.4 1.0
OD1 M:ASN102 2.5 10.9 0.5
O M:HOH376 2.6 15.9 1.0
CG M:ASP106 2.7 10.8 1.0
CG M:ASN102 3.3 11.0 0.5
ND2 M:ASN102 3.4 12.8 0.5
O M:HOH375 4.0 28.2 1.0
O M:HOH374 4.1 22.1 1.0
CB M:ASP106 4.2 6.6 1.0
O M:ASN102 4.2 9.8 0.5
NZ M:LYS46 4.4 21.3 1.0
ND2 M:ASN102 4.5 19.6 0.5
O M:ASN102 4.5 9.0 0.5
CB M:ASN102 4.7 11.5 0.5
CB M:ASN102 4.7 9.8 0.5
O M:HOH378 4.9 13.9 1.0
CA M:ASP106 5.0 6.7 1.0
C M:ASN102 5.0 9.8 0.5

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: Fri Jul 19 16:06:08 2024

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