Atomistry » Cadmium » PDB 3heq-3o7s » 3iis
Atomistry »
  Cadmium »
    PDB 3heq-3o7s »
      3iis »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy