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Chlorine 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:

Cadmium (Cd) 5 atoms
Magnesium (Mg) 1 atom
Potassium (K) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp), PDB code: 3iis:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3iis

Go back to Chlorine Binding Sites List in 3iis
Chlorine binding site 1 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl158

b:7.5
occ:0.90
 ND2 M:ASN25 3.2 10.1 1.0
O M:HOH308 3.7 13.1 1.0
CB M:ASP22 3.7 6.0 1.0
O M:HOH307 3.9 6.5 1.0
OD2 M:ASP22 3.9 8.1 1.0
CD1 M:LEU126 4.0 11.3 1.0
CG M:ASN25 4.2 8.5 1.0
CG M:ASP22 4.3 6.1 1.0
CB M:ASN25 4.4 8.0 1.0
CD2 M:LEU126 4.7 13.7 1.0
CG M:LEU126 4.7 9.6 1.0
CB M:LEU126 4.7 9.4 1.0
O M:HOH304 4.8 17.5 1.0
CA M:ASP22 4.9 5.5 1.0
N M:ASP22 5.0 5.9 1.0

Chlorine binding site 2 out of 7 in 3iis

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Chlorine binding site 2 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl159

b:25.1
occ:0.50
 CD M:CD152 1.6 11.5 0.2
CD M:CD152 2.5 9.0 0.5
O M:HOH264 2.7 22.3 1.0
O M:HOH436 3.3 14.5 1.0
OE1 M:GLU2 3.4 19.6 1.0
O M:HOH438 3.4 24.3 1.0
O M:HOH437 3.6 34.1 1.0
OE2 M:GLU2 3.7 17.2 1.0
CD M:GLU2 3.8 15.9 1.0
O M:HOH439 4.6 23.5 1.0
OD2 M:ASP5 4.9 9.4 1.0

Chlorine binding site 3 out of 7 in 3iis

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Chlorine binding site 3 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl160

b:21.0
occ:0.80
 CD M:CD153 2.3 7.6 0.8
CL M:CL161 3.2 9.7 0.8
O M:HOH288 3.3 32.1 1.0
O M:HOH289 3.3 9.9 1.0
OD2 M:ASP116 3.5 8.0 1.0
CL M:CL161 3.6 2.0 0.2
NZ M:LYS118 3.7 22.4 1.0
CM3 M:PID612 3.7 19.4 1.0
CD M:LYS118 3.8 14.8 1.0
C4 M:PID612 3.8 19.6 1.0
CG M:ASP116 3.9 7.0 1.0
OD1 M:ASP116 3.9 5.7 1.0
CE M:LYS118 4.1 18.2 1.0
O M:HOH290 4.1 25.6 1.0
K M:K157 4.2 8.1 0.8
C5 M:PID612 4.5 18.1 1.0
C3 M:PID612 4.5 22.3 1.0
O2 M:PID612 4.6 25.9 1.0
CG M:LYS118 4.7 11.4 1.0

Chlorine binding site 4 out of 7 in 3iis

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Chlorine binding site 4 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl161

b:2.0
occ:0.20
 CL M:CL161 0.0 2.0 0.2
CL M:CL161 1.1 9.7 0.8
CD M:CD153 2.5 7.6 0.8
OD1 M:ASP116 2.6 5.7 1.0
OD2 M:ASP116 3.1 8.0 1.0
CG M:ASP116 3.3 7.0 1.0
CG M:LYS118 3.3 11.4 1.0
CE M:LYS118 3.5 18.2 1.0
CD M:LYS118 3.5 14.8 1.0
CL M:CL160 3.6 21.0 0.8
CG M:PRO117 4.1 10.3 1.0
CB M:LYS118 4.2 9.6 1.0
CD M:PRO117 4.2 6.0 1.0
N M:LYS118 4.3 6.4 1.0
NZ M:LYS118 4.4 22.4 1.0
N M:PRO117 4.7 6.5 1.0
CB M:ASP116 4.7 6.5 1.0
CA M:LYS118 4.9 7.4 1.0
CB M:PRO117 4.9 8.6 1.0
O M:HOH289 5.0 9.9 1.0

Chlorine binding site 5 out of 7 in 3iis

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Chlorine binding site 5 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl161

b:9.7
occ:0.80
 CL M:CL161 0.0 9.7 0.8
CL M:CL161 1.1 2.0 0.2
CD M:CD153 1.5 7.6 0.8
OD2 M:ASP116 2.3 8.0 1.0
OD1 M:ASP116 2.6 5.7 1.0
CG M:ASP116 2.8 7.0 1.0
CL M:CL160 3.2 21.0 0.8
O M:HOH289 4.0 9.9 1.0
CG M:LYS118 4.2 11.4 1.0
CD M:LYS118 4.2 14.8 1.0
CD M:PRO117 4.2 6.0 1.0
CE M:LYS118 4.2 18.2 1.0
CB M:ASP116 4.3 6.5 1.0
CG M:PRO117 4.4 10.3 1.0
O M:HOH221 4.6 13.3 1.0
K M:K156 4.8 9.3 0.5
N M:PRO117 4.8 6.5 1.0
NZ M:LYS118 4.8 22.4 1.0
CB M:LYS118 4.8 9.6 1.0
N M:LYS118 4.9 6.4 1.0
O M:HOH288 4.9 32.1 1.0
K M:K157 4.9 8.1 0.8

Chlorine binding site 6 out of 7 in 3iis

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Chlorine binding site 6 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl162

b:4.2
occ:0.20
 CL M:CL162 0.0 4.2 0.2
CL M:CL162 1.3 15.4 0.6
K M:K155 2.6 11.4 0.8
N M:LEU38 3.4 7.0 1.0
CD M:PRO37 3.5 9.0 1.0
N M:PRO37 3.5 7.2 1.0
OE1 M:GLU39 3.6 20.5 0.8
CG M:LEU38 3.7 11.0 1.0
C M:GLN36 3.8 7.3 1.0
CB M:LEU38 3.8 9.6 1.0
O M:HOH284 3.9 32.1 1.0
CA M:GLN36 4.0 7.8 1.0
O M:HOH282 4.0 15.3 0.6
O M:HOH286 4.0 35.9 1.0
CD1 M:LEU38 4.1 12.1 1.0
CA M:LEU38 4.2 8.1 1.0
C M:PRO37 4.3 7.7 1.0
CA M:PRO37 4.4 8.1 1.0
O M:GLN36 4.4 7.0 1.0
CB M:GLN36 4.4 9.9 1.0
CB M:PRO37 4.6 7.5 1.0
CG M:PRO37 4.6 11.7 1.0
N M:GLU39 4.7 6.9 0.2
N M:GLU39 4.7 7.8 0.8
CD M:GLU39 4.7 20.7 0.8
O M:HOH287 4.7 39.5 1.0
CD2 M:LEU38 5.0 12.0 1.0

Chlorine binding site 7 out of 7 in 3iis

Go back to Chlorine Binding Sites List in 3iis
Chlorine binding site 7 out of 7 in the Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of the Reconstituted Peridinin-Chlorophyll A-Protein (Rfpcp) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cl162

b:15.4
occ:0.60
 CL M:CL162 0.0 15.4 0.6
CL M:CL162 1.3 4.2 0.2
K M:K155 1.9 11.4 0.8
OE1 M:GLU39 2.3 20.5 0.8
N M:LEU38 3.3 7.0 1.0
C M:GLN36 3.3 7.3 1.0
O M:HOH284 3.4 32.1 1.0
CD M:GLU39 3.5 20.7 0.8
O M:HOH282 3.5 15.3 0.6
CA M:GLN36 3.5 7.8 1.0
N M:PRO37 3.6 7.2 1.0
CB M:GLN36 3.6 9.9 1.0
CB M:LEU38 3.6 9.6 1.0
O M:GLN36 3.7 7.0 1.0
N M:GLU39 3.7 6.9 0.2
N M:GLU39 3.8 7.8 0.8
O M:HOH287 3.8 39.5 1.0
CA M:LEU38 3.9 8.1 1.0
CG M:GLU39 4.0 2.8 0.2
OE2 M:GLU39 4.0 24.6 0.8
O M:HOH286 4.0 35.9 1.0
CG M:LEU38 4.0 11.0 1.0
CD M:PRO37 4.0 9.0 1.0
C M:PRO37 4.2 7.7 1.0
C M:LEU38 4.3 7.7 1.0
CB M:GLU39 4.4 5.7 0.2
CA M:PRO37 4.4 8.1 1.0
CD1 M:LEU38 4.4 12.1 1.0
CG M:GLN36 4.5 10.0 1.0
CG M:GLU39 4.7 15.3 0.8
CA M:GLU39 4.7 6.0 0.2
CB M:GLU39 4.7 9.0 0.8
OE2 M:GLU39 4.8 7.6 0.2
CA M:GLU39 4.9 7.9 0.8
CD M:GLU39 5.0 4.7 0.2
N M:GLN36 5.0 8.1 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: Sat Jul 20 21:33:21 2024

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