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Mercury in PDB 2ped: Crystallographic Model of 9-Cis-Rhodopsin

Protein crystallography data

The structure of Crystallographic Model of 9-Cis-Rhodopsin, PDB code: 2ped was solved by H.Nakamichi, T.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.95
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 95.960, 95.960, 150.840, 90.00, 90.00, 90.00
R / Rfree (%) 24.3 / 28.9

Other elements in 2ped:

The structure of Crystallographic Model of 9-Cis-Rhodopsin also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystallographic Model of 9-Cis-Rhodopsin (pdb code 2ped). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystallographic Model of 9-Cis-Rhodopsin, PDB code: 2ped:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 2ped

Go back to Mercury Binding Sites List in 2ped
Mercury binding site 1 out of 6 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:84.8
occ:0.81
SG A:CYS264 2.4 55.0 1.0
CB A:CYS264 2.9 51.9 1.0
OG1 A:THR297 3.2 50.3 1.0
CD2 A:TYR301 3.4 53.4 1.0
CA A:CYS264 3.6 51.6 1.0
CE2 A:TYR301 3.8 52.6 1.0
O A:ALA260 3.8 55.4 1.0
N A:CYS264 4.0 52.7 1.0
CZ A:PHE294 4.0 46.6 1.0
CG A:TYR301 4.2 53.2 1.0
CE2 A:PHE294 4.3 47.6 1.0
CB A:THR297 4.4 49.4 1.0
CB A:TYR301 4.6 52.0 1.0
CE1 A:PHE294 4.7 45.5 1.0
N A:SER298 4.8 48.7 1.0
CZ A:TYR301 4.8 53.4 1.0
C A:THR297 4.8 49.3 1.0
C A:ILE263 4.8 52.4 1.0
CG2 A:ILE263 4.9 49.1 1.0
C A:ALA260 4.9 54.1 1.0
O A:PHE294 4.9 44.9 1.0
C A:CYS264 5.0 50.5 1.0

Mercury binding site 2 out of 6 in 2ped

Go back to Mercury Binding Sites List in 2ped
Mercury binding site 2 out of 6 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:83.6
occ:0.77
SG B:CYS264 2.3 64.9 1.0
O B:HOH2112 2.6 45.7 1.0
CB B:CYS264 2.9 60.4 1.0
O B:HOH2094 3.0 33.6 1.0
O B:ALA260 3.5 60.9 1.0
OG1 B:THR297 3.5 52.3 1.0
CA B:CYS264 3.5 58.9 1.0
CD2 B:TYR301 3.6 58.6 1.0
N B:CYS264 3.7 59.9 1.0
CE2 B:TYR301 4.0 58.6 1.0
CG B:TYR301 4.2 57.3 1.0
CZ B:PHE294 4.4 53.9 1.0
C B:ALA260 4.4 61.0 1.0
C B:ILE263 4.5 60.4 1.0
CE2 B:PHE294 4.6 52.7 1.0
CB B:TYR301 4.6 55.7 1.0
CG2 B:ILE263 4.7 61.2 1.0
CZ B:TYR301 4.8 58.2 1.0
CB B:ILE263 4.8 61.3 1.0
CB B:THR297 4.8 53.3 1.0
CA B:ALA260 4.9 61.6 1.0
C B:CYS264 5.0 57.0 1.0
CD1 B:TYR301 5.0 57.7 1.0

Mercury binding site 3 out of 6 in 2ped

Go back to Mercury Binding Sites List in 2ped
Mercury binding site 3 out of 6 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:85.9
occ:0.68
SG A:CYS222 2.5 74.4 1.0
O A:ALA132 3.2 69.5 1.0
CB A:CYS222 3.4 76.9 1.0
C A:CYS222 3.5 79.4 1.0
O A:CYS222 3.6 79.8 1.0
N A:TYR223 3.7 81.6 1.0
CA A:ALA132 3.9 70.2 1.0
CA A:TYR223 4.0 84.0 1.0
C A:ALA132 4.0 70.4 1.0
CD2 A:LEU226 4.0 0.3 1.0
CA A:CYS222 4.1 77.8 1.0
CB A:ALA132 4.1 70.9 1.0
CD1 A:LEU226 4.3 0.9 1.0
CB A:ARG135 4.4 72.6 1.0
CG A:LEU226 4.5 0.6 1.0
CB A:LEU226 4.6 0.1 1.0
CB A:TYR223 4.7 84.1 1.0
N A:TYR136 4.8 75.7 1.0
O A:ILE219 4.8 72.0 1.0
CB A:TYR136 4.9 77.5 1.0
CG A:ARG135 5.0 72.4 1.0

Mercury binding site 4 out of 6 in 2ped

Go back to Mercury Binding Sites List in 2ped
Mercury binding site 4 out of 6 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:94.2
occ:0.61
SG B:CYS222 2.2 91.2 1.0
O B:CYS222 2.6 91.2 1.0
C B:CYS222 3.2 91.8 1.0
O B:ALA132 3.4 83.2 1.0
CB B:CYS222 3.4 91.3 1.0
N B:TYR223 3.8 93.5 1.0
CA B:CYS222 3.9 91.1 1.0
CA B:ALA132 3.9 83.2 1.0
CA B:TYR223 4.0 95.8 1.0
CB B:ARG135 4.1 91.7 1.0
C B:ALA132 4.1 83.8 1.0
CD2 B:LEU226 4.2 0.4 1.0
CB B:ALA132 4.3 83.2 1.0
CD1 B:LEU226 4.3 0.8 1.0
CG B:ARG135 4.6 89.9 1.0
CG B:LEU226 4.7 0.9 1.0
N B:TYR136 4.7 97.4 1.0
CB B:TYR223 4.8 94.2 1.0
O B:ILE219 4.9 81.2 1.0
CB B:LEU226 4.9 0.9 1.0

Mercury binding site 5 out of 6 in 2ped

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Mercury binding site 5 out of 6 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg905

b:89.4
occ:0.53
SG A:CYS316 2.4 63.1 1.0
O A:HOH2061 2.6 62.2 1.0
O A:GLN312 3.2 58.8 1.0
N A:CYS316 3.4 64.7 1.0
CG1 A:VAL337 3.5 0.6 1.0
N A:VAL337 3.6 0.8 1.0
CB A:CYS316 3.7 65.1 1.0
CA A:CYS316 3.8 65.8 1.0
O A:VAL337 3.8 0.1 1.0
CG A:GLN312 3.9 62.2 1.0
CB A:ASN315 3.9 64.1 1.0
CA A:THR336 4.0 0.3 1.0
C A:GLN312 4.1 58.3 1.0
C A:THR336 4.1 0.9 1.0
C A:ASN315 4.1 63.8 1.0
CA A:VAL337 4.4 0.2 1.0
CA A:GLN312 4.4 58.5 1.0
CB A:THR336 4.5 0.3 1.0
C A:VAL337 4.6 0.4 1.0
CB A:VAL337 4.6 0.7 1.0
CA A:ASN315 4.6 62.4 1.0
CG2 A:THR336 4.6 0.6 1.0
CB A:GLN312 4.8 59.6 1.0
O A:ASN315 4.9 64.9 1.0
O A:THR336 5.0 0.7 1.0

Mercury binding site 6 out of 6 in 2ped

Go back to Mercury Binding Sites List in 2ped
Mercury binding site 6 out of 6 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:0.7
occ:0.34
O B:VAL337 2.2 0.3 1.0
SG B:CYS316 2.4 73.0 1.0
O B:THR336 2.8 0.6 1.0
CB B:CYS316 2.9 72.8 1.0
ND1 B:HIS65 3.0 80.2 1.0
CA B:CYS316 3.3 72.8 1.0
C B:THR336 3.3 0.5 1.0
C B:VAL337 3.4 0.7 1.0
CE1 B:HIS65 3.5 81.0 1.0
OG B:SER338 3.8 0.2 1.0
N B:VAL337 3.9 0.5 1.0
N B:CYS316 4.1 72.5 1.0
CA B:THR336 4.1 0.5 1.0
CG B:HIS65 4.2 80.1 1.0
CA B:VAL337 4.2 0.2 1.0
N B:SER338 4.3 0.4 1.0
C B:CYS316 4.5 72.6 1.0
CB B:THR336 4.5 0.4 1.0
CA B:SER338 4.5 0.4 1.0
CE B:LYS67 4.6 87.4 1.0
O B:CYS316 4.7 72.1 1.0
CB B:HIS65 4.7 79.5 1.0
NE2 B:HIS65 4.7 80.5 1.0
CG2 B:VAL337 4.7 0.9 1.0
CB B:SER338 4.7 0.9 1.0
CG2 B:THR342 4.8 0.3 1.0
OG1 B:THR319 4.8 74.5 1.0
C B:ASN315 4.8 72.8 1.0
CB B:THR319 5.0 74.8 1.0
O B:ASN315 5.0 73.2 1.0

Reference:

H.Nakamichi, V.Buss, T.Okada. Photoisomerization Mechanism of Rhodopsin and 9-Cis-Rhodopsin Revealed By X-Ray Crystallography Biophys.J. V. 92 L106 2007.
ISSN: ISSN 0006-3495
PubMed: 17449675
DOI: 10.1529/BIOPHYSJ.107.108225
Page generated: Wed Oct 28 18:41:55 2020

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