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Mercury in PDB 1f88: Crystal Structure of Bovine Rhodopsin

Protein crystallography data

The structure of Crystal Structure of Bovine Rhodopsin, PDB code: 1f88 was solved by T.Okada, K.Palczewski, R.E.Stenkamp, M.Miyano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 97.246, 97.246, 149.544, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.8

Other elements in 1f88:

The structure of Crystal Structure of Bovine Rhodopsin also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Bovine Rhodopsin (pdb code 1f88). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the Crystal Structure of Bovine Rhodopsin, PDB code: 1f88:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 1f88

Go back to Mercury Binding Sites List in 1f88
Mercury binding site 1 out of 6 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:69.2
occ:1.00
SG A:CYS264 2.7 36.9 1.0
CB A:CYS264 2.9 36.9 1.0
OG1 A:THR297 3.1 15.6 1.0
CA A:CYS264 3.7 37.0 1.0
CD1 A:TYR301 3.8 28.2 1.0
CE1 A:TYR301 3.9 29.0 1.0
O A:ALA260 4.1 41.9 1.0
N A:CYS264 4.1 36.7 1.0
CZ A:PHE294 4.1 26.6 1.0
CG A:TYR301 4.3 27.3 1.0
CE1 A:PHE294 4.4 23.9 1.0
CZ A:TYR301 4.4 27.9 1.0
CB A:THR297 4.5 20.7 1.0
CE2 A:PHE294 4.8 27.9 1.0
CD2 A:TYR301 4.8 26.4 1.0
C A:ILE263 4.8 36.8 1.0
C A:THR297 4.9 24.6 1.0
CE2 A:TYR301 4.9 28.7 1.0
CB A:TYR301 5.0 28.1 1.0
C A:ALA260 5.0 39.7 1.0
O A:THR297 5.0 25.7 1.0
C A:CYS264 5.0 36.2 1.0

Mercury binding site 2 out of 6 in 1f88

Go back to Mercury Binding Sites List in 1f88
Mercury binding site 2 out of 6 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:85.6
occ:0.92
SG A:CYS222 2.2 56.9 1.0
CB A:CYS222 3.4 62.3 1.0
CD1 A:LEU226 3.4 92.5 1.0
O A:ALA132 3.4 45.9 1.0
N A:TYR223 3.5 65.6 1.0
C A:CYS222 3.5 64.7 1.0
CG A:LEU226 3.6 92.8 1.0
O A:CYS222 3.7 65.2 1.0
CA A:TYR223 3.8 67.2 1.0
CB A:ARG135 4.0 55.2 1.0
CA A:ALA132 4.0 45.6 1.0
CA A:CYS222 4.1 63.4 1.0
C A:ALA132 4.1 46.0 1.0
CB A:ALA132 4.3 44.8 1.0
CB A:LEU226 4.4 92.7 1.0
CB A:TYR223 4.5 66.0 1.0
CD1 A:ILE255 4.5 47.9 1.0
CG A:ARG135 4.5 53.2 1.0
O A:ILE219 4.7 57.8 1.0
CD2 A:LEU226 4.8 92.7 1.0
N A:TYR136 4.8 64.1 1.0

Mercury binding site 3 out of 6 in 1f88

Go back to Mercury Binding Sites List in 1f88
Mercury binding site 3 out of 6 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg905

b:0.8
occ:0.95
SG A:CYS316 2.3 57.5 1.0
O A:GLN312 3.3 37.8 1.0
CB A:CYS316 3.6 54.1 1.0
CB A:SER338 3.6 64.1 1.0
N A:SER338 3.8 66.8 1.0
CA A:CYS316 3.9 52.0 1.0
N A:CYS316 3.9 51.5 1.0
CG A:GLN312 4.2 41.9 1.0
CA A:SER338 4.2 65.7 1.0
C A:GLN312 4.2 37.6 1.0
N A:VAL337 4.3 68.6 1.0
C A:ASN315 4.4 50.7 1.0
CB A:ASN315 4.6 51.8 1.0
CA A:GLN312 4.7 38.5 1.0
C A:VAL337 4.8 67.8 1.0
CA A:VAL337 5.0 68.4 1.0
O A:ASN315 5.0 52.1 1.0
CD1 A:LEU68 5.0 46.1 1.0

Mercury binding site 4 out of 6 in 1f88

Go back to Mercury Binding Sites List in 1f88
Mercury binding site 4 out of 6 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:70.8
occ:0.98
SG B:CYS264 2.1 42.6 1.0
O B:ALA260 3.1 47.0 1.0
OG1 B:THR297 3.4 32.5 1.0
CB B:CYS264 3.5 41.1 1.0
N B:CYS264 3.8 40.8 1.0
CA B:CYS264 3.9 41.8 1.0
CZ B:PHE294 4.1 24.8 1.0
CD1 B:TYR301 4.2 37.8 1.0
C B:ALA260 4.2 47.4 1.0
CG B:TYR301 4.3 38.1 1.0
C B:ILE263 4.4 40.9 1.0
CE2 B:PHE294 4.4 25.9 1.0
CB B:ILE263 4.5 39.3 1.0
CG2 B:ILE263 4.5 38.4 1.0
CB B:TYR301 4.6 39.1 1.0
CE1 B:TYR301 4.6 37.2 1.0
CE1 B:PHE294 4.8 25.1 1.0
CB B:THR297 4.8 34.1 1.0
CA B:ALA260 4.9 47.6 1.0
O B:ILE263 4.9 41.1 1.0
CB B:ALA260 4.9 47.0 1.0
CD2 B:TYR301 4.9 37.4 1.0
CA B:ILE263 5.0 40.5 1.0

Mercury binding site 5 out of 6 in 1f88

Go back to Mercury Binding Sites List in 1f88
Mercury binding site 5 out of 6 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:98.6
occ:0.93
SG B:CYS222 3.0 86.4 1.0
O B:ALA132 3.2 66.3 1.0
O B:CYS222 3.4 88.6 1.0
CA B:TYR223 3.4 91.6 1.0
C B:CYS222 3.5 88.2 1.0
N B:TYR223 3.5 89.7 1.0
CD1 B:LEU226 3.6 92.3 1.0
CB B:TYR223 3.8 93.0 1.0
C B:ALA132 4.0 67.0 1.0
CA B:ALA132 4.0 66.8 1.0
CB B:CYS222 4.0 87.2 1.0
CB B:ALA132 4.1 67.8 1.0
CB B:ARG135 4.2 68.3 1.0
CA B:CYS222 4.4 87.5 1.0
CG B:LEU226 4.6 90.8 1.0
O B:ILE219 4.6 75.6 1.0
CG B:TYR223 4.8 94.1 1.0
CD1 B:TYR223 4.8 94.9 1.0
C B:TYR223 4.8 92.3 1.0
C B:ARG135 4.9 71.9 1.0
N B:TYR136 4.9 73.8 1.0
CG B:ARG135 4.9 67.7 1.0

Mercury binding site 6 out of 6 in 1f88

Go back to Mercury Binding Sites List in 1f88
Mercury binding site 6 out of 6 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:0.5
occ:0.73
SG B:CYS316 2.1 69.1 1.0
CB B:CYS316 3.3 69.2 1.0
CE1 B:HIS65 3.4 75.1 1.0
ND1 B:HIS65 3.5 74.7 1.0
CA B:CYS316 3.8 67.8 1.0
NE2 B:HIS65 4.1 75.0 1.0
CG B:HIS65 4.3 74.2 1.0
NZ B:LYS66 4.3 72.3 1.0
N B:CYS316 4.4 69.3 1.0
CD2 B:HIS65 4.6 73.6 1.0
O B:GLN312 4.7 76.4 1.0

Reference:

K.Palczewski, T.Kumasaka, T.Hori, C.A.Behnke, H.Motoshima, B.A.Fox, I.Le Trong, D.C.Teller, T.Okada, R.E.Stenkamp, M.Yamamoto, M.Miyano. Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor. Science V. 289 739 2000.
ISSN: ISSN 0036-8075
PubMed: 10926528
DOI: 10.1126/SCIENCE.289.5480.739
Page generated: Sun Dec 13 19:02:39 2020

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