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Mercury in PDB 3oax: Crystal Structure of Bovine Rhodopsin with Beta-Ionone

Protein crystallography data

The structure of Crystal Structure of Bovine Rhodopsin with Beta-Ionone, PDB code: 3oax was solved by C.L.Makino, C.K.Riley, J.Looney, R.K.Crouch, T.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 96.990, 96.990, 149.800, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.2

Other elements in 3oax:

The structure of Crystal Structure of Bovine Rhodopsin with Beta-Ionone also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone (pdb code 3oax). 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 with Beta-Ionone, PDB code: 3oax:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 3oax

Go back to Mercury Binding Sites List in 3oax
Mercury binding site 1 out of 6 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:73.7
occ:0.82
 SG A:CYS264 2.6 56.9 1.0
CB A:CYS264 2.9 52.9 1.0
OG1 A:THR297 2.9 48.0 1.0
CA A:CYS264 3.7 50.5 1.0
CD2 A:TYR301 3.7 45.7 1.0
CZ A:PHE294 3.8 40.7 1.0
CE2 A:TYR301 4.0 46.6 1.0
CB A:THR297 4.1 47.4 1.0
N A:CYS264 4.2 51.7 1.0
CE1 A:PHE294 4.2 42.1 1.0
O A:ALA260 4.3 52.5 1.0
CE2 A:PHE294 4.4 41.1 1.0
CG A:TYR301 4.4 47.2 1.0
C A:THR297 4.7 49.6 1.0
N A:SER298 4.7 50.4 1.0
O A:PHE294 4.7 43.4 1.0
CB A:TYR301 4.8 47.3 1.0
C A:ILE263 4.9 51.2 1.0
CZ A:TYR301 4.9 45.4 1.0
C A:CYS264 5.0 50.7 1.0
O A:THR297 5.0 46.6 1.0
CA A:THR297 5.0 48.7 1.0

Mercury binding site 2 out of 6 in 3oax

Go back to Mercury Binding Sites List in 3oax
Mercury binding site 2 out of 6 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:82.0
occ:0.71
 SG A:CYS222 2.3 79.9 1.0
O A:ALA132 3.4 67.0 1.0
CB A:CYS222 3.5 80.0 1.0
C A:CYS222 3.6 82.1 1.0
N A:TYR223 3.7 83.1 1.0
O A:CYS222 3.7 82.9 1.0
CD1 A:LEU226 3.9 0.0 1.0
CA A:TYR223 3.9 84.2 1.0
CA A:ALA132 4.0 66.8 1.0
CD2 A:LEU226 4.0 0.4 1.0
CB A:ALA132 4.1 66.0 1.0
C A:ALA132 4.1 67.8 1.0
CA A:CYS222 4.1 80.9 1.0
CG A:LEU226 4.5 0.7 1.0
CB A:ARG135 4.5 70.8 1.0
O A:ILE219 4.7 71.1 1.0
CB A:TYR223 4.7 83.2 1.0
N A:TYR136 4.8 78.9 1.0
CB A:TYR136 5.0 81.4 1.0

Mercury binding site 3 out of 6 in 3oax

Go back to Mercury Binding Sites List in 3oax
Mercury binding site 3 out of 6 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg905

b:81.2
occ:0.52
 SG A:CYS316 2.2 54.5 1.0
O A:HOH2061 2.5 58.1 1.0
O A:GLN312 3.2 55.3 1.0
CG2 A:THR336 3.3 0.0 1.0
CB A:CYS316 3.5 61.3 1.0
N A:CYS316 3.5 61.6 1.0
N A:VAL337 3.6 0.5 1.0
CB A:THR336 3.6 0.4 1.0
CA A:THR336 3.7 0.9 1.0
CA A:CYS316 3.7 62.6 1.0
CG A:GLN312 3.8 60.2 1.0
O A:VAL337 3.9 0.6 1.0
CG1 A:VAL337 4.0 0.2 1.0
C A:THR336 4.0 0.8 1.0
CB A:ASN315 4.0 64.7 1.0
C A:GLN312 4.1 55.2 1.0
C A:ASN315 4.1 61.5 1.0
CA A:GLN312 4.4 55.1 1.0
CG A:GLU332 4.4 0.3 1.0
CA A:VAL337 4.6 0.1 1.0
CA A:ASN315 4.6 61.7 1.0
C A:VAL337 4.7 0.1 1.0
O A:ASN315 4.7 62.6 1.0
CB A:GLN312 4.8 56.6 1.0
O A:ASP331 4.8 0.6 1.0
O A:THR335 4.9 0.7 1.0
CD A:GLN312 4.9 62.2 1.0
CB A:VAL337 5.0 0.0 1.0
ND1 A:HIS65 5.0 71.8 1.0

Mercury binding site 4 out of 6 in 3oax

Go back to Mercury Binding Sites List in 3oax
Mercury binding site 4 out of 6 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:79.5
occ:0.81
 O B:HOH2112 2.3 43.9 1.0
SG B:CYS264 2.6 62.9 1.0
CB B:CYS264 3.0 59.1 1.0
O B:HOH2094 3.1 44.7 1.0
OG1 B:THR297 3.5 57.8 1.0
CD2 B:TYR301 3.6 53.9 1.0
O B:ALA260 3.6 64.1 1.0
CA B:CYS264 3.7 59.0 1.0
CE2 B:TYR301 3.8 55.1 1.0
N B:CYS264 4.0 59.5 1.0
CZ B:PHE294 4.2 47.6 1.0
CE2 B:PHE294 4.3 46.5 1.0
CG B:TYR301 4.4 52.7 1.0
C B:ALA260 4.6 62.8 1.0
CZ B:TYR301 4.7 55.5 1.0
C B:ILE263 4.7 59.5 1.0
CB B:THR297 4.8 53.6 1.0
CB B:TYR301 4.9 53.5 1.0

Mercury binding site 5 out of 6 in 3oax

Go back to Mercury Binding Sites List in 3oax
Mercury binding site 5 out of 6 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:98.8
occ:0.62
 SG B:CYS222 2.1 89.1 1.0
O B:CYS222 2.4 92.7 1.0
C B:CYS222 3.0 92.9 1.0
CB B:CYS222 3.1 92.3 1.0
CA B:CYS222 3.6 92.2 1.0
N B:TYR223 3.7 93.9 1.0
CD2 B:LEU226 4.0 0.9 1.0
O B:ALA132 4.0 85.1 1.0
CA B:TYR223 4.0 95.7 1.0
CB B:ARG135 4.1 92.3 1.0
CD1 B:LEU226 4.1 0.3 1.0
CA B:ALA132 4.2 83.2 1.0
CG B:ARG135 4.2 91.8 1.0
CB B:ALA132 4.4 82.5 1.0
C B:ALA132 4.6 84.0 1.0
N B:TYR136 4.6 96.5 1.0
CG B:LEU226 4.6 0.1 1.0
O B:ILE219 4.7 81.2 1.0
N B:CYS222 4.8 92.2 1.0
CB B:TYR223 4.8 93.5 1.0
CB B:TYR136 5.0 97.4 1.0

Mercury binding site 6 out of 6 in 3oax

Go back to Mercury Binding Sites List in 3oax
Mercury binding site 6 out of 6 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:0.8
occ:0.35
 SG B:CYS316 2.4 71.1 1.0
CG2 B:THR336 2.7 1.0 1.0
N B:VAL337 2.8 0.3 1.0
CA B:THR336 3.1 0.8 1.0
O B:GLN312 3.2 70.0 1.0
C B:THR336 3.3 0.2 1.0
N B:CYS316 3.3 65.6 1.0
CB B:CYS316 3.4 69.4 1.0
CB B:THR336 3.4 0.2 1.0
CA B:CYS316 3.5 67.5 1.0
CG B:GLU332 3.7 0.1 1.0
O B:VAL337 3.7 0.7 1.0
CA B:VAL337 3.9 0.2 1.0
C B:ASN315 3.9 66.3 1.0
CG2 B:VAL337 4.0 0.8 1.0
CB B:ASN315 4.0 68.1 1.0
OE1 B:GLU341 4.1 0.8 1.0
C B:GLN312 4.2 68.7 1.0
CB B:VAL337 4.2 0.6 1.0
CG B:GLN312 4.2 78.8 1.0
C B:VAL337 4.3 0.4 1.0
O B:THR335 4.4 0.0 1.0
N B:THR336 4.4 0.0 1.0
OG1 B:THR336 4.4 0.5 1.0
CA B:GLN312 4.5 70.1 1.0
O B:THR336 4.5 0.8 1.0
O B:ASN315 4.5 66.7 1.0
CA B:ASN315 4.5 66.2 1.0
O B:ASP331 4.6 0.5 1.0
CB B:GLU332 4.6 0.6 1.0
CD B:GLU332 4.8 0.3 1.0
C B:THR335 4.8 0.2 1.0
CB B:GLN312 4.9 73.3 1.0

Reference:

C.L.Makino, C.K.Riley, J.Looney, R.K.Crouch, T.Okada. Binding of More Than One Retinoid to Visual Opsins Biophys.J. V. 99 2366 2010.
ISSN: ISSN 0006-3495
PubMed: 20923672
DOI: 10.1016/J.BPJ.2010.08.003
Page generated: Fri Aug 8 10:14:38 2025

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