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Mercury in PDB 1u19: Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution

Protein crystallography data

The structure of Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution, PDB code: 1u19 was solved by T.Okada, M.Sugihara, A.N.Bondar, M.Elstner, P.Entel, V.Buss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 96.680, 96.680, 150.200, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.2

Other elements in 1u19:

The structure of Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution 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 at 2.2 Angstroms Resolution (pdb code 1u19). 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 at 2.2 Angstroms Resolution, PDB code: 1u19:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 1u19

Go back to Mercury Binding Sites List in 1u19
Mercury binding site 1 out of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution


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 at 2.2 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:77.5
occ:0.89
 SG A:CYS264 2.8 48.6 1.0
CB A:CYS264 3.0 43.8 1.0
OG1 A:THR297 3.1 39.2 1.0
CD2 A:TYR301 3.6 41.3 1.0
CA A:CYS264 3.7 42.5 1.0
CZ A:PHE294 3.9 34.7 1.0
CE2 A:TYR301 3.9 42.5 1.0
O A:ALA260 4.0 45.9 1.0
N A:CYS264 4.1 42.4 1.0
CB A:THR297 4.2 39.2 1.0
CE1 A:PHE294 4.4 34.1 1.0
CG A:TYR301 4.4 41.4 1.0
CE2 A:PHE294 4.4 34.8 1.0
C A:THR297 4.7 39.5 1.0
N A:SER298 4.7 39.9 1.0
O A:PHE294 4.8 38.2 1.0
CB A:TYR301 4.8 41.7 1.0
O A:THR297 4.8 39.2 1.0
CG2 A:ILE263 5.0 37.5 1.0
C A:ILE263 5.0 42.0 1.0
CZ A:TYR301 5.0 42.8 1.0

Mercury binding site 2 out of 6 in 1u19

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Mercury binding site 2 out of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution


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 at 2.2 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:82.6
occ:0.75
 SG A:CYS222 2.3 69.1 1.0
O A:CYS222 3.4 70.6 1.0
O A:ALA132 3.4 54.8 1.0
C A:CYS222 3.5 70.1 1.0
CB A:CYS222 3.5 68.2 1.0
N A:TYR223 3.7 71.6 1.0
CD2 A:LEU226 3.8 92.0 1.0
CA A:ALA132 3.9 54.9 1.0
CA A:TYR223 4.0 73.2 1.0
C A:ALA132 4.1 55.1 1.0
CD1 A:LEU226 4.1 91.9 1.0
CA A:CYS222 4.1 68.8 1.0
CB A:ALA132 4.2 54.9 1.0
CB A:ARG135 4.2 59.0 1.0
CG A:ARG135 4.3 58.4 1.0
CG A:LEU226 4.4 92.2 1.0
O A:ILE219 4.6 59.9 1.0
CB A:LEU226 4.6 92.2 1.0
N A:TYR136 4.6 65.0 1.0
CB A:TYR223 4.8 73.1 1.0
CB A:TYR136 4.9 66.8 1.0
CA A:TYR136 5.0 66.7 1.0

Mercury binding site 3 out of 6 in 1u19

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Mercury binding site 3 out of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution


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 at 2.2 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg905

b:74.9
occ:0.58
 SG A:CYS316 2.5 55.8 1.0
O A:HOH2061 2.6 47.2 1.0
O A:GLN312 3.2 50.5 1.0
N A:VAL337 3.3 84.8 1.0
N A:CYS316 3.5 55.5 1.0
CB A:CYS316 3.6 56.6 1.0
CG1 A:VAL337 3.7 82.2 1.0
O A:VAL337 3.7 77.6 1.0
CA A:THR336 3.7 89.7 1.0
CA A:CYS316 3.7 57.0 1.0
C A:THR336 3.8 87.3 1.0
CG A:GLN312 3.8 54.4 1.0
CG2 A:THR336 4.1 90.4 1.0
CB A:ASN315 4.1 52.2 1.0
CB A:THR336 4.1 90.0 1.0
C A:GLN312 4.2 50.1 1.0
C A:ASN315 4.2 53.6 1.0
CA A:VAL337 4.3 81.9 1.0
C A:VAL337 4.4 79.7 1.0
CA A:GLN312 4.5 51.0 1.0
CB A:VAL337 4.6 82.0 1.0
NE2 A:GLN312 4.7 56.4 1.0
CA A:ASN315 4.8 51.8 1.0
CD A:GLN312 4.8 55.8 1.0
CB A:GLN312 4.8 51.9 1.0
O A:THR336 4.8 86.9 1.0
O A:ASN315 4.8 54.3 1.0
ND1 A:HIS65 4.9 61.0 1.0
N A:THR336 5.0 92.5 1.0

Mercury binding site 4 out of 6 in 1u19

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Mercury binding site 4 out of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution


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 at 2.2 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:79.3
occ:0.83
 SG B:CYS264 2.7 54.7 1.0
CB B:CYS264 3.3 50.9 1.0
OG1 B:THR297 3.5 44.6 1.0
O B:ALA260 3.6 51.8 1.0
CD2 B:TYR301 3.7 46.2 1.0
CA B:CYS264 3.8 50.0 1.0
CE2 B:TYR301 3.9 47.8 1.0
N B:CYS264 4.1 50.4 1.0
CZ B:PHE294 4.2 40.1 1.0
CG B:TYR301 4.3 46.3 1.0
C B:ALA260 4.5 50.9 1.0
CE2 B:PHE294 4.6 40.3 1.0
C B:ILE263 4.6 50.7 1.0
CB B:THR297 4.7 43.3 1.0
CZ B:TYR301 4.8 47.8 1.0
CB B:TYR301 4.8 45.7 1.0
CE1 B:PHE294 4.9 40.6 1.0
CG2 B:ILE263 4.9 48.2 1.0
CA B:ALA260 4.9 51.3 1.0
O B:ILE263 5.0 51.3 1.0
CB B:ILE263 5.0 48.5 1.0

Mercury binding site 5 out of 6 in 1u19

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Mercury binding site 5 out of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution


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 at 2.2 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:96.2
occ:0.66
 SG B:CYS222 2.3 79.0 1.0
O B:CYS222 3.3 76.8 1.0
O B:ALA132 3.3 68.2 1.0
C B:CYS222 3.4 76.9 1.0
CB B:CYS222 3.6 77.8 1.0
N B:TYR223 3.6 77.3 1.0
CA B:ALA132 3.8 67.0 1.0
CA B:TYR223 3.8 78.1 1.0
CB B:ARG135 4.0 75.5 1.0
C B:ALA132 4.0 68.2 1.0
CA B:CYS222 4.1 76.8 1.0
CD2 B:LEU226 4.1 93.2 1.0
CB B:ALA132 4.2 66.0 1.0
CD1 B:LEU226 4.2 93.5 1.0
CG B:ARG135 4.3 75.1 1.0
O B:ILE219 4.5 66.2 1.0
CB B:TYR223 4.6 77.1 1.0
CG B:LEU226 4.6 93.9 1.0
N B:TYR136 4.7 78.4 1.0
CB B:LEU226 4.9 93.8 1.0
C B:TYR223 5.0 79.7 1.0

Mercury binding site 6 out of 6 in 1u19

Go back to Mercury Binding Sites List in 1u19
Mercury binding site 6 out of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution


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 at 2.2 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:0.3
occ:0.36
 O B:VAL337 2.0 0.1 1.0
O B:THR336 2.0 0.2 1.0
CB B:CYS316 2.3 62.5 1.0
SG B:CYS316 2.4 63.0 1.0
ND1 B:HIS65 2.7 69.0 1.0
CA B:CYS316 2.9 62.9 1.0
C B:THR336 3.1 0.4 1.0
C B:VAL337 3.2 0.6 1.0
CE1 B:HIS65 3.5 68.9 1.0
OG B:SER338 3.6 0.6 1.0
CG B:HIS65 3.8 68.8 1.0
N B:VAL337 3.9 0.1 1.0
C B:CYS316 3.9 62.7 1.0
O B:CYS316 4.0 62.6 1.0
N B:CYS316 4.0 62.9 1.0
CA B:VAL337 4.0 0.4 1.0
N B:SER338 4.1 0.1 1.0
CA B:THR336 4.2 0.8 1.0
CB B:HIS65 4.2 68.5 1.0
CE B:LYS67 4.2 75.9 1.0
CA B:SER338 4.4 1.0 1.0
CB B:SER338 4.6 0.0 1.0
NZ B:LYS67 4.7 77.1 1.0
NE2 B:HIS65 4.7 68.8 1.0
CB B:THR336 4.7 0.6 1.0
OG1 B:THR319 4.8 70.1 1.0
CG2 B:THR342 4.8 0.2 1.0
CG2 B:VAL337 4.8 0.3 1.0
CD1 B:LEU68 4.9 62.5 1.0
CD2 B:HIS65 4.9 68.7 1.0
CD B:LYS67 4.9 74.0 1.0
C B:ASN315 4.9 63.0 1.0
O B:GLN312 5.0 62.6 1.0

Reference:

T.Okada, M.Sugihara, A.N.Bondar, M.Elstner, P.Entel, V.Buss. The Retinal Conformation and Its Environment in Rhodopsin in Light of A New 2.2 A Crystal Structure J.Mol.Biol. V. 342 571 2004.
ISSN: ISSN 0022-2836
PubMed: 15327956
DOI: 10.1016/J.JMB.2004.07.044
Page generated: Sun Dec 13 19:05:22 2020

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