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Mercury in PDB 2hpy: Crystallographic Model of Lumirhodopsin

Protein crystallography data

The structure of Crystallographic Model of Lumirhodopsin, PDB code: 2hpy 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 / 2.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 96.720, 96.720, 150.400, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 23.8

Other elements in 2hpy:

The structure of Crystallographic Model of Lumirhodopsin also contains other interesting chemical elements:

Zinc (Zn) 7 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystallographic Model of Lumirhodopsin (pdb code 2hpy). 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 Lumirhodopsin, PDB code: 2hpy:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 2hpy

Go back to Mercury Binding Sites List in 2hpy
Mercury binding site 1 out of 6 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg901

b:82.5
occ:0.89
CB A:CYS264 2.8 57.9 0.4
OG1 A:THR297 3.2 52.4 0.4
SG A:CYS264 3.4 60.2 0.4
CD2 A:TYR301 3.5 54.0 0.4
CA A:CYS264 3.5 57.6 0.4
O A:ALA260 3.7 55.1 0.4
N A:CYS264 3.8 56.9 0.4
CE2 A:TYR301 3.9 54.0 0.4
CZ A:PHE294 4.0 47.0 0.4
CG2 A:ILE263 4.1 49.7 0.4
CG A:TYR301 4.1 53.0 0.4
CE1 A:PHE294 4.2 47.8 0.4
CB A:THR297 4.3 54.1 0.4
CB A:TYR301 4.5 53.5 0.4
C A:ALA260 4.7 54.8 0.4
C A:ILE263 4.7 55.1 0.4
CE2 A:PHE294 4.8 47.6 0.4
C A:THR297 4.8 54.7 0.4
CZ A:TYR301 4.8 53.5 0.4
N A:SER298 4.8 55.1 0.4
O A:PHE294 4.9 47.5 0.4
CB A:ILE263 4.9 49.4 0.4
CD1 A:TYR301 4.9 53.7 0.4
C A:CYS264 5.0 58.4 0.4

Mercury binding site 2 out of 6 in 2hpy

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Mercury binding site 2 out of 6 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg903

b:96.7
occ:0.75
SG A:CYS222 2.6 76.0 1.0
C A:CYS222 3.5 80.6 1.0
O A:CYS222 3.5 80.7 1.0
N A:TYR223 3.6 83.0 1.0
CB A:CYS222 3.6 78.2 1.0
O A:ALA132 3.7 77.8 0.4
CA A:TYR223 3.7 85.2 1.0
CB A:ALA132 4.0 76.9 0.4
CA A:ALA132 4.1 76.6 0.4
CD2 A:LEU226 4.1 0.2 1.0
CA A:CYS222 4.2 79.0 1.0
C A:ALA132 4.3 77.5 0.4
CD1 A:LEU226 4.4 0.3 1.0
CB A:TYR223 4.4 84.7 1.0
O A:ILE219 4.5 77.0 0.4
CB A:ARG135 4.5 81.2 1.0
CG A:LEU226 4.7 0.4 1.0
CG A:ARG135 4.8 81.6 1.0
CB A:LEU226 4.9 0.2 1.0

Mercury binding site 3 out of 6 in 2hpy

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Mercury binding site 3 out of 6 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg905

b:99.0
occ:0.58
SG A:CYS316 2.8 64.6 1.0
O A:GLN312 3.4 61.5 0.4
N A:CYS316 3.5 65.9 1.0
O A:HOH2061 3.5 72.3 1.0
N A:VAL337 3.5 0.8 1.0
CA A:CYS316 3.7 66.8 1.0
O A:VAL337 3.8 0.6 1.0
CB A:CYS316 3.8 65.7 1.0
CA A:THR336 3.9 0.9 1.0
CG1 A:VAL337 4.0 0.8 1.0
CB A:ASN315 4.0 65.2 0.4
CG A:GLN312 4.0 65.4 0.4
C A:THR336 4.0 0.5 1.0
C A:ASN315 4.1 65.3 0.4
CG2 A:THR336 4.1 0.8 1.0
CB A:THR336 4.2 0.8 1.0
C A:GLN312 4.3 60.5 0.4
CA A:VAL337 4.5 0.4 1.0
NE2 A:GLN312 4.5 66.6 0.4
CA A:GLN312 4.5 61.0 0.4
C A:VAL337 4.6 0.8 1.0
CA A:ASN315 4.7 64.0 0.4
O A:ASN315 4.7 66.0 0.4
CD A:GLN312 4.8 67.2 0.4
CB A:GLN312 4.8 61.2 0.4
CB A:VAL337 4.9 0.6 1.0

Mercury binding site 4 out of 6 in 2hpy

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Mercury binding site 4 out of 6 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg902

b:80.3
occ:0.83
CB B:CYS264 3.0 60.6 0.4
O B:ALA260 3.2 69.2 0.4
OG1 B:THR297 3.3 56.3 0.4
CD2 B:TYR301 3.4 56.5 0.4
SG B:CYS264 3.4 64.6 0.4
CE2 B:TYR301 3.6 56.1 0.4
CA B:CYS264 3.6 60.4 0.4
N B:CYS264 3.9 60.8 0.4
CG2 B:ILE263 4.0 64.2 0.4
CG B:TYR301 4.1 55.1 0.4
C B:ALA260 4.2 67.9 0.4
CZ B:TYR301 4.4 56.4 0.4
CZ B:PHE294 4.4 50.6 0.4
C B:ILE263 4.5 62.4 0.4
CB B:THR297 4.6 55.8 0.4
CA B:ALA260 4.6 67.8 0.4
CE2 B:PHE294 4.6 51.9 0.4
CB B:TYR301 4.7 55.4 0.4
CB B:ILE263 4.8 63.3 0.4
CD1 B:TYR301 4.9 56.3 0.4
CB B:ALA260 4.9 66.3 0.4
O B:ILE263 4.9 62.0 0.4
N B:SER298 5.0 54.6 0.4

Mercury binding site 5 out of 6 in 2hpy

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Mercury binding site 5 out of 6 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg904

b:0.1
occ:0.66
SG B:CYS222 2.2 90.6 1.0
O B:CYS222 3.3 92.1 1.0
C B:CYS222 3.3 92.3 1.0
CB B:CYS222 3.3 91.4 1.0
N B:TYR223 3.6 94.0 1.0
CA B:ALA132 3.7 79.5 0.4
O B:ALA132 3.8 79.9 0.4
CB B:ALA132 3.8 79.0 0.4
CA B:TYR223 3.8 96.3 1.0
CA B:CYS222 4.0 91.1 1.0
C B:ALA132 4.2 79.8 0.4
CB B:ARG135 4.2 84.1 1.0
CD1 B:LEU226 4.4 0.7 1.0
O B:ILE219 4.4 76.2 0.4
CD2 B:LEU226 4.4 0.6 1.0
CG B:ARG135 4.6 82.5 1.0
CB B:TYR223 4.6 93.7 1.0
CG B:LEU226 4.9 0.0 1.0
N B:ALA132 4.9 79.7 0.4
N B:CYS222 5.0 89.6 1.0
N B:TYR136 5.0 89.0 1.0

Mercury binding site 6 out of 6 in 2hpy

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Mercury binding site 6 out of 6 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg906

b:0.2
occ:0.36
O B:VAL337 2.2 0.4 1.0
ND1 B:HIS65 2.7 82.9 0.4
CB B:CYS316 2.8 74.0 1.0
SG B:CYS316 2.8 76.8 1.0
OG B:SER338 2.9 1.0 1.0
CE1 B:HIS65 3.1 83.2 0.4
CA B:CYS316 3.1 72.9 1.0
O B:THR336 3.1 0.7 1.0
C B:VAL337 3.4 0.5 1.0
C B:THR336 3.9 0.6 1.0
O B:CYS316 3.9 70.9 1.0
C B:CYS316 4.0 72.2 1.0
CB B:SER338 4.0 0.7 1.0
CG B:HIS65 4.1 83.3 0.4
N B:CYS316 4.2 71.3 1.0
CA B:SER338 4.2 0.1 1.0
N B:SER338 4.2 0.1 1.0
OG1 B:THR319 4.3 80.0 1.0
NE2 B:HIS65 4.4 83.0 0.4
CB B:THR319 4.4 78.1 1.0
N B:VAL337 4.4 0.1 1.0
CA B:VAL337 4.5 0.3 1.0
CG2 B:THR342 4.5 0.8 1.0
OE1 B:GLU341 4.7 0.7 1.0
CB B:HIS65 4.8 82.9 0.4
CA B:THR336 4.8 0.9 1.0
CG2 B:THR319 4.8 77.6 1.0
CD2 B:HIS65 4.9 83.0 0.4
O B:ASN315 4.9 71.9 0.4
C B:ASN315 4.9 72.0 0.4

Reference:

H.Nakamichi, T.Okada. Local Peptide Movement in the Photoreaction Intermediate of Rhodopsin Proc.Natl.Acad.Sci.Usa V. 103 12729 2006.
ISSN: ISSN 0027-8424
PubMed: 16908857
DOI: 10.1073/PNAS.0601765103
Page generated: Sun Dec 13 19:07:10 2020

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