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Mercury in PDB 2g87: Crystallographic Model of Bathorhodopsin

Protein crystallography data

The structure of Crystallographic Model of Bathorhodopsin, PDB code: 2g87 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 / 2.60
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 96.490, 96.490, 150.400, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 18.1

Other elements in 2g87:

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

Zinc (Zn) 7 atoms

Mercury Binding Sites:

The binding sites of Mercury atom in the Crystallographic Model of Bathorhodopsin (pdb code 2g87). 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 Bathorhodopsin, PDB code: 2g87:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 2g87

Go back to Mercury Binding Sites List in 2g87
Mercury binding site 1 out of 6 in the Crystallographic Model of Bathorhodopsin


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

b:84.4
occ:0.89
SG A:CYS264 2.7 55.4 1.0
CB A:CYS264 3.0 50.6 1.0
OG1 A:THR297 3.1 46.0 1.0
CD2 A:TYR301 3.6 48.1 1.0
CA A:CYS264 3.7 49.3 1.0
CE2 A:TYR301 3.9 49.3 1.0
CZ A:PHE294 3.9 41.5 1.0
O A:ALA260 3.9 52.7 1.0
N A:CYS264 4.1 49.2 1.0
CB A:THR297 4.2 46.0 1.0
CG A:TYR301 4.3 48.2 1.0
CE1 A:PHE294 4.4 40.9 1.0
CE2 A:PHE294 4.5 41.6 1.0
C A:THR297 4.6 46.3 1.0
N A:SER298 4.7 46.7 1.0
CB A:TYR301 4.7 48.5 1.0
O A:PHE294 4.8 45.1 1.0
O A:THR297 4.8 46.0 1.0
CZ A:TYR301 4.9 49.6 1.0
C A:ILE263 5.0 48.8 1.0
CA A:THR297 5.0 46.6 1.0

Mercury binding site 2 out of 6 in 2g87

Go back to Mercury Binding Sites List in 2g87
Mercury binding site 2 out of 6 in the Crystallographic Model of Bathorhodopsin


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

b:89.5
occ:0.75
SG A:CYS222 2.3 75.9 1.0
O A:CYS222 3.2 77.4 1.0
O A:ALA132 3.4 61.7 1.0
C A:CYS222 3.4 76.9 1.0
CB A:CYS222 3.6 75.0 1.0
N A:TYR223 3.7 78.4 1.0
CD2 A:LEU226 3.8 98.8 1.0
CA A:TYR223 3.9 80.0 1.0
CA A:ALA132 3.9 61.7 1.0
CD1 A:LEU226 4.0 98.8 1.0
C A:ALA132 4.1 61.9 1.0
CA A:CYS222 4.2 75.7 1.0
CB A:ARG135 4.2 65.8 1.0
CB A:ALA132 4.2 61.7 1.0
CG A:LEU226 4.3 99.0 1.0
CG A:ARG135 4.4 65.2 1.0
CB A:LEU226 4.6 99.0 1.0
N A:TYR136 4.7 71.8 1.0
CB A:TYR223 4.7 79.9 1.0
O A:ILE219 4.7 66.8 1.0
CB A:TYR136 4.9 73.7 1.0

Mercury binding site 3 out of 6 in 2g87

Go back to Mercury Binding Sites List in 2g87
Mercury binding site 3 out of 6 in the Crystallographic Model of Bathorhodopsin


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

b:81.7
occ:0.58
O A:HOH2061 2.5 54.0 1.0
SG A:CYS316 2.5 62.7 1.0
O A:GLN312 3.0 57.4 1.0
N A:VAL337 3.5 91.6 1.0
N A:CYS316 3.6 62.3 1.0
CB A:CYS316 3.6 63.4 1.0
CG A:GLN312 3.7 61.2 1.0
CG1 A:VAL337 3.7 89.1 1.0
CA A:CYS316 3.8 63.9 1.0
O A:VAL337 3.8 84.5 1.0
CA A:THR336 3.9 96.5 1.0
C A:THR336 4.0 94.1 1.0
CB A:ASN315 4.0 59.0 1.0
C A:GLN312 4.0 56.9 1.0
C A:ASN315 4.3 60.4 1.0
CA A:GLN312 4.3 57.8 1.0
CG2 A:THR336 4.3 97.2 1.0
CA A:VAL337 4.4 88.7 1.0
CB A:THR336 4.4 96.9 1.0
C A:VAL337 4.5 86.5 1.0
CB A:GLN312 4.6 58.8 1.0
CB A:VAL337 4.7 88.8 1.0
CA A:ASN315 4.7 58.6 1.0
CD A:GLN312 4.7 62.6 1.0
NE2 A:GLN312 4.8 63.2 1.0
O A:THR336 5.0 93.7 1.0
O A:ASN315 5.0 61.1 1.0

Mercury binding site 4 out of 6 in 2g87

Go back to Mercury Binding Sites List in 2g87
Mercury binding site 4 out of 6 in the Crystallographic Model of Bathorhodopsin


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

b:86.1
occ:0.83
SG B:CYS264 2.4 61.5 1.0
CB B:CYS264 3.2 57.7 1.0
OG1 B:THR297 3.5 51.4 1.0
O B:ALA260 3.5 58.6 1.0
CD2 B:TYR301 3.6 53.0 1.0
CA B:CYS264 3.8 56.9 1.0
CE2 B:TYR301 4.0 54.6 1.0
N B:CYS264 4.1 57.2 1.0
CG B:TYR301 4.2 53.1 1.0
CZ B:PHE294 4.2 46.9 1.0
C B:ALA260 4.5 57.8 1.0
CB B:TYR301 4.6 52.5 1.0
CE2 B:PHE294 4.6 47.1 1.0
C B:ILE263 4.7 57.6 1.0
CB B:THR297 4.7 50.2 1.0
CZ B:TYR301 4.8 54.6 1.0
CE1 B:PHE294 4.9 47.4 1.0
CD1 B:TYR301 5.0 54.7 1.0

Mercury binding site 5 out of 6 in 2g87

Go back to Mercury Binding Sites List in 2g87
Mercury binding site 5 out of 6 in the Crystallographic Model of Bathorhodopsin


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

b:0.1
occ:0.66
SG B:CYS222 2.1 85.8 1.0
O B:CYS222 3.2 83.6 1.0
C B:CYS222 3.4 83.7 1.0
O B:ALA132 3.4 75.0 1.0
CB B:CYS222 3.4 84.7 1.0
N B:TYR223 3.7 84.1 1.0
CA B:ALA132 3.8 73.8 1.0
CA B:TYR223 3.9 85.0 1.0
C B:ALA132 4.0 75.0 1.0
CA B:CYS222 4.1 83.7 1.0
CB B:ARG135 4.1 82.3 1.0
CB B:ALA132 4.2 72.8 1.0
CD2 B:LEU226 4.2 0.0 1.0
CD1 B:LEU226 4.4 0.3 1.0
CG B:ARG135 4.4 81.9 1.0
O B:ILE219 4.6 73.1 1.0
CB B:TYR223 4.6 83.9 1.0
CG B:LEU226 4.8 0.7 1.0
N B:TYR136 4.8 85.2 1.0
CB B:LEU226 5.0 0.6 1.0

Mercury binding site 6 out of 6 in 2g87

Go back to Mercury Binding Sites List in 2g87
Mercury binding site 6 out of 6 in the Crystallographic Model of Bathorhodopsin


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

b:0.1
occ:0.36
O B:VAL337 2.0 0.9 1.0
O B:THR336 2.2 0.0 1.0
SG B:CYS316 2.3 69.8 1.0
CB B:CYS316 2.4 69.4 1.0
CA B:CYS316 3.1 69.7 1.0
ND1 B:HIS65 3.1 75.8 1.0
C B:THR336 3.1 0.2 1.0
C B:VAL337 3.2 0.5 1.0
OG B:SER338 3.5 0.4 1.0
CE1 B:HIS65 3.8 75.7 1.0
N B:VAL337 3.9 0.9 1.0
CA B:VAL337 4.1 0.2 1.0
N B:CYS316 4.1 69.7 1.0
CA B:THR336 4.1 0.6 1.0
C B:CYS316 4.1 69.5 1.0
O B:CYS316 4.2 69.5 1.0
CG B:HIS65 4.2 75.6 1.0
N B:SER338 4.2 1.0 1.0
CE B:LYS67 4.4 82.7 1.0
CA B:SER338 4.5 0.8 1.0
CB B:HIS65 4.6 75.4 1.0
CB B:SER338 4.6 0.8 1.0
CB B:THR336 4.7 0.4 1.0
CG2 B:THR342 4.7 0.0 1.0
NZ B:LYS67 4.8 83.9 1.0
OG1 B:THR319 4.9 76.9 1.0
C B:ASN315 4.9 69.8 1.0
O B:GLN312 5.0 69.4 1.0

Reference:

H.Nakamichi, T.Okada. Crystallographic Analysis of Primary Visual Photochemistry Angew.Chem.Int.Ed.Engl. V. 45 4270 2006.
ISSN: ISSN 1433-7851
PubMed: 16586416
DOI: 10.1002/ANIE.200600595
Page generated: Wed Oct 28 18:41:32 2020

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