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Mercury in PDB 2wcd: Crystal Structure of the Assembled Cytolysin A Pore

Protein crystallography data

The structure of Crystal Structure of the Assembled Cytolysin A Pore, PDB code: 2wcd was solved by M.Mueller, U.Grauschopf, T.Maier, R.Glockshuber, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.37 / 3.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 111.430, 114.410, 270.550, 94.44, 85.92, 102.55
R / Rfree (%) 22.8 / 24.4

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of the Assembled Cytolysin A Pore (pdb code 2wcd). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 48 binding sites of Mercury where determined in the Crystal Structure of the Assembled Cytolysin A Pore, PDB code: 2wcd:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 48 in 2wcd

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Mercury binding site 1 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


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 the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg304

b:0.8
occ:0.51
HG A:EMC304 0.0 0.8 0.5
C1 A:EMC304 2.2 88.8 0.5
SG A:CYS87 2.3 96.1 1.0
CB A:CYS285 3.2 0.4 1.0
C2 A:EMC304 3.3 40.5 0.5
CB A:CYS87 3.5 0.8 1.0
CA A:CYS87 3.6 0.1 1.0
CZ3 A:TRP86 3.6 96.7 1.0
O A:CYS87 3.8 0.8 1.0
SG A:CYS285 3.9 0.0 1.0
CG2 A:ILE253 4.0 97.1 1.0
CH2 A:TRP86 4.1 82.1 1.0
CA A:CYS285 4.1 0.6 1.0
C A:CYS87 4.2 96.5 1.0
CE3 A:TRP86 4.4 94.6 1.0
O A:MET281 4.4 0.7 1.0
CD1 A:ILE253 4.5 0.8 1.0
CE A:MET281 4.7 0.7 1.0
OG1 A:THR91 4.8 0.9 1.0
N A:CYS285 4.8 0.6 1.0
N A:CYS87 4.8 95.5 1.0
CB A:ALA90 5.0 71.6 1.0

Mercury binding site 2 out of 48 in 2wcd

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Mercury binding site 2 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


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 the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg305

b:0.8
occ:0.26
HG A:EMC305 0.0 0.8 0.3
C1 A:EMC305 2.2 55.0 0.3
SG A:CYS285 2.4 0.0 1.0
C2 A:EMC305 3.2 60.6 0.3
OG1 A:THR91 3.8 0.9 1.0
CG A:GLN289 4.0 0.8 1.0
CB A:CYS285 4.0 0.4 1.0
N A:ASN286 4.2 0.3 1.0
C A:CYS285 4.3 0.5 1.0
OD1 A:ASN286 4.3 0.1 1.0
CA A:ASN286 4.3 0.0 1.0
O A:CYS285 4.5 0.5 1.0
O A:CYS87 4.6 0.8 1.0
NE2 A:GLN289 4.7 0.8 1.0
CB A:THR91 4.7 93.5 1.0
CD A:GLN289 4.7 0.9 1.0
CA A:CYS285 4.8 0.6 1.0
CG2 A:THR91 4.9 93.1 1.0
CB A:ASN286 4.9 0.6 1.0

Mercury binding site 3 out of 48 in 2wcd

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Mercury binding site 3 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


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 the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg304

b:0.1
occ:0.51
HG B:EMC304 0.0 0.1 0.5
C1 B:EMC304 2.2 91.5 0.5
SG B:CYS87 2.3 90.8 1.0
CB B:CYS285 3.1 0.1 1.0
C2 B:EMC304 3.3 29.9 0.5
CB B:CYS87 3.5 0.2 1.0
CA B:CYS87 3.6 0.4 1.0
CZ3 B:TRP86 3.6 87.1 1.0
O B:CYS87 3.8 0.9 1.0
SG B:CYS285 3.9 0.9 1.0
CG2 B:ILE253 4.0 99.5 1.0
CA B:CYS285 4.0 0.7 1.0
C B:CYS87 4.2 0.0 1.0
CH2 B:TRP86 4.2 84.8 1.0
O B:MET281 4.3 0.2 1.0
CD1 B:ILE253 4.4 0.6 1.0
CE3 B:TRP86 4.4 86.9 1.0
N B:CYS285 4.7 0.2 1.0
OG1 B:THR91 4.7 0.8 1.0
CE B:MET281 4.8 0.1 1.0
N B:CYS87 4.9 89.8 1.0

Mercury binding site 4 out of 48 in 2wcd

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Mercury binding site 4 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


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 the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg305

b:0.0
occ:0.26
HG B:EMC305 0.0 0.0 0.3
C1 B:EMC305 2.2 56.2 0.3
SG B:CYS285 2.4 0.9 1.0
C2 B:EMC305 3.2 60.2 0.3
OG1 B:THR91 3.7 0.8 1.0
CB B:CYS285 4.0 0.1 1.0
CG B:GLN289 4.0 0.2 1.0
N B:ASN286 4.1 0.3 1.0
OD1 B:ASN286 4.2 0.6 1.0
CA B:ASN286 4.2 0.2 1.0
C B:CYS285 4.3 0.1 1.0
O B:CYS285 4.5 0.7 1.0
CB B:THR91 4.6 94.7 1.0
O B:CYS87 4.6 0.9 1.0
NE2 B:GLN289 4.7 0.3 1.0
CG2 B:THR91 4.8 89.7 1.0
CD B:GLN289 4.8 0.7 1.0
CB B:ASN286 4.8 0.2 1.0
CA B:CYS285 4.8 0.7 1.0
CG B:ASN286 5.0 0.1 1.0

Mercury binding site 5 out of 48 in 2wcd

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Mercury binding site 5 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


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 the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg304

b:0.7
occ:0.51
HG C:EMC304 0.0 0.7 0.5
C1 C:EMC304 2.2 91.0 0.5
SG C:CYS87 2.4 95.3 1.0
CB C:CYS285 3.3 0.8 1.0
C2 C:EMC304 3.3 42.6 0.5
CZ3 C:TRP86 3.5 91.1 1.0
CB C:CYS87 3.5 0.4 1.0
CA C:CYS87 3.6 0.0 1.0
O C:CYS87 3.8 0.2 1.0
CG2 C:ILE253 3.9 0.9 1.0
SG C:CYS285 4.0 0.6 1.0
CH2 C:TRP86 4.1 89.2 1.0
CA C:CYS285 4.2 0.5 1.0
C C:CYS87 4.2 0.8 1.0
O C:MET281 4.3 0.5 1.0
CE3 C:TRP86 4.3 86.4 1.0
CD1 C:ILE253 4.4 0.7 1.0
CE C:MET281 4.6 0.4 1.0
N C:CYS285 4.8 0.6 1.0
N C:CYS87 4.9 93.8 1.0
OG1 C:THR91 4.9 0.4 1.0
CB C:ALA90 4.9 73.7 1.0

Mercury binding site 6 out of 48 in 2wcd

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Mercury binding site 6 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


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 the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg305

b:0.6
occ:0.26
HG C:EMC305 0.0 0.6 0.3
C1 C:EMC305 2.2 63.6 0.3
SG C:CYS285 2.4 0.6 1.0
C2 C:EMC305 3.2 62.9 0.3
OG1 C:THR91 3.8 0.4 1.0
CG C:GLN289 4.0 0.4 1.0
CB C:CYS285 4.0 0.8 1.0
N C:ASN286 4.2 0.3 1.0
OD1 C:ASN286 4.2 0.7 1.0
CA C:ASN286 4.2 0.8 1.0
C C:CYS285 4.3 0.9 1.0
O C:CYS285 4.5 0.2 1.0
O C:CYS87 4.6 0.2 1.0
NE2 C:GLN289 4.7 0.1 1.0
CD C:GLN289 4.8 0.8 1.0
CB C:THR91 4.8 95.2 1.0
CB C:ASN286 4.8 0.5 1.0
CA C:CYS285 4.8 0.5 1.0
CG2 C:THR91 4.9 88.0 1.0
CG C:ASN286 5.0 0.8 1.0

Mercury binding site 7 out of 48 in 2wcd

Go back to Mercury Binding Sites List in 2wcd
Mercury binding site 7 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg304

b:0.5
occ:0.51
HG D:EMC304 0.0 0.5 0.5
C1 D:EMC304 2.2 93.3 0.5
SG D:CYS87 2.3 90.7 1.0
C2 D:EMC304 3.4 51.3 0.5
CB D:CYS285 3.4 0.8 1.0
CB D:CYS87 3.5 0.6 1.0
CZ3 D:TRP86 3.5 97.5 1.0
CA D:CYS87 3.6 0.1 1.0
CG2 D:ILE253 3.8 87.1 1.0
O D:CYS87 3.9 0.4 1.0
CH2 D:TRP86 4.0 94.8 1.0
SG D:CYS285 4.1 0.3 1.0
C D:CYS87 4.2 0.7 1.0
CE3 D:TRP86 4.3 91.2 1.0
CA D:CYS285 4.3 0.2 1.0
CD1 D:ILE253 4.4 0.8 1.0
O D:MET281 4.4 0.5 1.0
CE D:MET281 4.7 1.0 1.0
N D:CYS87 4.8 94.0 1.0
N D:CYS285 4.9 1.0 1.0
OG1 D:THR91 4.9 0.5 1.0
CB D:ALA90 5.0 74.8 1.0

Mercury binding site 8 out of 48 in 2wcd

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Mercury binding site 8 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg305

b:0.3
occ:0.26
HG D:EMC305 0.0 0.3 0.3
C1 D:EMC305 2.2 72.4 0.3
SG D:CYS285 2.3 0.3 1.0
C2 D:EMC305 3.4 70.6 0.3
OG1 D:THR91 3.6 0.5 1.0
CB D:CYS285 3.9 0.8 1.0
N D:ASN286 4.1 0.2 1.0
CG D:GLN289 4.2 0.9 1.0
CA D:ASN286 4.2 0.4 1.0
OD1 D:ASN286 4.2 0.8 1.0
C D:CYS285 4.3 0.1 1.0
CB D:THR91 4.5 92.5 1.0
CG2 D:THR91 4.5 90.1 1.0
O D:CYS285 4.6 0.7 1.0
O D:CYS87 4.6 0.4 1.0
O D:ILE282 4.7 0.5 1.0
CB D:ASN286 4.7 0.3 1.0
CA D:CYS285 4.8 0.2 1.0
CG D:ASN286 4.9 0.7 1.0
NE2 D:GLN289 4.9 0.8 1.0

Mercury binding site 9 out of 48 in 2wcd

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Mercury binding site 9 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Crystal Structure of the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg304

b:0.5
occ:0.51
HG E:EMC304 0.0 0.5 0.5
C1 E:EMC304 2.2 87.2 0.5
SG E:CYS87 2.3 0.8 1.0
C2 E:EMC304 3.2 45.2 0.5
CB E:CYS285 3.3 0.8 1.0
CB E:CYS87 3.5 0.1 1.0
CA E:CYS87 3.6 0.2 1.0
CZ3 E:TRP86 3.6 94.2 1.0
O E:CYS87 3.8 0.2 1.0
CG2 E:ILE253 3.9 98.5 1.0
SG E:CYS285 4.0 0.3 1.0
CH2 E:TRP86 4.1 93.8 1.0
C E:CYS87 4.2 0.3 1.0
CA E:CYS285 4.2 0.9 1.0
CE3 E:TRP86 4.4 85.5 1.0
O E:MET281 4.4 0.4 1.0
CD1 E:ILE253 4.4 1.0 1.0
OG1 E:THR91 4.7 0.9 1.0
CE E:MET281 4.7 0.5 1.0
N E:CYS285 4.8 0.2 1.0
N E:CYS87 4.9 96.4 1.0
CB E:ALA90 4.9 70.2 1.0

Mercury binding site 10 out of 48 in 2wcd

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Mercury binding site 10 out of 48 in the Crystal Structure of the Assembled Cytolysin A Pore


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Crystal Structure of the Assembled Cytolysin A Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg305

b:0.2
occ:0.26
HG E:EMC305 0.0 0.2 0.3
C1 E:EMC305 2.2 59.5 0.3
SG E:CYS285 2.3 0.3 1.0
C2 E:EMC305 3.2 58.0 0.3
CG E:GLN289 3.9 0.4 1.0
OG1 E:THR91 3.9 0.9 1.0
CB E:CYS285 4.0 0.8 1.0
N E:ASN286 4.2 0.3 1.0
C E:CYS285 4.2 0.2 1.0
CA E:ASN286 4.2 0.8 1.0
OD1 E:ASN286 4.3 0.2 1.0
O E:CYS285 4.4 0.1 1.0
NE2 E:GLN289 4.6 0.2 1.0
O E:CYS87 4.6 0.2 1.0
CD E:GLN289 4.6 0.3 1.0
CB E:THR91 4.7 90.3 1.0
CA E:CYS285 4.8 0.9 1.0
CB E:ASN286 4.9 0.2 1.0
CG2 E:THR91 4.9 90.0 1.0

Reference:

M.Mueller, U.Grauschopf, T.Maier, R.Glockshuber, N.Ban. The Structure of A Cytolytic Alpha-Helical Toxin Pore Reveals Its Assembly Mechanism Nature V. 459 726 2009.
ISSN: ISSN 0028-0836
PubMed: 19421192
DOI: 10.1038/NATURE08026
Page generated: Wed Oct 28 18:42:12 2020

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