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Mercury in PDB 5ec5: Crystal Structure of Lysenin Pore

Protein crystallography data

The structure of Crystal Structure of Lysenin Pore, PDB code: 5ec5 was solved by M.Podobnik, P.Savory, N.Rojko, M.Kisovec, M.Bruce, L.Jayasinghe, G.Anderluh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 3.10
Space group P 43 21 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.994, 192.994, 493.202, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.8

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Mercury atom in the Crystal Structure of Lysenin Pore (pdb code 5ec5). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 36 binding sites of Mercury where determined in the Crystal Structure of Lysenin Pore, PDB code: 5ec5:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 36 in 5ec5

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Mercury binding site 1 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg301

b:61.6
occ:1.00
HG A:MBO301 0.0 61.6 1.0
SG A:CYS283 2.3 58.5 1.0
CE1 A:MBO301 2.3 66.5 1.0
O A:CYS283 2.6 56.2 1.0
OG A:SER226 2.9 59.9 1.0
OG A:SER269 2.9 65.9 1.0
CB A:CYS283 3.2 54.8 1.0
CE2 A:MBO301 3.2 69.3 1.0
CE6 A:MBO301 3.2 69.7 1.0
C A:CYS283 3.3 53.5 1.0
CB A:SER269 3.6 63.7 1.0
CD2 A:PHE266 3.7 64.9 1.0
CA A:CYS283 3.8 52.8 1.0
CB A:SER226 3.8 59.2 1.0
CG A:PHE266 4.0 62.8 1.0
CB A:PHE266 4.0 60.5 1.0
N A:LEU284 4.2 54.5 1.0
CA A:GLY230 4.3 69.5 1.0
CE2 A:PHE266 4.4 63.8 1.0
O A:GLY230 4.5 59.1 1.0
CE3 A:MBO301 4.5 73.2 1.0
CE5 A:MBO301 4.6 75.3 1.0
CA A:LEU284 4.7 57.8 1.0
N A:CYS283 4.8 52.0 1.0
CD1 A:PHE266 4.9 64.4 1.0
C A:GLY230 4.9 63.4 1.0
CB A:ASN263 5.0 54.4 1.0

Mercury binding site 2 out of 36 in 5ec5

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Mercury binding site 2 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg302

b:68.9
occ:1.00
HG A:MBO302 0.0 68.9 1.0
CE1 A:MBO302 2.3 80.2 1.0
SG A:CYS272 2.5 53.9 1.0
O A:TYR273 2.7 56.1 1.0
CE2 A:MBO302 3.2 84.2 1.0
CE6 A:MBO302 3.3 78.6 1.0
CD A:ARG287 3.4 72.5 1.0
CD1 A:LEU284 3.4 56.0 1.0
C A:TYR273 3.6 55.7 1.0
CB A:CYS272 3.7 54.0 1.0
CB A:ASP274 3.8 67.8 1.0
CB A:ARG287 4.1 63.1 1.0
CG A:ARG287 4.2 65.9 1.0
N A:ASP274 4.3 57.9 1.0
N A:TYR273 4.3 51.6 1.0
CA A:ASP274 4.4 63.0 1.0
OD1 A:ASP274 4.4 74.9 1.0
CG A:LEU284 4.4 55.3 1.0
NE A:ARG287 4.5 77.4 1.0
CE3 A:MBO302 4.5 87.6 1.0
CG A:ASP274 4.6 72.0 1.0
C A:CYS272 4.6 52.1 1.0
CE5 A:MBO302 4.6 84.2 1.0
CA A:TYR273 4.6 53.1 1.0
CA A:CYS272 4.8 53.3 1.0
CB A:LEU284 4.9 54.9 1.0

Mercury binding site 3 out of 36 in 5ec5

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Mercury binding site 3 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg301

b:79.8
occ:1.00
HG B:MBO301 0.0 79.8 1.0
CE1 B:MBO301 2.3 90.2 1.0
SG B:CYS272 2.3 63.0 1.0
O B:TYR273 2.7 71.0 1.0
CE2 B:MBO301 3.2 93.4 1.0
CE6 B:MBO301 3.3 90.2 1.0
CG B:ARG287 3.4 66.7 1.0
CB B:CYS272 3.6 60.1 1.0
C B:TYR273 3.6 63.5 1.0
CB B:ASP274 3.8 73.7 1.0
CB B:ARG287 3.9 66.0 1.0
CD B:ARG287 4.2 69.6 1.0
CD1 B:LEU284 4.2 68.2 1.0
N B:ASP274 4.2 65.5 1.0
NE B:ARG287 4.2 76.3 1.0
N B:TYR273 4.3 58.0 1.0
CA B:ASP274 4.4 68.8 1.0
OD1 B:ASP274 4.4 80.2 1.0
CE3 B:MBO301 4.5 97.2 1.0
C B:CYS272 4.6 57.8 1.0
CE5 B:MBO301 4.6 97.3 1.0
CG B:ASP274 4.6 78.8 1.0
CA B:TYR273 4.6 59.4 1.0
CA B:CYS272 4.7 58.1 1.0
CB B:LEU284 4.8 67.8 1.0
CG B:LEU284 5.0 69.8 1.0

Mercury binding site 4 out of 36 in 5ec5

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Mercury binding site 4 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg302

b:76.4
occ:1.00
HG B:MBO302 0.0 76.4 1.0
SG B:CYS283 2.3 70.9 1.0
CE1 B:MBO302 2.3 95.0 1.0
O B:CYS283 2.5 62.4 1.0
OG B:SER269 2.7 85.4 1.0
OG B:SER226 3.0 69.1 1.0
CB B:CYS283 3.2 65.3 1.0
C B:CYS283 3.2 62.4 1.0
CE6 B:MBO302 3.2 0.4 1.0
CE2 B:MBO302 3.2 95.6 1.0
CB B:SER269 3.5 78.3 1.0
CA B:CYS283 3.8 61.0 1.0
CB B:PHE266 3.9 79.3 1.0
CB B:SER226 3.9 70.5 1.0
CG B:PHE266 4.0 82.4 1.0
CD2 B:PHE266 4.0 85.8 1.0
N B:LEU284 4.2 65.0 1.0
CE5 B:MBO302 4.5 1.0 1.0
CE3 B:MBO302 4.5 0.5 1.0
CA B:GLY230 4.6 79.8 1.0
CA B:LEU284 4.6 69.3 1.0
O B:GLY230 4.7 87.0 1.0
CD1 B:PHE266 4.7 80.0 1.0
CE2 B:PHE266 4.7 83.3 1.0
N B:CYS283 4.8 58.0 1.0
CA B:SER269 4.9 75.1 1.0

Mercury binding site 5 out of 36 in 5ec5

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Mercury binding site 5 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg301

b:80.7
occ:1.00
HG C:MBO301 0.0 80.7 1.0
SG C:CYS283 2.2 78.8 1.0
CE1 C:MBO301 2.3 93.6 1.0
O C:CYS283 2.7 62.7 1.0
OG C:SER269 2.8 88.2 1.0
OG C:SER226 3.0 76.0 1.0
CB C:CYS283 3.2 72.7 1.0
CE6 C:MBO301 3.2 95.9 1.0
CE2 C:MBO301 3.2 95.1 1.0
C C:CYS283 3.3 67.1 1.0
CB C:SER269 3.6 82.3 1.0
CB C:PHE266 3.8 80.6 1.0
CA C:CYS283 3.8 68.4 1.0
CB C:SER226 3.9 73.7 1.0
CD2 C:PHE266 3.9 81.0 1.0
CG C:PHE266 4.0 81.5 1.0
N C:LEU284 4.2 66.6 1.0
CA C:GLY230 4.4 95.4 1.0
CE5 C:MBO301 4.6 0.0 1.0
CE3 C:MBO301 4.6 96.7 1.0
O C:GLY230 4.7 0.2 1.0
N C:CYS283 4.8 67.7 1.0
CE2 C:PHE266 4.8 82.1 1.0
CA C:LEU284 4.9 69.5 1.0
CD1 C:PHE266 5.0 83.0 1.0
CA C:SER269 5.0 78.8 1.0
CB C:ASN263 5.0 79.4 1.0
O C:SER227 5.0 87.5 1.0

Mercury binding site 6 out of 36 in 5ec5

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Mercury binding site 6 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg302

b:80.1
occ:1.00
SG C:CYS272 2.2 59.5 1.0
O C:TYR273 2.8 81.8 1.0
NE C:ARG287 3.2 78.0 1.0
CB C:CYS272 3.6 59.6 1.0
NH2 C:ARG287 3.7 69.7 1.0
C C:TYR273 3.8 76.9 1.0
CZ C:ARG287 3.9 78.4 1.0
CB C:ASP274 4.0 88.1 1.0
CB C:ARG287 4.0 70.1 1.0
CD C:ARG287 4.1 72.5 1.0
N C:TYR273 4.3 70.4 1.0
CG C:ARG287 4.3 71.9 1.0
CB C:LEU284 4.4 63.4 1.0
N C:ASP274 4.5 77.3 1.0
CG C:LEU284 4.5 61.6 1.0
C C:CYS272 4.6 67.5 1.0
OD1 C:ASP274 4.6 99.3 1.0
CA C:ASP274 4.7 80.7 1.0
CA C:TYR273 4.7 72.6 1.0
CA C:CYS272 4.7 63.7 1.0
CG C:ASP274 4.8 92.0 1.0

Mercury binding site 7 out of 36 in 5ec5

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Mercury binding site 7 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg301

b:61.2
occ:1.00
HG D:MBO301 0.0 61.2 1.0
SG D:CYS283 2.1 52.8 1.0
CE1 D:MBO301 2.3 68.2 1.0
O D:CYS283 2.6 52.2 1.0
OG D:SER226 2.7 59.9 1.0
OG D:SER269 2.9 51.1 1.0
CE2 D:MBO301 3.2 69.6 1.0
CE6 D:MBO301 3.2 71.3 1.0
C D:CYS283 3.3 51.8 1.0
CB D:CYS283 3.5 55.2 1.0
CB D:SER269 3.6 51.8 1.0
CB D:SER226 3.7 61.5 1.0
CB D:PHE266 3.8 59.0 1.0
CA D:CYS283 3.9 52.1 1.0
CG D:PHE266 3.9 60.9 1.0
CD2 D:PHE266 4.0 60.9 1.0
CA D:GLY230 4.2 74.1 1.0
N D:LEU284 4.3 50.6 1.0
O D:GLY230 4.4 76.1 1.0
CE3 D:MBO301 4.5 75.8 1.0
CE5 D:MBO301 4.5 79.2 1.0
N D:CYS283 4.6 52.4 1.0
CD1 D:PHE266 4.6 61.8 1.0
CE2 D:PHE266 4.7 60.9 1.0
C D:GLY230 4.8 72.7 1.0
CA D:LEU284 4.8 49.9 1.0
O D:SER227 4.9 73.2 1.0

Mercury binding site 8 out of 36 in 5ec5

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Mercury binding site 8 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg302

b:73.5
occ:1.00
SG D:CYS272 2.3 48.1 1.0
O D:TYR273 2.8 61.1 1.0
CD D:ARG287 3.2 80.1 1.0
CG D:ARG287 3.5 70.8 1.0
C D:TYR273 3.6 57.6 1.0
CB D:CYS272 3.7 49.0 1.0
CB D:ASP274 3.7 69.3 1.0
CB D:ARG287 3.9 64.2 1.0
CD1 D:LEU284 4.0 46.1 1.0
N D:ASP274 4.2 61.1 1.0
OD1 D:ASP274 4.2 82.4 1.0
N D:TYR273 4.3 54.5 1.0
CA D:ASP274 4.3 65.4 1.0
NE D:ARG287 4.3 89.4 1.0
CG D:ASP274 4.5 74.1 1.0
C D:CYS272 4.6 52.3 1.0
CA D:TYR273 4.6 54.8 1.0
CB D:LEU284 4.8 47.0 1.0
CA D:CYS272 4.8 50.1 1.0

Mercury binding site 9 out of 36 in 5ec5

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Mercury binding site 9 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg301

b:50.4
occ:1.00
HG E:MBO301 0.0 50.4 1.0
SG E:CYS283 2.2 41.8 1.0
CE1 E:MBO301 2.3 52.1 1.0
O E:CYS283 2.5 45.3 1.0
OG E:SER226 2.9 56.4 1.0
OG E:SER269 3.0 53.8 1.0
CB E:CYS283 3.1 40.9 1.0
CE2 E:MBO301 3.1 56.5 1.0
CE6 E:MBO301 3.2 53.7 1.0
C E:CYS283 3.2 42.7 1.0
CD2 E:PHE266 3.5 47.8 1.0
CB E:SER269 3.6 48.4 1.0
CA E:CYS283 3.7 41.0 1.0
CB E:SER226 3.8 53.4 1.0
CG E:PHE266 3.9 47.1 1.0
CB E:PHE266 3.9 46.6 1.0
CE2 E:PHE266 4.2 46.0 1.0
CA E:GLY230 4.2 56.5 1.0
N E:LEU284 4.3 44.1 1.0
O E:GLY230 4.5 62.4 1.0
CE3 E:MBO301 4.5 62.0 1.0
CE5 E:MBO301 4.5 58.7 1.0
N E:CYS283 4.7 41.7 1.0
CD1 E:PHE266 4.7 45.0 1.0
CA E:LEU284 4.8 44.7 1.0
C E:GLY230 4.8 54.1 1.0
CA E:SER269 5.0 46.3 1.0
O E:SER227 5.0 60.1 1.0

Mercury binding site 10 out of 36 in 5ec5

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Mercury binding site 10 out of 36 in the Crystal Structure of Lysenin 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 Lysenin Pore within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg302

b:66.6
occ:1.00
SG E:CYS272 2.4 45.1 1.0
O E:TYR273 2.5 64.1 1.0
CD1 E:LEU284 3.3 44.7 1.0
CD E:ARG287 3.4 64.6 1.0
CG E:ARG287 3.5 58.5 1.0
C E:TYR273 3.5 54.8 1.0
CB E:ASP274 3.6 61.8 1.0
CB E:CYS272 3.6 47.8 1.0
CB E:ARG287 3.9 55.0 1.0
OD1 E:ASP274 4.0 69.8 1.0
N E:ASP274 4.1 54.4 1.0
CA E:ASP274 4.1 58.1 1.0
CG E:ASP274 4.2 65.2 1.0
CG E:LEU284 4.3 44.9 1.0
N E:TYR273 4.3 49.6 1.0
NH1 E:ARG287 4.4 86.3 1.0
C E:CYS272 4.6 48.2 1.0
CA E:TYR273 4.6 50.3 1.0
NE E:ARG287 4.6 74.7 1.0
CB E:LEU284 4.7 43.7 1.0
CA E:CYS272 4.7 47.1 1.0
CZ E:ARG287 5.0 81.2 1.0

Reference:

M.Podobnik, P.Savory, N.Rojko, M.Kisovec, N.Wood, R.Hambley, J.Pugh, E.J.Wallace, L.Mcneill, M.Bruce, I.Liko, T.M.Allison, S.Mehmood, N.Yilmaz, T.Kobayashi, R.J.Gilbert, C.V.Robinson, L.Jayasinghe, G.Anderluh. Crystal Structure of An Invertebrate Cytolysin Pore Reveals Unique Properties and Mechanism of Assembly. Nat Commun V. 7 11598 2016.
ISSN: ESSN 2041-1723
PubMed: 27176125
DOI: 10.1038/NCOMMS11598
Page generated: Sun Dec 13 19:12:34 2020

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