Atomistry » Mercury » PDB 5ca2-5l9w » 5ec5
Atomistry »
  Mercury »
    PDB 5ca2-5l9w »
      5ec5 »

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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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

Go back to Mercury Binding Sites List in 5ec5
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 Aug 11 06:19:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy