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Mercury in PDB 2jes: Portal Protein (GP6) From Bacteriophage SPP1

Protein crystallography data

The structure of Portal Protein (GP6) From Bacteriophage SPP1, PDB code: 2jes was solved by A.A.Lebedev, M.H.Krause, A.L.Isidro, A.A.Vagin, E.V.Orlova, J.Turner, E.J.Dodson, P.Tavares, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.81 / 3.40
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 174.314, 221.405, 421.866, 90.00, 90.00, 90.00
R / Rfree (%) 28.8 / 31.9

Other elements in 2jes:

The structure of Portal Protein (GP6) From Bacteriophage SPP1 also contains other interesting chemical elements:

Calcium (Ca) 13 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Mercury atom in the Portal Protein (GP6) From Bacteriophage SPP1 (pdb code 2jes). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 13 binding sites of Mercury where determined in the Portal Protein (GP6) From Bacteriophage SPP1, PDB code: 2jes:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 13 in 2jes

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Mercury binding site 1 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg701

b:0.2
occ:0.30
 O C:PHE259 3.0 0.2 1.0
O A:SER85 3.0 0.2 1.0
SG A:CYS55 3.4 0.2 1.0
C C:PHE259 3.4 0.2 1.0
CA C:TYR260 3.6 0.2 1.0
N C:TYR260 3.7 0.2 1.0
OD2 C:ASP262 3.7 0.2 1.0
CB C:ASP262 3.8 0.2 1.0
CB A:CYS55 3.8 0.2 1.0
C C:TYR260 4.1 0.2 1.0
CG C:ASP262 4.2 0.2 1.0
N C:ASP262 4.2 0.2 1.0
C A:SER85 4.2 0.2 1.0
N C:LYS261 4.2 0.2 1.0
O C:LYS258 4.3 0.2 1.0
CA C:PHE259 4.3 0.2 1.0
N A:ALA87 4.5 0.2 1.0
CA C:ASP262 4.6 0.2 1.0
CB A:ALA87 4.7 0.2 1.0
CA A:HIS86 4.8 0.2 1.0
OG A:SER85 4.9 0.2 1.0
CB C:TYR260 4.9 0.2 1.0
N C:LEU263 4.9 0.2 1.0
O C:TYR260 4.9 0.2 1.0
C A:HIS86 5.0 0.2 1.0

Mercury binding site 2 out of 13 in 2jes

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Mercury binding site 2 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg701

b:0.2
occ:0.30
 O C:SER85 2.9 0.2 1.0
O E:PHE259 2.9 0.2 1.0
C E:PHE259 3.4 0.2 1.0
SG C:CYS55 3.6 0.2 1.0
CA E:TYR260 3.7 0.2 1.0
N E:TYR260 3.8 0.2 1.0
CB E:ASP262 3.8 0.2 1.0
CB C:CYS55 4.0 0.2 1.0
C C:SER85 4.1 0.2 1.0
OD2 E:ASP262 4.1 0.2 1.0
C E:TYR260 4.3 0.2 1.0
N C:ALA87 4.3 0.2 1.0
N E:ASP262 4.3 0.2 1.0
CA E:PHE259 4.4 0.2 1.0
CG E:ASP262 4.4 0.2 1.0
N E:LYS261 4.5 0.2 1.0
CA C:HIS86 4.6 0.2 1.0
CB C:ALA87 4.6 0.2 1.0
CA E:ASP262 4.6 0.2 1.0
O E:LYS258 4.6 0.2 1.0
CG E:LEU263 4.7 0.2 1.0
C C:HIS86 4.7 0.2 1.0
N E:LEU263 4.8 0.2 1.0
N C:HIS86 4.8 0.2 1.0
CB E:TYR260 4.9 0.2 1.0
CA C:ALA87 4.9 0.2 1.0
OG C:SER85 5.0 0.2 1.0

Mercury binding site 3 out of 13 in 2jes

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Mercury binding site 3 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg701

b:0.2
occ:0.30
 O G:PHE259 2.9 0.2 1.0
O E:SER85 3.0 0.2 1.0
C G:PHE259 3.3 0.2 1.0
SG E:CYS55 3.4 0.2 1.0
N G:TYR260 3.7 0.2 1.0
CA G:TYR260 3.7 0.2 1.0
CB E:CYS55 3.8 0.2 1.0
CB G:ASP262 4.1 0.2 1.0
CA G:PHE259 4.1 0.2 1.0
C E:SER85 4.2 0.2 1.0
N E:ALA87 4.2 0.2 1.0
CB E:ALA87 4.3 0.2 1.0
C G:TYR260 4.3 0.2 1.0
N G:ASP262 4.5 0.2 1.0
O G:LYS258 4.5 0.2 1.0
N G:LYS261 4.5 0.2 1.0
CA E:HIS86 4.6 0.2 1.0
C E:HIS86 4.7 0.2 1.0
OD2 G:ASP262 4.7 0.2 1.0
CA E:ALA87 4.7 0.2 1.0
CG G:ASP262 4.8 0.2 1.0
N E:HIS86 4.9 0.2 1.0
CA G:ASP262 4.9 0.2 1.0
CB G:TYR260 4.9 0.2 1.0
OG E:SER85 5.0 0.2 1.0

Mercury binding site 4 out of 13 in 2jes

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Mercury binding site 4 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Hg701

b:0.2
occ:0.30
 O G:SER85 2.9 0.2 1.0
O I:PHE259 3.0 0.2 1.0
C I:PHE259 3.4 0.2 1.0
CA I:TYR260 3.5 0.2 1.0
SG G:CYS55 3.5 0.2 1.0
N I:TYR260 3.6 0.2 1.0
CB I:ASP262 4.0 0.2 1.0
OD2 I:ASP262 4.0 0.2 1.0
CB G:CYS55 4.1 0.2 1.0
C G:SER85 4.1 0.2 1.0
C I:TYR260 4.1 0.2 1.0
N G:ALA87 4.2 0.2 1.0
N I:ASP262 4.3 0.2 1.0
N I:LYS261 4.4 0.2 1.0
CA I:PHE259 4.4 0.2 1.0
CA G:HIS86 4.5 0.2 1.0
CG I:ASP262 4.5 0.2 1.0
CB G:ALA87 4.5 0.2 1.0
O I:LYS258 4.6 0.2 1.0
CB I:TYR260 4.7 0.2 1.0
CG I:LEU263 4.7 0.2 1.0
C G:HIS86 4.7 0.2 1.0
CA I:ASP262 4.7 0.2 1.0
N G:HIS86 4.8 0.2 1.0
N I:LEU263 4.8 0.2 1.0
CA G:ALA87 4.9 0.2 1.0
O I:TYR260 4.9 0.2 1.0
CD2 I:LEU263 5.0 0.2 1.0

Mercury binding site 5 out of 13 in 2jes

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Mercury binding site 5 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Hg701

b:0.2
occ:0.30
 O K:PHE259 3.0 0.2 1.0
O I:SER85 3.1 0.2 1.0
C K:PHE259 3.4 0.2 1.0
SG I:CYS55 3.4 0.2 1.0
CA K:TYR260 3.5 0.2 1.0
N K:TYR260 3.6 0.2 1.0
CB I:CYS55 3.9 0.2 1.0
CB K:ASP262 4.0 0.2 1.0
N I:ALA87 4.1 0.2 1.0
C K:TYR260 4.1 0.2 1.0
C I:SER85 4.2 0.2 1.0
CA K:PHE259 4.3 0.2 1.0
CB I:ALA87 4.4 0.2 1.0
OD2 K:ASP262 4.4 0.2 1.0
N K:LYS261 4.4 0.2 1.0
N K:ASP262 4.4 0.2 1.0
CA I:HIS86 4.5 0.2 1.0
C I:HIS86 4.6 0.2 1.0
O K:LYS258 4.6 0.2 1.0
CG K:ASP262 4.6 0.2 1.0
O K:TYR260 4.7 0.2 1.0
CB K:TYR260 4.7 0.2 1.0
CA I:ALA87 4.8 0.2 1.0
CA K:ASP262 4.8 0.2 1.0
N I:HIS86 4.8 0.2 1.0
CG K:LEU263 4.9 0.2 1.0
N K:LEU263 4.9 0.2 1.0

Mercury binding site 6 out of 13 in 2jes

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Mercury binding site 6 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Hg701

b:0.2
occ:0.30
 O K:SER85 2.9 0.2 1.0
O M:PHE259 3.0 0.2 1.0
C M:PHE259 3.4 0.2 1.0
SG K:CYS55 3.4 0.2 1.0
CA M:TYR260 3.5 0.2 1.0
N M:TYR260 3.6 0.2 1.0
CB M:ASP262 3.7 0.2 1.0
OD2 M:ASP262 3.9 0.2 1.0
CB K:CYS55 3.9 0.2 1.0
C M:TYR260 4.1 0.2 1.0
C K:SER85 4.1 0.2 1.0
N K:ALA87 4.1 0.2 1.0
CG M:ASP262 4.2 0.2 1.0
N M:ASP262 4.3 0.2 1.0
N M:LYS261 4.3 0.2 1.0
CA M:PHE259 4.4 0.2 1.0
CB K:ALA87 4.5 0.2 1.0
O M:LYS258 4.5 0.2 1.0
CA M:ASP262 4.6 0.2 1.0
CA K:HIS86 4.6 0.2 1.0
CB M:TYR260 4.7 0.2 1.0
C K:HIS86 4.8 0.2 1.0
N M:LEU263 4.8 0.2 1.0
O M:TYR260 4.8 0.2 1.0
CA K:ALA87 4.9 0.2 1.0
N K:HIS86 4.9 0.2 1.0
CG M:LEU263 5.0 0.2 1.0

Mercury binding site 7 out of 13 in 2jes

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Mercury binding site 7 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Hg701

b:0.2
occ:0.30
 O M:SER85 2.9 0.2 1.0
O O:PHE259 3.0 0.2 1.0
SG M:CYS55 3.4 0.2 1.0
C O:PHE259 3.5 0.2 1.0
CB O:ASP262 3.6 0.2 1.0
CA O:TYR260 3.8 0.2 1.0
CB M:CYS55 3.8 0.2 1.0
OD2 O:ASP262 3.9 0.2 1.0
N O:TYR260 3.9 0.2 1.0
CG O:ASP262 4.1 0.2 1.0
C M:SER85 4.1 0.2 1.0
N M:ALA87 4.2 0.2 1.0
N O:ASP262 4.3 0.2 1.0
C O:TYR260 4.3 0.2 1.0
CA O:PHE259 4.5 0.2 1.0
CB M:ALA87 4.5 0.2 1.0
CA O:ASP262 4.5 0.2 1.0
CA M:HIS86 4.6 0.2 1.0
N O:LYS261 4.6 0.2 1.0
O O:LYS258 4.7 0.2 1.0
C M:HIS86 4.7 0.2 1.0
N M:HIS86 4.8 0.2 1.0
CA M:ALA87 4.9 0.2 1.0
N O:LEU263 4.9 0.2 1.0
O O:TYR260 5.0 0.2 1.0

Mercury binding site 8 out of 13 in 2jes

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Mercury binding site 8 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Hg701

b:0.2
occ:0.30
 O O:SER85 2.8 0.2 1.0
SG O:CYS55 2.9 0.2 1.0
O Q:PHE259 3.1 0.2 1.0
CB O:CYS55 3.6 0.2 1.0
C Q:PHE259 3.6 0.2 1.0
CB Q:ASP262 3.9 0.2 1.0
C O:SER85 4.0 0.2 1.0
CA Q:TYR260 4.0 0.2 1.0
N Q:TYR260 4.1 0.2 1.0
N O:ALA87 4.1 0.2 1.0
CB O:ALA87 4.4 0.2 1.0
OD2 Q:ASP262 4.4 0.2 1.0
O Q:LYS258 4.4 0.2 1.0
CA O:HIS86 4.5 0.2 1.0
CA Q:PHE259 4.5 0.2 1.0
C O:HIS86 4.5 0.2 1.0
N Q:ASP262 4.6 0.2 1.0
C Q:TYR260 4.6 0.2 1.0
CG Q:ASP262 4.6 0.2 1.0
N O:HIS86 4.7 0.2 1.0
N Q:LYS261 4.8 0.2 1.0
CA O:ALA87 4.8 0.2 1.0
CA Q:ASP262 4.8 0.2 1.0
OG O:SER85 4.9 0.2 1.0
CA O:CYS55 4.9 0.2 1.0

Mercury binding site 9 out of 13 in 2jes

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Mercury binding site 9 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Hg701

b:0.2
occ:0.30
 SG Q:CYS55 2.9 0.2 1.0
O Q:SER85 3.0 0.2 1.0
O S:PHE259 3.1 0.2 1.0
CB Q:CYS55 3.4 0.2 1.0
C S:PHE259 3.5 0.2 1.0
N S:TYR260 4.0 0.2 1.0
CA S:TYR260 4.1 0.2 1.0
N Q:ALA87 4.1 0.2 1.0
CB S:ASP262 4.1 0.2 1.0
C Q:SER85 4.2 0.2 1.0
CA S:PHE259 4.2 0.2 1.0
CB Q:ALA87 4.3 0.2 1.0
O S:LYS258 4.3 0.2 1.0
C Q:HIS86 4.6 0.2 1.0
CA Q:ALA87 4.6 0.2 1.0
C S:TYR260 4.6 0.2 1.0
CA Q:HIS86 4.6 0.2 1.0
N S:ASP262 4.7 0.2 1.0
N S:LYS261 4.8 0.2 1.0
CG S:ASP262 4.8 0.2 1.0
CA Q:CYS55 4.8 0.2 1.0
N Q:HIS86 4.9 0.2 1.0
OD2 S:ASP262 4.9 0.2 1.0
OG Q:SER85 4.9 0.2 1.0

Mercury binding site 10 out of 13 in 2jes

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Mercury binding site 10 out of 13 in the Portal Protein (GP6) From Bacteriophage SPP1


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Portal Protein (GP6) From Bacteriophage SPP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Hg701

b:0.2
occ:0.30
 O U:PHE259 3.0 0.2 1.0
O S:SER85 3.1 0.2 1.0
SG S:CYS55 3.4 0.2 1.0
C U:PHE259 3.5 0.2 1.0
CA U:TYR260 3.6 0.2 1.0
N U:TYR260 3.8 0.2 1.0
CB U:ASP262 3.9 0.2 1.0
CB S:CYS55 4.0 0.2 1.0
N S:ALA87 4.2 0.2 1.0
C U:TYR260 4.2 0.2 1.0
C S:SER85 4.3 0.2 1.0
CB S:ALA87 4.4 0.2 1.0
N U:ASP262 4.4 0.2 1.0
CA U:PHE259 4.5 0.2 1.0
N U:LYS261 4.5 0.2 1.0
CA S:HIS86 4.6 0.2 1.0
CG U:LEU263 4.7 0.2 1.0
C S:HIS86 4.7 0.2 1.0
CA U:ASP262 4.7 0.2 1.0
OD2 U:ASP262 4.7 0.2 1.0
CB U:TYR260 4.7 0.2 1.0
O U:TYR260 4.8 0.2 1.0
N U:LEU263 4.8 0.2 1.0
CA S:ALA87 4.8 0.2 1.0
O U:LYS258 4.8 0.2 1.0
CG U:ASP262 4.8 0.2 1.0
N S:HIS86 4.9 0.2 1.0

Reference:

A.A.Lebedev, M.H.Krause, A.L.Isidro, A.A.Vagin, E.V.Orlova, J.Turner, E.J.Dodson, P.Tavares, A.A.Antson. Structural Framework For Dna Translocation Via the Viral Portal Protein Embo J. V. 26 1984 2007.
ISSN: ISSN 0261-4189
PubMed: 17363899
DOI: 10.1038/SJ.EMBOJ.7601643
Page generated: Sun Dec 13 19:07:26 2020

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