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Mercury in PDB 3erz: Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel

Enzymatic activity of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel

All present enzymatic activity of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel:
1.16.3.1;

Protein crystallography data

The structure of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel, PDB code: 3erz was solved by L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.80 / 3.06
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 170.941, 170.941, 190.144, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 25.6

Other elements in 3erz:

The structure of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Zinc (Zn) 5 atoms

Mercury Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Mercury atom in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel (pdb code 3erz). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 12 binding sites of Mercury where determined in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel, PDB code: 3erz:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Mercury binding site 1 out of 12 in 3erz

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Mercury binding site 1 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg524

b:66.0
occ:0.50
SG A:CYS130 2.5 42.0 1.0
O A:HOH823 2.9 28.8 1.0
O A:ASP126 3.5 42.5 1.0
CB A:CYS130 3.6 46.7 1.0
CA A:PRO127 3.7 46.6 1.0
C A:ASP126 3.7 44.3 1.0
CA A:THR122 3.8 43.8 1.0
N A:PRO127 3.8 45.0 1.0
O A:ALA121 4.0 42.9 1.0
OG1 A:THR122 4.1 46.9 1.0
N A:THR122 4.1 42.1 1.0
N A:ASP126 4.2 46.5 1.0
C A:ALA121 4.3 42.1 1.0
CB A:THR122 4.5 43.8 1.0
CB A:PRO127 4.6 46.0 1.0
CA A:ASP126 4.6 44.1 1.0
C A:PRO127 4.6 43.7 1.0
C A:THR122 4.7 46.4 1.0
O A:THR122 4.8 47.2 1.0
O A:PRO127 4.8 43.6 1.0
C A:ASN125 4.8 45.5 1.0
CD A:PRO127 4.9 44.1 1.0
CA A:CYS130 4.9 45.0 1.0
CA A:ASN125 4.9 47.3 1.0
CB A:ALA121 5.0 45.4 1.0

Mercury binding site 2 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 2 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Hg526

b:53.7
occ:0.50
SG B:CYS130 2.3 31.4 1.0
CB B:CYS130 3.5 37.0 1.0
O B:ALA121 3.6 49.3 1.0
O B:ASP126 3.7 39.4 1.0
CA B:THR122 3.7 41.9 1.0
C B:ASP126 3.8 37.8 1.0
CA B:PRO127 3.8 37.8 1.0
N B:PRO127 3.8 37.6 1.0
OG1 B:THR122 3.9 40.8 1.0
N B:ASP126 4.0 43.9 1.0
O B:HOH717 4.1 35.2 1.0
C B:ALA121 4.2 44.1 1.0
O F:HOH558 4.2 32.6 1.0
N B:THR122 4.3 41.5 1.0
CB B:THR122 4.3 39.1 1.0
C B:ASN125 4.5 43.3 1.0
CA B:ASP126 4.6 41.5 1.0
CA B:ASN125 4.6 41.5 1.0
CB B:PRO127 4.7 40.7 1.0
CG2 B:THR122 4.7 38.5 1.0
C B:THR122 4.8 44.3 1.0
CD B:PRO127 4.8 42.2 1.0
O B:THR122 4.8 47.7 1.0
CA B:CYS130 4.8 39.3 1.0
C B:PRO127 4.8 36.4 1.0
O B:PRO127 5.0 36.1 1.0
N B:CYS130 5.0 40.5 1.0

Mercury binding site 3 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 3 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Hg525

b:66.0
occ:0.50
SG C:CYS130 2.4 45.2 1.0
O A:HOH832 2.8 35.7 1.0
O A:HOH830 3.4 36.1 1.0
CB C:CYS130 3.5 48.5 1.0
O C:ASP126 3.7 46.8 1.0
C C:ASP126 3.8 47.1 1.0
N C:PRO127 3.8 46.7 1.0
CA C:PRO127 3.8 45.2 1.0
CA C:THR122 3.8 51.3 1.0
OG1 C:THR122 4.0 50.0 1.0
O C:ALA121 4.0 46.4 1.0
N C:ASP126 4.0 54.6 1.0
N C:THR122 4.3 50.3 1.0
CB C:THR122 4.3 48.2 1.0
CG2 C:THR122 4.3 50.0 1.0
C C:ALA121 4.3 48.8 1.0
CA C:ASP126 4.6 48.0 1.0
CB C:PRO127 4.6 43.1 1.0
CD C:PRO127 4.6 46.6 1.0
CA C:CYS130 4.8 47.9 1.0
C C:ASN125 4.8 55.8 1.0
C C:PRO127 4.9 47.0 1.0
CA C:ASN125 4.9 54.2 1.0
C C:THR122 4.9 51.0 1.0
O C:THR122 4.9 48.9 1.0

Mercury binding site 4 out of 12 in 3erz

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Mercury binding site 4 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Hg527

b:63.3
occ:0.50
SG D:CYS130 2.4 41.9 1.0
CB D:CYS130 3.4 44.5 1.0
CA D:THR122 3.5 40.0 1.0
OG1 D:THR122 3.6 40.5 1.0
C D:ASP126 3.7 43.5 1.0
O D:ASP126 3.8 42.6 1.0
N D:PRO127 3.8 40.2 1.0
CA D:PRO127 3.8 38.7 1.0
N D:ASP126 3.9 43.0 1.0
O D:ALA121 3.9 37.4 1.0
CB D:THR122 4.0 36.5 1.0
N D:THR122 4.1 39.7 1.0
C D:ALA121 4.2 40.9 1.0
CG2 D:THR122 4.4 35.5 1.0
CA D:ASP126 4.5 41.7 1.0
C D:THR122 4.6 42.0 1.0
O D:THR122 4.6 40.9 1.0
CB D:PRO127 4.7 39.7 1.0
C D:ASN125 4.7 44.0 1.0
CA D:ASN125 4.7 43.9 1.0
CA D:CYS130 4.8 42.8 1.0
CD D:PRO127 4.8 40.5 1.0
C D:PRO127 4.9 39.9 1.0

Mercury binding site 5 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 5 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Hg523

b:66.1
occ:0.50
SG E:CYS130 2.4 36.4 1.0
O E:HOH638 3.1 29.4 1.0
CB E:CYS130 3.4 41.4 1.0
O C:HOH542 3.4 32.7 1.0
CA E:THR122 3.7 43.8 1.0
CA E:PRO127 3.7 43.3 1.0
O E:ASP126 3.8 45.3 1.0
N E:PRO127 3.8 45.1 1.0
C E:ASP126 3.9 46.9 1.0
O E:ALA121 3.9 40.0 1.0
OG1 E:THR122 4.1 41.9 1.0
N E:ASP126 4.2 44.3 1.0
N E:THR122 4.2 42.0 1.0
C E:ALA121 4.3 41.3 1.0
CB E:THR122 4.4 40.7 1.0
CB E:PRO127 4.6 40.1 1.0
CG2 E:THR122 4.6 42.5 1.0
O E:THR122 4.7 45.0 1.0
C E:THR122 4.7 44.2 1.0
CA E:ASP126 4.7 48.1 1.0
CA E:CYS130 4.7 43.2 1.0
C E:PRO127 4.8 42.5 1.0
CD E:PRO127 4.8 42.8 1.0
O E:PRO127 4.9 42.5 1.0
C E:ASN125 4.9 45.7 1.0
CA E:ASN125 4.9 42.9 1.0

Mercury binding site 6 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 6 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Hg528

b:61.5
occ:0.50
SG F:CYS130 2.3 40.6 1.0
O F:HOH565 3.1 45.9 1.0
CB F:CYS130 3.3 39.9 1.0
CA F:PRO127 3.6 39.5 1.0
O F:ASP126 3.6 40.3 1.0
CA F:THR122 3.6 41.4 1.0
N F:PRO127 3.7 39.6 1.0
C F:ASP126 3.8 41.1 1.0
OG1 F:THR122 4.0 44.5 1.0
N F:THR122 4.2 42.3 1.0
CB F:THR122 4.2 44.2 1.0
N F:ASP126 4.3 44.7 1.0
O F:ALA121 4.3 45.0 1.0
CB F:PRO127 4.3 36.6 1.0
CG2 F:THR122 4.4 43.0 1.0
C F:ALA121 4.5 43.9 1.0
CA F:CYS130 4.6 40.0 1.0
C F:PRO127 4.6 40.6 1.0
O F:THR122 4.7 48.4 1.0
CD F:PRO127 4.7 39.3 1.0
C F:THR122 4.7 44.8 1.0
CA F:ASP126 4.7 43.7 1.0
O F:PRO127 4.8 41.5 1.0
O F:HOH560 4.8 35.3 1.0
N F:CYS130 4.9 40.1 1.0
C F:ASN125 4.9 45.7 1.0

Mercury binding site 7 out of 12 in 3erz

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Mercury binding site 7 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Hg529

b:70.3
occ:0.50
SG G:CYS130 2.3 37.7 1.0
O G:HOH823 2.4 21.7 1.0
O G:HOH824 3.2 32.8 1.0
O G:HOH819 3.3 45.7 1.0
CB G:CYS130 3.4 46.6 1.0
CA G:THR122 3.5 45.1 1.0
OG1 G:THR122 3.7 38.8 1.0
O G:ASP126 3.7 45.5 1.0
N G:THR122 3.9 48.2 1.0
O G:ALA121 4.0 45.5 1.0
C G:ASP126 4.0 46.8 1.0
CA G:PRO127 4.1 41.7 1.0
C G:ALA121 4.1 45.5 1.0
CB G:THR122 4.1 43.5 1.0
N G:PRO127 4.2 43.4 1.0
N G:ASP126 4.4 48.4 1.0
C G:THR122 4.6 46.1 1.0
O G:THR122 4.6 44.9 1.0
CG2 G:THR122 4.8 45.4 1.0
CA G:CYS130 4.8 48.8 1.0
CB G:ALA121 4.8 44.4 1.0
CA G:ASP126 4.9 48.2 1.0
C G:PRO127 4.9 44.2 1.0
O G:PRO127 5.0 44.9 1.0
N G:CYS130 5.0 46.2 1.0

Mercury binding site 8 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 8 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Hg533

b:59.6
occ:0.50
SG H:CYS130 2.5 31.7 1.0
CB H:CYS130 3.7 41.5 1.0
O H:ALA121 3.8 38.8 1.0
O L:HOH541 3.8 34.0 1.0
CA H:PRO127 3.8 40.7 1.0
N H:PRO127 3.8 41.0 1.0
CA H:THR122 3.8 42.8 1.0
O H:ASP126 3.8 38.4 1.0
C H:ASP126 3.8 40.6 1.0
OG1 H:THR122 4.0 40.0 1.0
N H:ASP126 4.0 43.9 1.0
C H:ALA121 4.3 42.2 1.0
N H:THR122 4.4 43.1 1.0
CB H:THR122 4.4 41.3 1.0
C H:ASN125 4.5 43.7 1.0
CA H:ASN125 4.5 44.2 1.0
CB H:PRO127 4.6 40.1 1.0
CA H:ASP126 4.6 41.8 1.0
CD H:PRO127 4.7 42.4 1.0
CG2 H:THR122 4.7 40.4 1.0
O H:THR122 4.8 45.0 1.0
C H:THR122 4.8 44.3 1.0
C H:PRO127 4.9 37.9 1.0

Mercury binding site 9 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 9 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 9 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Hg531

b:65.6
occ:0.50
SG I:CYS130 2.6 35.4 1.0
O G:HOH820 2.8 38.2 1.0
CB I:CYS130 3.5 43.4 1.0
CA I:PRO127 3.6 46.6 1.0
N I:PRO127 3.6 45.2 1.0
O G:HOH826 3.7 34.7 1.0
C I:ASP126 3.7 45.3 1.0
O I:ASP126 3.8 45.2 1.0
N I:ASP126 4.1 51.5 1.0
CA I:THR122 4.1 45.7 1.0
O I:ALA121 4.2 45.8 1.0
OG1 I:THR122 4.3 48.4 1.0
CB I:PRO127 4.3 45.5 1.0
CD I:PRO127 4.4 49.5 1.0
CG2 I:THR122 4.5 44.8 1.0
CB I:THR122 4.5 45.1 1.0
CA I:ASP126 4.6 48.3 1.0
N I:THR122 4.6 41.9 1.0
C I:ALA121 4.6 42.0 1.0
C I:PRO127 4.7 45.4 1.0
C I:ASN125 4.8 51.6 1.0
CA I:CYS130 4.9 44.7 1.0
CA I:ASN125 4.9 51.0 1.0
O I:PRO127 5.0 45.0 1.0

Mercury binding site 10 out of 12 in 3erz

Go back to Mercury Binding Sites List in 3erz
Mercury binding site 10 out of 12 in the Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 10 of Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Mercury Ions on the Three-Fold Channel within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Hg532

b:63.2
occ:0.50
SG J:CYS130 2.4 35.7 1.0
O J:HOH819 3.4 18.9 1.0
CB J:CYS130 3.4 45.4 1.0
CA J:THR122 3.4 42.4 1.0
OG1 J:THR122 3.5 36.8 1.0
C J:ASP126 3.8 41.2 1.0
O J:ASP126 3.8 41.0 1.0
N J:PRO127 3.8 40.6 1.0
O H:HOH721 3.9 41.7 1.0
CA J:PRO127 3.9 42.4 1.0
O J:ALA121 3.9 34.7 1.0
CB J:THR122 4.0 37.5 1.0
N J:ASP126 4.0 47.8 1.0
N J:THR122 4.0 40.6 1.0
C J:ALA121 4.2 36.9 1.0
CG2 J:THR122 4.3 36.1 1.0
C J:THR122 4.5 45.3 1.0
O J:THR122 4.6 43.7 1.0
CA J:ASP126 4.6 43.0 1.0
C J:ASN125 4.7 47.1 1.0
CA J:CYS130 4.8 42.5 1.0
CA J:ASN125 4.8 44.4 1.0
CB J:PRO127 4.8 40.2 1.0
CD J:PRO127 4.8 41.4 1.0
C J:PRO127 4.9 42.6 1.0

Reference:

C.A.Butts, J.Swift, S.G.Kang, L.Di Costanzo, D.W.Christianson, J.G.Saven, I.J.Dmochowski. Directing Noble Metal Ion Chemistry Within A Designed Ferritin Protein. Biochemistry V. 47 12729 2008.
ISSN: ISSN 0006-2960
PubMed: 18991401
DOI: 10.1021/BI8016735
Page generated: Wed Oct 28 18:42:30 2020

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