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Gadolinium in PDB 4x8i: De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase

Enzymatic activity of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase

All present enzymatic activity of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase:
3.4.11.15;

Protein crystallography data

The structure of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase, PDB code: 4x8i was solved by M.Colombo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.06 / 2.50
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 203.908, 203.908, 112.443, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.8

Other elements in 4x8i:

The structure of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase also contains other interesting chemical elements:

Cobalt (Co) 3 atoms
Zinc (Zn) 3 atoms
Chlorine (Cl) 3 atoms

Gadolinium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Gadolinium atom in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase (pdb code 4x8i). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 11 binding sites of Gadolinium where determined in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase, PDB code: 4x8i:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gadolinium binding site 1 out of 11 in 4x8i

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Gadolinium binding site 1 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd404

b:87.3
occ:0.60
OE2 A:GLU299 3.5 65.9 1.0
NH1 A:ARG298 4.0 57.7 1.0
CD A:GLU299 4.2 61.1 1.0
CG A:GLU299 4.5 48.2 1.0
OD2 A:ASP222 4.6 53.2 1.0

Gadolinium binding site 2 out of 11 in 4x8i

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Gadolinium binding site 2 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd405

b:0.5
occ:0.60
OE2 A:GLU168 2.6 96.6 1.0
CD A:GLU168 3.7 90.6 1.0
OE1 A:GLU168 4.4 94.2 1.0
CG A:GLU168 4.6 82.1 1.0

Gadolinium binding site 3 out of 11 in 4x8i

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Gadolinium binding site 3 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd406

b:86.7
occ:0.60
OD2 A:ASP132 2.7 95.4 1.0
CG A:ASP132 3.5 92.1 1.0
O A:HOH554 3.6 44.2 1.0
OD2 A:ASP130 3.9 90.8 1.0
OD1 A:ASP130 3.9 90.3 1.0
OD1 A:ASP132 4.0 93.0 1.0
CG A:ASP130 4.3 88.7 1.0
CB A:ASP132 4.5 88.9 1.0
CE B:LYS242 4.7 70.7 1.0

Gadolinium binding site 4 out of 11 in 4x8i

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Gadolinium binding site 4 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd404

b:96.4
occ:0.60
OE2 B:GLU275 2.7 77.8 1.0
OE1 B:GLU275 2.7 81.8 1.0
CD B:GLU275 3.0 74.5 1.0
CG B:GLU275 4.4 66.4 1.0

Gadolinium binding site 5 out of 11 in 4x8i

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Gadolinium binding site 5 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd405

b:0.4
occ:0.60
OE1 B:GLU194 3.6 99.9 1.0
CD B:GLU194 4.7 95.0 1.0

Gadolinium binding site 6 out of 11 in 4x8i

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Gadolinium binding site 6 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd406

b:80.0
occ:0.60
O B:HOH560 2.8 50.5 1.0
O B:HOH561 2.9 49.7 1.0
O A:HOH580 3.7 63.6 1.0
OE2 B:GLU299 3.9 74.6 1.0
NH1 B:ARG298 4.3 49.2 1.0
CD B:GLU299 4.5 69.4 1.0
OD2 B:ASP222 4.5 49.9 1.0
CG B:GLU299 4.7 61.0 1.0

Gadolinium binding site 7 out of 11 in 4x8i

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Gadolinium binding site 7 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 7 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Gd407

b:85.8
occ:0.60
OD2 B:ASP132 2.7 97.9 1.0
OD1 B:ASP132 2.8 0.4 1.0
CG B:ASP132 3.0 95.5 1.0
NZ C:LYS242 3.8 65.3 1.0
OD1 B:ASP130 3.8 90.4 1.0
OD2 B:ASP130 4.2 91.4 1.0
CB B:ASP132 4.3 89.3 1.0
CE C:LYS242 4.5 63.8 1.0
CG B:ASP130 4.5 90.4 1.0
N B:ASP132 4.6 77.1 1.0
CA B:ASP132 5.0 81.6 1.0

Gadolinium binding site 8 out of 11 in 4x8i

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Gadolinium binding site 8 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 8 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd404

b:61.4
occ:0.60
N4 C:DO3408 2.3 81.3 0.6
O3 C:DO3408 2.5 81.0 0.6
O5 C:DO3408 2.5 76.8 0.6
OE2 C:GLU275 2.7 73.1 1.0
O1 C:DO3408 2.7 94.9 0.6
OE1 C:GLU275 2.7 70.3 1.0
N3 C:DO3408 2.8 80.7 0.6
C13 C:DO3408 2.9 77.3 0.6
N2 C:DO3408 3.0 82.4 0.6
N1 C:DO3408 3.0 85.9 0.6
CD C:GLU275 3.0 68.0 1.0
C11 C:DO3408 3.3 81.4 0.6
C14 C:DO3408 3.3 79.0 0.6
C7 C:DO3408 3.4 82.3 0.6
C6 C:DO3408 3.4 80.8 0.6
C9 C:DO3408 3.4 93.4 0.6
C5 C:DO3408 3.5 80.0 0.6
O6 C:DO3408 3.6 76.5 0.6
C12 C:DO3408 3.6 81.9 0.6
C10 C:DO3408 3.7 89.4 0.6
C4 C:DO3408 3.7 81.0 0.6
C8 C:DO3408 3.7 84.0 0.6
C3 C:DO3408 3.8 81.6 0.6
C1 C:DO3408 4.0 86.1 0.6
C2 C:DO3408 4.0 85.1 0.6
O4 C:DO3408 4.3 82.7 0.6
O2 C:DO3408 4.4 95.8 0.6
CG C:GLU275 4.5 61.7 1.0

Gadolinium binding site 9 out of 11 in 4x8i

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Gadolinium binding site 9 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 9 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd405

b:0.3
occ:0.60
OE2 C:GLU148 2.8 78.1 1.0
OE1 C:GLU148 2.8 77.5 1.0
CD C:GLU148 3.1 74.3 1.0
CG C:GLU148 4.7 66.1 1.0
NZ C:LYS104 4.9 58.8 1.0

Gadolinium binding site 10 out of 11 in 4x8i

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Gadolinium binding site 10 out of 11 in the De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 10 of De Novo Crystal Structure of the Pyrococcus Furiosus TET3 Aminopeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Gd406

b:0.9
occ:0.60
OE2 C:GLU299 3.4 75.8 1.0
CD C:GLU299 3.9 73.4 1.0
CG C:GLU299 4.2 62.2 1.0
OD2 C:ASP222 4.3 54.0 1.0
NE C:ARG298 4.5 41.7 1.0
OE1 C:GLU299 4.8 82.5 1.0

Reference:

M.Colombo, E.Girard, B.Franzetti. Tuned By Metals: the Tet Peptidase Activity Is Controlled By 3 Metal Binding Sites. Sci Rep V. 6 20876 2016.
ISSN: ESSN 2045-2322
PubMed: 26853450
DOI: 10.1038/SREP20876
Page generated: Sun Dec 13 19:00:00 2020

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