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Tantalum in PDB 5eul: Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate

Protein crystallography data

The structure of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate, PDB code: 5eul was solved by L.Li, E.Park, J.Ling, J.Ingram, H.Ploegh, T.A.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.85 / 3.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 127.798, 127.798, 554.772, 90.00, 90.00, 120.00
R / Rfree (%) 29.5 / 31.5

Other elements in 5eul:

The structure of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 1 atom
Bromine (Br) 216 atoms

Tantalum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 108;

Binding sites:

The binding sites of Tantalum atom in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate (pdb code 5eul). This binding sites where shown within 5.0 Angstroms radius around Tantalum atom.
In total 108 binding sites of Tantalum where determined in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate, PDB code: 5eul:
Jump to Tantalum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tantalum binding site 1 out of 108 in 5eul

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Tantalum binding site 1 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 1 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1004

b:0.9
occ:0.93
TA1 A:TBR1004 0.0 0.9 0.9
BR3 A:TBR1004 2.6 0.1 0.9
BR2 A:TBR1004 2.6 0.9 0.9
BR1 A:TBR1004 2.6 0.8 0.9
BR4 A:TBR1004 2.6 0.1 0.9
TA5 A:TBR1004 2.9 0.2 0.9
TA2 A:TBR1004 2.9 0.6 0.9
TA6 A:TBR1004 2.9 0.1 0.9
TA3 A:TBR1004 2.9 0.0 0.9
NE2 A:GLN598 4.0 0.7 1.0
TA4 A:TBR1004 4.1 0.8 0.9
BR6 A:TBR1004 4.1 0.8 0.9
BRC A:TBR1004 4.2 0.3 0.9
BRB A:TBR1004 4.2 0.4 0.9
BR5 A:TBR1004 4.2 0.5 0.9
OE1 A:GLN598 4.4 0.7 1.0
CD A:GLN598 4.7 0.5 1.0

Tantalum binding site 2 out of 108 in 5eul

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Tantalum binding site 2 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 2 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1004

b:0.6
occ:0.93
TA2 A:TBR1004 0.0 0.6 0.9
BRC A:TBR1004 2.6 0.3 0.9
BR5 A:TBR1004 2.6 0.5 0.9
BR9 A:TBR1004 2.6 0.5 0.9
BR1 A:TBR1004 2.6 0.8 0.9
TA4 A:TBR1004 2.9 0.8 0.9
TA1 A:TBR1004 2.9 0.9 0.9
TA3 A:TBR1004 2.9 0.0 0.9
TA6 A:TBR1004 2.9 0.1 0.9
TA5 A:TBR1004 4.1 0.2 0.9
BR2 A:TBR1004 4.1 0.9 0.9
BRA A:TBR1004 4.2 0.5 0.9
BR4 A:TBR1004 4.2 0.1 0.9
BR8 A:TBR1004 4.2 0.7 0.9
N Y:GLU103 4.4 0.8 1.0
OE1 Y:GLU103 4.4 0.4 1.0
CA Y:GLU103 4.8 0.2 1.0

Tantalum binding site 3 out of 108 in 5eul

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Tantalum binding site 3 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 3 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1004

b:0.0
occ:0.93
TA3 A:TBR1004 0.0 0.0 0.9
BRA A:TBR1004 2.6 0.5 0.9
BR6 A:TBR1004 2.6 0.8 0.9
BR5 A:TBR1004 2.6 0.5 0.9
BR2 A:TBR1004 2.6 0.9 0.9
TA2 A:TBR1004 2.9 0.6 0.9
TA4 A:TBR1004 2.9 0.8 0.9
TA1 A:TBR1004 2.9 0.9 0.9
TA5 A:TBR1004 2.9 0.2 0.9
BR1 A:TBR1004 4.2 0.8 0.9
BR9 A:TBR1004 4.2 0.5 0.9
BR3 A:TBR1004 4.2 0.1 0.9
TA6 A:TBR1004 4.2 0.1 0.9
BR7 A:TBR1004 4.2 0.6 0.9

Tantalum binding site 4 out of 108 in 5eul

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Tantalum binding site 4 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 4 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1004

b:0.8
occ:0.93
TA4 A:TBR1004 0.0 0.8 0.9
BR9 A:TBR1004 2.6 0.5 0.9
BR8 A:TBR1004 2.6 0.7 0.9
BR7 A:TBR1004 2.6 0.6 0.9
BRA A:TBR1004 2.6 0.5 0.9
TA2 A:TBR1004 2.9 0.6 0.9
TA5 A:TBR1004 2.9 0.2 0.9
TA3 A:TBR1004 2.9 0.0 0.9
TA6 A:TBR1004 2.9 0.1 0.9
TA1 A:TBR1004 4.1 0.9 0.9
BRC A:TBR1004 4.1 0.3 0.9
BR6 A:TBR1004 4.2 0.8 0.9
BR5 A:TBR1004 4.2 0.5 0.9
BRB A:TBR1004 4.2 0.4 0.9

Tantalum binding site 5 out of 108 in 5eul

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Tantalum binding site 5 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 5 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1004

b:0.2
occ:0.93
TA5 A:TBR1004 0.0 0.2 0.9
BR6 A:TBR1004 2.6 0.8 0.9
BRB A:TBR1004 2.6 0.4 0.9
BR7 A:TBR1004 2.6 0.6 0.9
BR3 A:TBR1004 2.6 0.1 0.9
TA1 A:TBR1004 2.9 0.9 0.9
TA4 A:TBR1004 2.9 0.8 0.9
TA6 A:TBR1004 2.9 0.1 0.9
TA3 A:TBR1004 2.9 0.0 0.9
TA2 A:TBR1004 4.1 0.6 0.9
BR8 A:TBR1004 4.2 0.7 0.9
BR4 A:TBR1004 4.2 0.1 0.9
BRA A:TBR1004 4.2 0.5 0.9
BR2 A:TBR1004 4.2 0.9 0.9

Tantalum binding site 6 out of 108 in 5eul

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Tantalum binding site 6 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 6 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1004

b:0.1
occ:0.93
TA6 A:TBR1004 0.0 0.1 0.9
BR4 A:TBR1004 2.6 0.1 0.9
BRC A:TBR1004 2.6 0.3 0.9
BRB A:TBR1004 2.6 0.4 0.9
BR8 A:TBR1004 2.6 0.7 0.9
TA5 A:TBR1004 2.9 0.2 0.9
TA1 A:TBR1004 2.9 0.9 0.9
TA4 A:TBR1004 2.9 0.8 0.9
TA2 A:TBR1004 2.9 0.6 0.9
BR7 A:TBR1004 4.2 0.6 0.9
BR3 A:TBR1004 4.2 0.1 0.9
BR9 A:TBR1004 4.2 0.5 0.9
TA3 A:TBR1004 4.2 0.0 0.9
BR1 A:TBR1004 4.2 0.8 0.9

Tantalum binding site 7 out of 108 in 5eul

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Tantalum binding site 7 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 7 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1005

b:0.1
occ:0.84
TA1 A:TBR1005 0.0 0.1 0.8
BR3 A:TBR1005 2.6 0.2 0.8
BR2 A:TBR1005 2.6 1.0 0.8
BR1 A:TBR1005 2.6 0.3 0.8
BR4 A:TBR1005 2.6 0.4 0.8
TA5 A:TBR1005 2.9 0.5 0.8
TA2 A:TBR1005 2.9 0.5 0.8
TA6 A:TBR1005 2.9 0.9 0.8
TA3 A:TBR1005 2.9 0.7 0.8
TA4 A:TBR1005 4.1 0.7 0.8
BR6 A:TBR1005 4.1 1.0 0.8
BRC A:TBR1005 4.2 0.2 0.8
BRB A:TBR1005 4.2 0.6 0.8
BR5 A:TBR1005 4.2 0.8 0.8
CE A:MET801 4.8 0.9 1.0

Tantalum binding site 8 out of 108 in 5eul

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Tantalum binding site 8 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 8 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1005

b:0.5
occ:0.84
TA2 A:TBR1005 0.0 0.5 0.8
BRC A:TBR1005 2.6 0.2 0.8
BR5 A:TBR1005 2.6 0.8 0.8
BR9 A:TBR1005 2.6 0.6 0.8
BR1 A:TBR1005 2.6 0.3 0.8
TA4 A:TBR1005 2.9 0.7 0.8
TA1 A:TBR1005 2.9 0.1 0.8
TA3 A:TBR1005 2.9 0.7 0.8
TA6 A:TBR1005 2.9 0.9 0.8
CG A:GLU798 3.4 0.9 1.0
OE2 A:GLU798 3.8 0.1 1.0
CD A:GLU798 3.9 0.2 1.0
TA5 A:TBR1005 4.1 0.5 0.8
BRA A:TBR1005 4.2 0.1 0.8
BR2 A:TBR1005 4.2 1.0 0.8
BR4 A:TBR1005 4.2 0.4 0.8
BR8 A:TBR1005 4.2 0.3 0.8
CB A:GLU798 4.6 0.4 1.0
OE1 A:GLU798 4.9 0.5 1.0

Tantalum binding site 9 out of 108 in 5eul

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Tantalum binding site 9 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 9 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1005

b:0.7
occ:0.84
TA3 A:TBR1005 0.0 0.7 0.8
BRA A:TBR1005 2.6 0.1 0.8
BR6 A:TBR1005 2.6 1.0 0.8
BR5 A:TBR1005 2.6 0.8 0.8
BR2 A:TBR1005 2.6 1.0 0.8
TA2 A:TBR1005 2.9 0.5 0.8
TA4 A:TBR1005 2.9 0.7 0.8
TA5 A:TBR1005 2.9 0.5 0.8
TA1 A:TBR1005 2.9 0.1 0.8
OE1 A:GLU802 3.7 0.3 1.0
CD A:GLU802 4.0 0.8 1.0
OE2 A:GLU802 4.0 0.1 1.0
BR1 A:TBR1005 4.2 0.3 0.8
BR3 A:TBR1005 4.2 0.2 0.8
BR9 A:TBR1005 4.2 0.6 0.8
TA6 A:TBR1005 4.2 0.9 0.8
BR7 A:TBR1005 4.2 0.9 0.8
CB A:GLU802 4.9 0.0 1.0
CG A:GLU802 4.9 0.3 1.0

Tantalum binding site 10 out of 108 in 5eul

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Tantalum binding site 10 out of 108 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 10 of Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1005

b:0.7
occ:0.84
TA4 A:TBR1005 0.0 0.7 0.8
BR9 A:TBR1005 2.6 0.6 0.8
BR8 A:TBR1005 2.6 0.3 0.8
BR7 A:TBR1005 2.6 0.9 0.8
BRA A:TBR1005 2.6 0.1 0.8
TA2 A:TBR1005 2.9 0.5 0.8
TA5 A:TBR1005 2.9 0.5 0.8
TA3 A:TBR1005 2.9 0.7 0.8
TA6 A:TBR1005 2.9 0.9 0.8
TA1 A:TBR1005 4.1 0.1 0.8
BRC A:TBR1005 4.1 0.2 0.8
BR6 A:TBR1005 4.2 1.0 0.8
BR5 A:TBR1005 4.2 0.8 0.8
BRB A:TBR1005 4.2 0.6 0.8

Reference:

L.Li, E.Park, J.Ling, J.Ingram, H.Ploegh, T.A.Rapoport. Crystal Structure of A Substrate-Engaged Secy Protein-Translocation Channel. Nature V. 531 395 2016.
ISSN: ESSN 1476-4687
PubMed: 26950603
DOI: 10.1038/NATURE17163
Page generated: Wed Dec 16 02:26:17 2020

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