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

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

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
Tantalum	(Ta)	108 atoms

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 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 216;

Binding sites:

The binding sites of Bromine 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 Bromine atom.
In total 216 binding sites of Bromine where determined in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate, PDB code: 5eul:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.8 occ:0.93 BR1 A:TBR1004 0.0 0.8 0.9 TA2 A:TBR1004 2.6 0.6 0.9 TA1 A:TBR1004 2.6 0.9 0.9 OE1 A:GLN598 3.5 0.7 1.0 BR2 A:TBR1004 3.6 0.9 0.9 BR5 A:TBR1004 3.6 0.5 0.9 BRC A:TBR1004 3.6 0.3 0.9 BR4 A:TBR1004 3.7 0.1 0.9 TA3 A:TBR1004 4.2 0.0 0.9 OE1 Y:GLU103 4.2 0.4 1.0 TA6 A:TBR1004 4.2 0.1 0.9 CD A:GLN598 4.4 0.5 1.0 NE2 A:GLN598 4.5 0.7 1.0 CB A:LYS594 4.5 0.6 1.0 NZ A:LYS594 4.8 0.8 1.0

Bromine binding site 2 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.9 occ:0.93 BR2 A:TBR1004 0.0 0.9 0.9 TA1 A:TBR1004 2.6 0.9 0.9 TA3 A:TBR1004 2.6 0.0 0.9 CB A:GLN595 3.5 0.7 1.0 BR1 A:TBR1004 3.6 0.8 0.9 BR3 A:TBR1004 3.6 0.1 0.9 BR5 A:TBR1004 3.6 0.5 0.9 BR6 A:TBR1004 3.6 0.8 0.9 O A:ASP591 3.7 0.7 1.0 CA A:GLN595 3.9 0.9 1.0 CG A:GLN595 4.0 0.9 1.0 N A:GLN595 4.1 0.6 1.0 TA2 A:TBR1004 4.1 0.6 0.9 TA5 A:TBR1004 4.2 0.2 0.9 CD A:GLN595 4.3 0.4 1.0 OE1 A:GLN595 4.5 0.4 1.0 C A:ASP591 4.6 0.5 1.0 NE2 A:GLN598 4.8 0.7 1.0 NE2 A:GLN595 4.8 0.9 1.0 C A:LYS594 4.9 0.1 1.0 CB A:ASP591 5.0 0.7 1.0

Bromine binding site 3 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.1 occ:0.93 BR3 A:TBR1004 0.0 0.1 0.9 TA1 A:TBR1004 2.6 0.9 0.9 TA5 A:TBR1004 2.6 0.2 0.9 OH A:TYR599 3.5 0.9 1.0 BR6 A:TBR1004 3.6 0.8 0.9 BR4 A:TBR1004 3.6 0.1 0.9 BR2 A:TBR1004 3.6 0.9 0.9 BRB A:TBR1004 3.6 0.4 0.9 TA3 A:TBR1004 4.2 0.0 0.9 TA6 A:TBR1004 4.2 0.1 0.9 NE2 A:GLN598 4.2 0.7 1.0 CZ A:TYR599 4.5 0.6 1.0 ND1 A:HIS739 4.7 0.6 1.0 NE2 A:GLN595 4.8 0.9 1.0 CG A:GLN595 4.9 0.9 1.0

Bromine binding site 4 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.1 occ:0.93 BR4 A:TBR1004 0.0 0.1 0.9 TA6 A:TBR1004 2.6 0.1 0.9 TA1 A:TBR1004 2.6 0.9 0.9 BR3 A:TBR1004 3.6 0.1 0.9 BRB A:TBR1004 3.6 0.4 0.9 BRC A:TBR1004 3.7 0.3 0.9 BR1 A:TBR1004 3.7 0.8 0.9 NE2 A:GLN598 3.8 0.7 1.0 TA5 A:TBR1004 4.2 0.2 0.9 TA2 A:TBR1004 4.2 0.6 0.9 OE1 A:GLN598 4.2 0.7 1.0 CD A:GLN598 4.4 0.5 1.0 CD1 A:LEU796 5.0 0.5 1.0

Bromine binding site 5 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.5 occ:0.93 BR5 A:TBR1004 0.0 0.5 0.9 TA2 A:TBR1004 2.6 0.6 0.9 TA3 A:TBR1004 2.6 0.0 0.9 OD2 A:ASP591 3.3 0.9 1.0 N Y:GLU103 3.3 0.8 1.0 BR1 A:TBR1004 3.6 0.8 0.9 BR9 A:TBR1004 3.6 0.5 0.9 BRA A:TBR1004 3.6 0.5 0.9 CG A:ASP591 3.6 0.0 1.0 BR2 A:TBR1004 3.6 0.9 0.9 CB A:ASP591 3.8 0.7 1.0 CA Y:GLU103 4.0 0.2 1.0 CB Y:GLU103 4.0 1.0 1.0 C Y:GLY102 4.1 0.5 1.0 TA4 A:TBR1004 4.2 0.8 0.9 TA1 A:TBR1004 4.2 0.9 0.9 OD1 A:ASP591 4.3 0.2 1.0 CA Y:GLY102 4.4 0.2 1.0 OE1 Y:GLU103 4.4 0.4 1.0 CA A:ASP591 4.5 0.3 1.0 O A:ASP591 5.0 0.7 1.0

Bromine binding site 6 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.8 occ:0.93 BR6 A:TBR1004 0.0 0.8 0.9 TA5 A:TBR1004 2.6 0.2 0.9 TA3 A:TBR1004 2.6 0.0 0.9 BR3 A:TBR1004 3.6 0.1 0.9 BR7 A:TBR1004 3.6 0.6 0.9 BR2 A:TBR1004 3.6 0.9 0.9 BRA A:TBR1004 3.7 0.5 0.9 TA1 A:TBR1004 4.1 0.9 0.9 TA4 A:TBR1004 4.2 0.8 0.9 NE2 A:GLN595 4.5 0.9 1.0 CD A:GLN595 4.9 0.4 1.0

Bromine binding site 7 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.6 occ:0.93 BR7 A:TBR1004 0.0 0.6 0.9 TA5 A:TBR1004 2.6 0.2 0.9 TA4 A:TBR1004 2.6 0.8 0.9 BR8 A:TBR1004 3.6 0.7 0.9 BRB A:TBR1004 3.6 0.4 0.9 BR6 A:TBR1004 3.6 0.8 0.9 BRA A:TBR1004 3.7 0.5 0.9 O A:LEU740 3.8 0.2 1.0 TA6 A:TBR1004 4.2 0.1 0.9 TA3 A:TBR1004 4.2 0.0 0.9 CA A:ARG741 4.9 0.9 1.0 C A:LEU740 4.9 0.2 1.0

Bromine binding site 8 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.7 occ:0.93 BR8 A:TBR1004 0.0 0.7 0.9 TA4 A:TBR1004 2.6 0.8 0.9 TA6 A:TBR1004 2.6 0.1 0.9 BR7 A:TBR1004 3.6 0.6 0.9 BRB A:TBR1004 3.6 0.4 0.9 BR9 A:TBR1004 3.6 0.5 0.9 BRC A:TBR1004 3.6 0.3 0.9 TA5 A:TBR1004 4.2 0.2 0.9 TA2 A:TBR1004 4.2 0.6 0.9

Bromine binding site 9 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.5 occ:0.93 BR9 A:TBR1004 0.0 0.5 0.9 TA4 A:TBR1004 2.6 0.8 0.9 TA2 A:TBR1004 2.6 0.6 0.9 N Y:GLU103 3.4 0.8 1.0 BRC A:TBR1004 3.6 0.3 0.9 BRA A:TBR1004 3.6 0.5 0.9 BR5 A:TBR1004 3.6 0.5 0.9 BR8 A:TBR1004 3.6 0.7 0.9 TA3 A:TBR1004 4.2 0.0 0.9 TA6 A:TBR1004 4.2 0.1 0.9 CA Y:GLY102 4.2 0.2 1.0 C Y:GLY102 4.2 0.5 1.0 CB Y:ARG106 4.2 0.4 1.0 CA Y:GLU103 4.2 0.2 1.0 N Y:ARG106 4.6 0.5 1.0

Bromine binding site 10 out of 216 in the Structure of the Seca-Secy Complex with A Translocating Polypeptide Substrate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br 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:Br1004 b:0.5 occ:0.93 BRA A:TBR1004 0.0 0.5 0.9 TA3 A:TBR1004 2.6 0.0 0.9 TA4 A:TBR1004 2.6 0.8 0.9 BR9 A:TBR1004 3.6 0.5 0.9 BR5 A:TBR1004 3.6 0.5 0.9 BR6 A:TBR1004 3.7 0.8 0.9 BR7 A:TBR1004 3.7 0.6 0.9 NH2 A:ARG741 3.9 0.2 1.0 TA2 A:TBR1004 4.2 0.6 0.9 TA5 A:TBR1004 4.2 0.2 0.9 CA Y:GLY102 4.2 0.2 1.0 O Y:GLN101 4.8 0.8 1.0 CZ A:ARG741 4.9 0.6 1.0 N Y:GLU103 4.9 0.8 1.0

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