Sodium in PDB 5ee5: Structure of Human ARL1 in Complex with the Dcb Domain of BIG1

The structure of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1, PDB code: 5ee5 was solved by A.Galindo, N.Soler, S.Munro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 2.28
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.166, 50.727, 103.837, 90.00, 111.98, 90.00
R / Rfree (%)	21.7 / 25.9

The structure of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	7 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 (pdb code 5ee5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1, PDB code: 5ee5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:74.3 occ:1.00 CA A:THR98 3.9 52.3 1.0 N A:THR98 4.1 52.9 1.0 OG1 A:THR98 4.1 63.8 1.0 CB A:ASP101 4.2 55.2 1.0 C A:SER97 4.2 57.4 1.0 O A:SER97 4.2 59.7 1.0 NZ A:LYS18 4.3 0.3 1.0 CB A:SER97 4.5 55.3 1.0 CG A:ASP101 4.5 57.9 1.0 CB A:THR98 4.6 55.9 1.0 OD2 A:ASP101 4.7 58.3 1.0 OE1 A:GLN150 4.9 50.2 1.0

Sodium binding site 2 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:67.7 occ:1.00 ND2 A:ASN187 3.3 69.5 1.0 OD1 A:ASN187 3.5 64.9 1.0 OD1 A:ASN190 3.5 61.9 1.0 NE2 B:GLN64 3.7 59.8 1.0 CG A:ASN187 3.7 63.4 1.0 CB A:ILE189 3.8 60.2 1.0 OE1 B:GLN64 3.9 66.3 1.0 CG2 A:ILE189 4.0 60.0 1.0 CD B:GLN64 4.2 62.7 1.0 CG A:ASN190 4.3 58.2 1.0 CD2 A:LEU149 4.3 51.6 1.0 O A:HOH419 4.4 66.7 1.0 CG1 A:ILE189 4.4 65.4 1.0 N A:ASN190 4.7 52.7 1.0 ND2 A:ASN190 4.8 58.8 1.0

Sodium binding site 3 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:91.7 occ:1.00 CD1 A:LEU41 4.0 79.0 1.0 NA A:NA306 4.1 78.8 1.0 CG A:GLU17 4.4 85.7 1.0 OE2 A:GLU17 4.7 0.1 1.0 CD1 A:LEU20 4.8 67.8 1.0 CD A:GLU17 4.9 98.3 1.0

Sodium binding site 4 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:98.5 occ:1.00 O A:HOH408 2.3 30.0 1.0 OE2 A:GLU47 2.8 0.2 1.0 OE1 A:GLN51 3.4 0.8 1.0 CD A:GLU47 3.8 0.3 1.0 OE1 A:GLU47 4.1 0.5 1.0 N A:PHE74 4.1 0.1 1.0 O A:PHE74 4.1 1.0 1.0 CD A:GLN51 4.4 0.3 1.0 CB A:GLN51 4.9 0.8 1.0

Sodium binding site 5 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range:

Sodium binding site 6 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:78.8 occ:1.00 CG A:GLU38 3.8 72.7 1.0 CA A:GLU38 3.8 73.4 1.0 O A:GLU38 3.9 80.4 1.0 CD1 A:LEU41 3.9 79.0 1.0 CB A:GLU38 4.0 70.8 1.0 CB A:LEU41 4.1 81.2 1.0 NA A:NA303 4.1 91.7 1.0 CD1 A:LEU20 4.3 67.8 1.0 C A:GLU38 4.3 75.2 1.0 CG A:LEU41 4.7 82.4 1.0 CD A:GLU38 4.9 80.4 1.0 CG A:GLU42 4.9 99.1 1.0

Sodium binding site 7 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:82.8 occ:1.00 CG B:GLU112 3.5 74.1 1.0 CA B:GLU112 4.0 65.8 1.0 O B:LEU111 4.2 65.9 1.0 CB B:GLU112 4.3 63.9 1.0 CD B:GLU112 4.6 84.2 1.0 OE2 B:GLU112 4.6 90.2 1.0 O B:GLU112 4.8 70.7 1.0 C B:GLU112 4.9 65.0 1.0 N B:GLU112 4.9 61.8 1.0 C B:LEU111 4.9 58.5 1.0

Sodium binding site 8 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:94.3 occ:1.00 OD2 B:ASP150 2.3 0.0 1.0 CG B:ASP150 3.3 0.0 1.0 OD1 B:ASP150 4.0 99.2 1.0 CB B:ASP150 4.2 94.4 1.0

Sodium binding site 9 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:81.2 occ:1.00 O B:VAL39 3.6 76.7 1.0 OE2 B:GLU41 3.8 0.2 1.0 O B:GLY40 4.0 76.2 1.0 C B:GLY40 4.5 70.5 1.0 CD B:GLU41 4.5 0.5 1.0 CB B:GLU41 4.6 74.7 1.0 CG B:GLU41 4.7 91.7 1.0 C B:VAL39 4.8 71.4 1.0 N B:GLU41 5.0 72.3 1.0

Sodium binding site 10 out of 14 in the Structure of Human ARL1 in Complex with the Dcb Domain of BIG1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Human ARL1 in Complex with the Dcb Domain of BIG1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:65.6 occ:1.00 ND2 B:ASN84 4.6 77.1 1.0 CG1 A:ILE189 4.8 65.4 1.0 CG B:ASN84 4.9 75.6 1.0 CB B:ASN84 5.0 74.5 1.0

A.Galindo, N.Soler, S.H.Mclaughlin, M.Yu, R.L.Williams, S.Munro. Structural Insights Into ARL1-Mediated Targeting of the Arf-Gef BIG1 to the Trans-Golgi. Cell Rep V. 16 839 2016.
ISSN: ESSN 2211-1247
PubMed: 27373159
DOI: 10.1016/J.CELREP.2016.06.022