Zinc in PDB 8qf5: Complex Between N-Lobe of Arc and Nanobody E5

The structure of Complex Between N-Lobe of Arc and Nanobody E5, PDB code: 8qf5 was solved by J.M.Godoy Munoz, P.Kursula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.83 / 1.50
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.5, 99.48, 138.43, 90, 90, 90
R / Rfree (%)	14.5 / 19.3

The structure of Complex Between N-Lobe of Arc and Nanobody E5 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Complex Between N-Lobe of Arc and Nanobody E5 (pdb code 8qf5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Complex Between N-Lobe of Arc and Nanobody E5, PDB code: 8qf5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Complex Between N-Lobe of Arc and Nanobody E5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Between N-Lobe of Arc and Nanobody E5 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:43.4 occ:0.46 HZ1 G:LYS66 1.5 74.2 1.0 HZ2 G:LYS66 1.7 74.2 1.0 NZ G:LYS66 1.9 61.9 1.0 OD1 G:ASP63 2.0 49.5 1.0 O G:HOH388 2.3 66.8 1.0 HE3 G:LYS66 2.4 65.2 1.0 CE G:LYS66 2.6 54.4 1.0 HZ3 G:LYS66 2.7 74.2 1.0 HE2 G:LYS66 3.0 65.2 1.0 CG G:ASP63 3.1 42.8 1.0 O G:HOH410 3.5 60.5 1.0 OD2 G:ASP63 3.6 51.9 1.0 O G:TYR61 3.8 37.2 1.0 CD G:LYS66 3.9 57.9 1.0 HD2 G:LYS66 3.9 69.4 1.0 HA G:ASP63 4.0 44.8 1.0 H G:ASP63 4.1 44.9 1.0 N G:ASP63 4.2 37.5 1.0 CB G:ASP63 4.3 37.5 1.0 O G:HOH396 4.3 53.0 1.0 HD3 G:LYS66 4.4 69.4 1.0 CA G:ASP63 4.4 37.4 1.0 HA G:VAL62 4.5 48.8 1.0 HG3 G:LYS66 4.8 63.8 1.0 O G:HOH389 4.8 44.3 1.0 HB2 G:ASP63 4.8 44.9 1.0 C G:VAL62 4.8 36.5 1.0 C G:TYR61 4.9 35.1 1.0 HB3 G:ASP63 5.0 44.9 1.0 CG G:LYS66 5.0 53.2 1.0

Zinc binding site 2 out of 5 in the Complex Between N-Lobe of Arc and Nanobody E5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Between N-Lobe of Arc and Nanobody E5 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:41.8 occ:0.47 ZN H:ZN301 0.0 41.8 0.5 HE1 H:HIS223 1.7 65.6 0.4 OE1 H:GLU219 2.0 41.2 1.0 NE2 H:HIS223 2.3 34.9 0.6 CE1 H:HIS223 2.5 54.7 0.4 CD H:GLU219 2.6 55.4 1.0 OE2 H:GLU219 2.6 57.1 1.0 CE1 H:HIS223 3.1 43.9 0.6 ZN H:ZN301 3.1 36.3 0.5 HE1 H:HIS223 3.2 52.6 0.6 NE2 H:HIS223 3.2 51.5 0.4 HE2 H:HIS223 3.2 61.8 0.4 CD2 H:HIS223 3.3 43.4 0.6 HD2 H:HIS223 3.5 52.0 0.6 ND1 H:HIS223 3.5 54.3 0.4 O H:HOH458 3.8 42.5 1.0 CG H:GLU219 4.1 51.9 1.0 HG H:SER222 4.2 67.9 1.0 ND1 H:HIS223 4.2 47.2 0.6 HG3 H:GLU219 4.3 62.2 1.0 CG H:HIS223 4.4 45.7 0.6 CD2 H:HIS223 4.4 50.8 0.4 HB3 H:GLU219 4.6 53.0 1.0 HG2 H:GLU219 4.6 62.2 1.0 CG H:HIS223 4.6 50.4 0.4 OG H:SER222 4.7 56.6 1.0 HA H:GLU219 4.8 54.6 1.0 CB H:GLU219 4.9 44.2 1.0 HD1 H:HIS223 5.0 56.6 0.6

Zinc binding site 3 out of 5 in the Complex Between N-Lobe of Arc and Nanobody E5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Between N-Lobe of Arc and Nanobody E5 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:36.3 occ:0.53 ZN H:ZN301 0.0 36.3 0.5 HE1 H:HIS223 1.1 52.6 0.6 CE1 H:HIS223 1.5 43.9 0.6 HE2 H:HIS223 2.0 61.8 0.4 O H:HOH458 2.1 42.5 1.0 NE2 H:HIS223 2.1 34.9 0.6 NE2 H:HIS223 2.3 51.5 0.4 OE2 H:GLU226 2.4 63.2 1.0 ND1 H:HIS223 2.6 47.2 0.6 CE1 H:HIS223 2.9 54.7 0.4 HD1 H:HIS223 3.0 56.6 0.6 CD2 H:HIS223 3.1 50.8 0.4 HE1 H:HIS223 3.1 65.6 0.4 ZN H:ZN301 3.1 41.8 0.5 CD2 H:HIS223 3.3 43.4 0.6 HD2 H:HIS223 3.4 60.9 0.4 CD H:GLU226 3.5 60.7 1.0 CG H:HIS223 3.6 45.7 0.6 ND1 H:HIS223 3.8 54.3 0.4 OE1 H:GLU226 3.9 62.9 1.0 CG H:HIS223 3.9 50.4 0.4 HD2 H:HIS223 4.1 52.0 0.6 HG H:SER222 4.3 67.9 1.0 OG H:SER222 4.7 56.6 1.0 OE1 H:GLU219 4.7 41.2 1.0 HG3 H:GLU226 4.8 65.4 1.0 HA H:HIS223 4.8 53.3 0.4 CG H:GLU226 4.8 54.6 1.0 OE2 H:GLU219 4.8 57.1 1.0 HA H:HIS223 4.9 52.4 0.6 CB H:HIS223 4.9 35.0 0.6

Zinc binding site 4 out of 5 in the Complex Between N-Lobe of Arc and Nanobody E5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Between N-Lobe of Arc and Nanobody E5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:52.3 occ:0.43 ZN B:ZN301 0.0 52.3 0.4 ZN B:ZN301 1.7 37.7 0.6 NE2 B:HIS223 2.3 37.1 1.0 O B:HOH467 2.3 46.1 1.0 CE1 B:HIS223 3.2 35.4 1.0 CD2 B:HIS223 3.2 36.4 1.0 HD2 B:HIS223 3.4 43.6 1.0 HE1 B:HIS223 3.4 42.5 1.0 ND1 B:HIS223 4.3 33.4 1.0 CG B:HIS223 4.3 35.0 1.0 O B:HOH412 4.5 50.6 1.0 O B:HOH471 4.9 40.2 0.4

Zinc binding site 5 out of 5 in the Complex Between N-Lobe of Arc and Nanobody E5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex Between N-Lobe of Arc and Nanobody E5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:37.7 occ:0.57 ZN B:ZN301 0.0 37.7 0.6 ZN B:ZN301 1.7 52.3 0.4 O B:HOH467 2.2 46.1 1.0 NE2 B:HIS223 2.2 37.1 1.0 CE1 B:HIS223 3.1 35.4 1.0 HE1 B:HIS223 3.2 42.5 1.0 CD2 B:HIS223 3.2 36.4 1.0 HD2 B:HIS223 3.4 43.6 1.0 ND1 B:HIS223 4.2 33.4 1.0 OE1 B:GLU226 4.3 50.4 1.0 CG B:HIS223 4.3 35.0 1.0 O B:HOH471 4.6 40.2 0.4 OE2 B:GLU226 4.8 51.3 1.0 HD1 B:HIS223 5.0 40.0 1.0 CD B:GLU226 5.0 41.0 1.0

J.M.Godoy Munoz, P.Kursula. Complex Between N-Lobe of Arc and Nanobody E5 To Be Published.