Zinc in PDB 5w7h: Supercharged Arpte Variant R5

The structure of Supercharged Arpte Variant R5, PDB code: 5w7h was solved by E.Campbell, J.Grant, Y.Wang, M.Sandhu, R.J.Williams, D.R.Nisbet, A.Perriman, D.Lupton, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.391, 110.076, 112.277, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27.6

The binding sites of Zinc atom in the Supercharged Arpte Variant R5 (pdb code 5w7h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Supercharged Arpte Variant R5, PDB code: 5w7h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Supercharged Arpte Variant R5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Supercharged Arpte Variant R5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.9 occ:1.00 OD1 A:ASP301 2.0 34.5 1.0 NE2 A:HIS57 2.0 27.9 1.0 NE2 A:HIS55 2.0 34.1 1.0 OQ2 A:KCX169 2.1 50.0 1.0 CG A:ASP301 2.8 30.1 1.0 CX A:KCX169 2.8 50.0 1.0 CD2 A:HIS55 2.8 29.7 1.0 CD2 A:HIS57 3.0 22.5 1.0 CE1 A:HIS57 3.0 22.0 1.0 OD2 A:ASP301 3.0 31.2 1.0 ZN A:ZN402 3.2 40.5 1.0 CE1 A:HIS55 3.2 30.5 1.0 OQ1 A:KCX169 3.4 51.4 1.0 NZ A:KCX169 3.6 26.1 1.0 O A:HOH516 3.9 30.4 1.0 CE1 A:HIS230 4.0 70.9 1.0 CG A:HIS55 4.1 27.2 1.0 CB A:ASP301 4.1 26.0 1.0 ND1 A:HIS57 4.1 22.5 1.0 CG A:HIS57 4.1 21.2 1.0 NE2 A:HIS230 4.1 67.9 1.0 ND1 A:HIS55 4.2 30.8 1.0 CG2 A:VAL101 4.3 23.4 1.0 CA A:ASP301 4.6 24.6 1.0 CE A:KCX169 4.8 29.9 1.0

Zinc binding site 2 out of 4 in the Supercharged Arpte Variant R5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Supercharged Arpte Variant R5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:40.5 occ:1.00 OQ1 A:KCX169 2.0 51.4 1.0 NE2 A:HIS230 2.0 67.9 1.0 ND1 A:HIS201 2.0 49.7 1.0 O A:HOH516 2.4 30.4 1.0 CE1 A:HIS201 2.7 46.8 1.0 CX A:KCX169 2.8 50.0 1.0 CE1 A:HIS230 3.0 70.9 1.0 CD2 A:HIS230 3.1 28.8 1.0 OQ2 A:KCX169 3.1 50.0 1.0 ZN A:ZN401 3.2 28.9 1.0 CG A:HIS201 3.2 43.3 1.0 NE2 A:HIS55 3.6 34.1 1.0 OD2 A:ASP301 3.7 31.2 1.0 CE1 A:HIS55 3.7 30.5 1.0 CB A:HIS201 3.8 40.1 1.0 NE2 A:HIS201 3.9 48.2 1.0 NZ A:KCX169 3.9 26.1 1.0 ND1 A:HIS230 4.1 70.8 1.0 CG A:HIS230 4.2 28.2 1.0 CD2 A:HIS201 4.2 47.0 1.0 NE1 A:TRP131 4.4 24.5 1.0 CE A:KCX169 4.4 29.9 1.0 CG A:ASP301 4.4 30.1 1.0 OD1 A:ASP301 4.5 34.5 1.0 CA A:HIS201 4.6 34.5 1.0 NE2 A:HIS57 4.9 27.9 1.0 CD2 A:HIS55 4.9 29.7 1.0 ND1 A:HIS55 4.9 30.8 1.0

Zinc binding site 3 out of 4 in the Supercharged Arpte Variant R5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Supercharged Arpte Variant R5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:25.7 occ:1.00 OD1 B:ASP301 2.0 36.8 1.0 NE2 B:HIS57 2.0 34.0 1.0 NE2 B:HIS55 2.0 39.1 1.0 OQ2 B:KCX169 2.1 34.6 1.0 CD2 B:HIS55 2.9 23.9 1.0 CD2 B:HIS57 2.9 36.9 1.0 CG B:ASP301 3.0 35.7 1.0 CE1 B:HIS57 3.1 38.1 1.0 CX B:KCX169 3.1 34.1 1.0 CE1 B:HIS55 3.1 39.7 1.0 OD2 B:ASP301 3.4 36.8 1.0 OQ1 B:KCX169 3.6 37.1 1.0 ZN B:ZN402 3.7 31.4 1.0 O B:HOH517 3.9 33.2 1.0 CG B:HIS55 4.1 40.5 1.0 CG B:HIS57 4.1 37.6 1.0 ND1 B:HIS57 4.2 38.9 1.0 ND1 B:HIS55 4.2 39.7 1.0 CE1 B:HIS230 4.2 41.5 1.0 NZ B:KCX169 4.2 32.2 1.0 CB B:ASP301 4.3 32.7 1.0 CG2 B:VAL101 4.4 21.7 1.0 NE2 B:HIS230 4.4 46.5 1.0 CA B:ASP301 4.6 28.6 1.0

Zinc binding site 4 out of 4 in the Supercharged Arpte Variant R5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Supercharged Arpte Variant R5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:31.4 occ:1.00 NE2 B:HIS230 2.0 46.5 1.0 ND1 B:HIS201 2.0 44.5 1.0 OQ1 B:KCX169 2.1 37.1 1.0 CX B:KCX169 2.8 34.1 1.0 CE1 B:HIS201 2.8 41.1 1.0 OQ2 B:KCX169 2.8 34.6 1.0 O B:HOH517 2.9 33.2 1.0 CD2 B:HIS230 3.0 43.3 1.0 CE1 B:HIS230 3.0 41.5 1.0 CG B:HIS201 3.2 38.0 1.0 ZN B:ZN401 3.7 25.7 1.0 CB B:HIS201 3.8 35.5 1.0 NE2 B:HIS201 4.0 41.4 1.0 NZ B:KCX169 4.1 32.2 1.0 CE1 B:HIS55 4.1 39.7 1.0 ND1 B:HIS230 4.1 41.9 1.0 CG B:HIS230 4.1 40.3 1.0 OD2 B:ASP301 4.2 36.8 1.0 NE2 B:HIS55 4.2 39.1 1.0 CD2 B:HIS201 4.2 41.3 1.0 NE1 B:TRP131 4.4 36.4 1.0 CA B:HIS201 4.5 33.3 1.0 CE B:KCX169 4.7 31.6 1.0 NH1 B:ARG254 4.8 43.6 1.0 OD1 B:ASP301 4.8 36.8 1.0 CG B:ASP301 4.9 35.7 1.0

E.Campbell, J.Grant, Y.Wang, M.Sandhu, D.Nisbet, A.Perriman, D.Lupton, C.J.Jackson. Hydrogel-Immobilized Supercharged Proteins Adv Biosyst 2018.
ISSN: ESSN 2366-7478
DOI: 10.1002/ADBI.201700240