Zinc in PDB 5ld9: Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1.

The structure of Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1., PDB code: 5ld9 was solved by J.A.Maupin-Furlow, B.Franzetti, S.Cao, E.Girard, F.Gabel, S.Engilberge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.39 / 1.73
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.202, 37.147, 60.131, 97.29, 104.18, 100.07
R / Rfree (%)	15.7 / 18.9

The structure of Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1. also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1. (pdb code 5ld9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1., PDB code: 5ld9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:24.8 occ:0.90 OD2 A:ASP101 2.0 15.8 1.0 NE2 A:HIS90 2.0 18.2 1.0 NE2 A:HIS88 2.0 16.8 1.0 O A:HOH360 2.1 19.9 1.0 CG A:ASP101 2.7 17.0 1.0 OD1 A:ASP101 2.7 18.6 1.0 CD2 A:HIS90 2.9 18.1 1.0 CD2 A:HIS88 3.0 17.1 1.0 HD2 A:HIS90 3.0 21.7 1.0 CE1 A:HIS88 3.0 21.9 1.0 CE1 A:HIS90 3.1 18.9 1.0 HD2 A:HIS88 3.2 20.5 1.0 HE1 A:HIS88 3.2 26.3 1.0 HE1 A:HIS90 3.4 22.7 1.0 H A:SER98 3.6 19.5 1.0 HG A:SER98 3.8 23.4 1.0 HD13 A:ILE114 3.8 22.4 1.0 HB3 A:SER98 3.9 26.1 1.0 HE1 A:PHE62 3.9 21.8 1.0 OG A:SER98 3.9 19.5 1.0 O A:HOH354 4.0 37.8 1.0 CG A:HIS90 4.1 15.7 1.0 ND1 A:HIS88 4.1 16.2 1.0 CB A:ASP101 4.1 14.5 1.0 CG A:HIS88 4.2 17.3 1.0 ND1 A:HIS90 4.2 15.9 1.0 HD1 A:PHE62 4.2 21.9 1.0 HB2 A:ASP101 4.4 17.4 1.0 CB A:SER98 4.4 21.7 1.0 HG23 A:ILE114 4.4 21.0 1.0 HA A:PRO97 4.4 18.2 1.0 HG21 A:ILE114 4.4 21.0 1.0 N A:SER98 4.5 16.2 1.0 OE1 A:GLU34 4.5 20.0 1.0 O A:HOH339 4.5 28.5 1.0 HB3 A:ASP101 4.5 17.4 1.0 O A:HOH377 4.6 27.3 1.0 CE1 A:PHE62 4.7 18.2 1.0 CD1 A:ILE114 4.7 18.7 1.0 OE2 A:GLU34 4.7 21.8 1.0 HD11 A:ILE114 4.7 22.4 1.0 CD1 A:PHE62 4.8 18.2 1.0 CG2 A:ILE114 4.9 17.5 1.0 H A:ASP101 4.9 23.5 1.0 HG12 A:ILE114 4.9 16.7 1.0 HZ3 A:TRP112 4.9 23.1 1.0 CD A:GLU34 5.0 20.3 1.0 O A:SER89 5.0 18.2 1.0

Zinc binding site 2 out of 2 in the Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Deubiquitinating Enzyme Homolog, Pyrococcus Furiosus JAMM1. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:27.9 occ:0.90 OD2 B:ASP101 1.9 23.4 1.0 NE2 B:HIS90 2.0 21.4 1.0 NE2 B:HIS88 2.0 18.9 1.0 O B:HOH357 2.1 23.1 1.0 CG B:ASP101 2.6 18.8 1.0 OD1 B:ASP101 2.6 19.3 1.0 CD2 B:HIS90 2.9 22.8 1.0 HD2 B:HIS90 3.0 27.4 1.0 CD2 B:HIS88 3.0 22.2 1.0 CE1 B:HIS88 3.0 22.1 1.0 CE1 B:HIS90 3.1 24.9 1.0 HD2 B:HIS88 3.2 26.6 1.0 HE1 B:HIS88 3.2 26.5 1.0 HE1 B:HIS90 3.4 29.8 1.0 H B:SER98 3.7 23.2 1.0 HD13 B:ILE114 3.8 26.5 1.0 O B:HOH343 3.8 36.3 1.0 HE1 B:PHE62 4.0 28.4 1.0 HG B:SER98 4.0 24.6 1.0 CG B:HIS90 4.1 18.1 1.0 CB B:ASP101 4.1 21.4 1.0 OG B:SER98 4.1 20.5 1.0 ND1 B:HIS88 4.1 17.9 1.0 CG B:HIS88 4.2 19.2 1.0 ND1 B:HIS90 4.2 22.1 1.0 O B:HOH337 4.2 39.3 1.0 HB3 B:SER98 4.2 29.6 1.0 HA B:PRO97 4.4 25.4 1.0 HB2 B:ASP101 4.4 25.7 1.0 HG23 B:ILE114 4.4 24.9 1.0 OE1 B:GLU34 4.4 25.8 1.0 HB3 B:ASP101 4.4 25.7 1.0 HD1 B:PHE62 4.4 26.1 1.0 HG21 B:ILE114 4.4 24.9 1.0 O B:HOH379 4.5 38.3 1.0 OE2 B:GLU34 4.5 27.2 1.0 N B:SER98 4.6 19.4 1.0 CB B:SER98 4.7 24.7 1.0 CD1 B:ILE114 4.7 22.1 1.0 HD11 B:ILE114 4.7 26.5 1.0 CE1 B:PHE62 4.8 23.6 1.0 CD B:GLU34 4.8 24.1 1.0 CG2 B:ILE114 4.9 20.8 1.0 O B:HOH314 4.9 33.3 1.0 HG12 B:ILE114 4.9 26.8 1.0 O B:SER89 4.9 21.5 1.0 HZ3 B:TRP112 5.0 23.4 1.0

S.Cao, S.Engilberge, E.Girard, F.Gabel, B.Franzetti, J.A.Maupin-Furlow. Structural Insight Into Ubiquitin-Like Protein Recognition and Oligomeric States of Jamm/Mpn(+) Proteases. Structure V. 25 823 2017.
ISSN: ISSN 1878-4186
PubMed: 28479062
DOI: 10.1016/J.STR.2017.04.002