Zinc in PDB 4k1r: Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin

The structure of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin, PDB code: 4k1r was solved by R.K.Shrestha, C.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.24 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.292, 74.457, 139.292, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.5

The structure of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin (pdb code 4k1r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin, PDB code: 4k1r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:14.3 occ:1.00 OE2 C:GLU327 2.0 13.7 1.0 NE2 A:HIS304 2.0 12.5 1.0 NE2 A:HIS332 2.1 13.6 1.0 CL A:CL504 2.2 14.6 1.0 CD C:GLU327 2.7 13.4 1.0 OE1 C:GLU327 2.8 14.3 1.0 CD2 A:HIS304 3.0 14.6 1.0 CE1 A:HIS304 3.0 14.5 1.0 CD2 A:HIS332 3.0 13.9 1.0 CE1 A:HIS332 3.1 17.5 1.0 NE2 A:GLN428 3.9 14.0 1.0 ND1 A:HIS304 4.1 14.3 1.0 CG A:HIS304 4.1 13.4 1.0 ND1 A:HIS332 4.1 16.1 1.0 CG A:HIS332 4.2 15.8 1.0 CG C:GLU327 4.2 13.2 1.0 CG A:GLN428 4.3 12.7 1.0 O C:GLU327 4.3 15.6 1.0 CA C:PHE328 4.3 13.3 1.0 N C:PHE328 4.4 12.6 1.0 C C:GLU327 4.4 15.1 1.0 CD A:GLN428 4.6 14.3 1.0 CB A:GLN428 4.7 12.2 1.0 CB C:GLU327 4.7 13.2 1.0 CZ A:PHE328 4.8 15.7 1.0 CB C:PHE328 4.9 14.2 1.0 CD1 A:LEU334 4.9 15.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:15.1 occ:1.00 OD2 A:ASP354 1.9 13.8 1.0 OXT B:GLY76 1.9 15.2 1.0 NE2 A:HIS343 2.0 15.2 1.0 NE2 A:HIS341 2.0 11.6 1.0 CG A:ASP354 2.7 14.4 1.0 OD1 A:ASP354 2.8 14.7 1.0 C B:GLY76 2.9 15.9 1.0 CE1 A:HIS341 2.9 13.5 1.0 CD2 A:HIS343 3.0 16.3 1.0 CE1 A:HIS343 3.0 16.4 1.0 CD2 A:HIS341 3.2 15.7 1.0 O B:GLY76 3.4 16.7 1.0 N B:GLY76 3.8 15.4 1.0 OG A:SER351 3.9 15.2 1.0 CA B:GLY76 3.9 16.7 1.0 ND1 A:HIS341 4.1 13.6 1.0 ND1 A:HIS343 4.1 16.5 1.0 CG A:HIS343 4.1 15.1 1.0 CB A:ASP354 4.1 14.1 1.0 CG A:HIS341 4.2 12.8 1.0 O A:PHE349 4.2 16.8 1.0 CB A:SER351 4.3 16.9 1.0 N A:SER351 4.4 14.7 1.0 CG1 A:VAL372 4.7 15.7 1.0 O1 A:EDO506 4.8 31.7 1.0 CG2 A:VAL372 4.9 13.8 1.0 C B:GLY75 4.9 17.0 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:16.8 occ:1.00 NE2 A:HIS406 2.0 17.0 1.0 NE2 A:HIS404 2.0 17.9 1.0 NE2 A:HIS356 2.1 14.6 1.0 SG A:CYS397 2.3 15.1 1.0 CE1 A:HIS406 2.9 18.1 1.0 CE1 A:HIS356 3.0 17.1 1.0 CD2 A:HIS404 3.0 17.5 1.0 CD2 A:HIS406 3.0 17.3 1.0 CE1 A:HIS404 3.0 18.2 1.0 CD2 A:HIS356 3.1 18.3 1.0 CB A:CYS397 3.3 16.2 1.0 ND1 A:HIS406 4.0 19.6 1.0 CG A:HIS406 4.1 18.0 1.0 ND1 A:HIS356 4.1 15.3 1.0 ND1 A:HIS404 4.1 19.5 1.0 CG A:HIS404 4.1 20.0 1.0 CG A:HIS356 4.2 14.3 1.0 OG A:SER352 4.3 22.8 1.0 CD1 A:ILE394 4.5 16.5 1.0 O A:HOH683 4.7 18.4 1.0 CA A:CYS397 4.7 14.5 1.0 CB A:LYS399 4.8 20.4 1.0 C A:CYS397 5.0 17.9 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:13.8 occ:1.00 OXT D:GLY76 1.9 15.1 1.0 OD2 C:ASP354 2.0 11.9 1.0 NE2 C:HIS343 2.0 14.3 1.0 NE2 C:HIS341 2.0 13.3 1.0 CG C:ASP354 2.7 14.4 1.0 C D:GLY76 2.8 15.3 1.0 OD1 C:ASP354 2.9 13.7 1.0 CE1 C:HIS341 2.9 13.1 1.0 CD2 C:HIS343 3.0 14.3 1.0 CE1 C:HIS343 3.1 13.9 1.0 CD2 C:HIS341 3.2 12.7 1.0 O D:GLY76 3.4 14.5 1.0 N D:GLY76 3.8 15.2 1.0 CA D:GLY76 3.9 16.6 1.0 OG C:SER351 3.9 14.4 1.0 ND1 C:HIS341 4.1 13.6 1.0 CG C:HIS343 4.1 13.6 1.0 ND1 C:HIS343 4.1 12.8 1.0 CB C:ASP354 4.2 12.2 1.0 O C:PHE349 4.2 15.3 1.0 CG C:HIS341 4.2 12.0 1.0 N C:SER351 4.4 14.2 1.0 CB C:SER351 4.4 15.2 1.0 CG1 C:VAL372 4.7 14.3 1.0 CG2 C:VAL372 4.8 13.4 1.0 C D:GLY75 4.9 15.1 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:17.6 occ:1.00 NE2 C:HIS406 1.9 18.7 1.0 NE2 C:HIS356 2.0 15.7 1.0 NE2 C:HIS404 2.1 19.1 1.0 SG C:CYS397 2.3 17.5 1.0 CE1 C:HIS406 2.9 19.4 1.0 CD2 C:HIS406 2.9 18.2 1.0 CE1 C:HIS356 3.0 17.6 1.0 CE1 C:HIS404 3.0 20.6 1.0 CD2 C:HIS404 3.1 20.2 1.0 CD2 C:HIS356 3.1 19.8 1.0 CB C:CYS397 3.3 21.0 1.0 ND1 C:HIS406 4.0 21.9 1.0 CG C:HIS406 4.0 20.4 1.0 ND1 C:HIS356 4.1 18.5 1.0 ND1 C:HIS404 4.1 20.4 1.0 OG C:SER352 4.2 23.9 1.0 CG C:HIS356 4.2 16.6 1.0 CG C:HIS404 4.2 21.7 1.0 CD1 C:ILE394 4.5 18.7 1.0 CB C:LYS399 4.6 21.4 1.0 CA C:CYS397 4.7 23.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Schizosaccharomyces Pombe SST2 Catalytic Domain and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn503 b:15.0 occ:1.00 OE1 A:GLU327 2.0 14.9 1.0 NE2 C:HIS304 2.0 12.3 1.0 NE2 C:HIS332 2.0 15.0 1.0 CL C:CL504 2.3 14.3 1.0 CD A:GLU327 2.7 16.4 1.0 OE2 A:GLU327 2.8 14.7 1.0 CE1 C:HIS332 3.0 14.5 1.0 CD2 C:HIS304 3.0 14.5 1.0 CD2 C:HIS332 3.0 15.1 1.0 CE1 C:HIS304 3.0 16.3 1.0 NE2 C:GLN428 4.0 14.9 1.0 ND1 C:HIS332 4.1 15.2 1.0 ND1 C:HIS304 4.1 13.6 1.0 CG C:HIS332 4.1 15.5 1.0 CG C:HIS304 4.1 12.9 1.0 CG A:GLU327 4.2 15.2 1.0 CG C:GLN428 4.3 16.0 1.0 O A:GLU327 4.4 14.5 1.0 CA A:PHE328 4.4 13.2 1.0 N A:PHE328 4.4 14.2 1.0 C A:GLU327 4.5 14.8 1.0 CD C:GLN428 4.7 14.4 1.0 CB C:GLN428 4.7 15.9 1.0 CB A:GLU327 4.7 14.8 1.0 CZ C:PHE328 4.8 12.9 1.0 CB A:PHE328 4.9 13.7 1.0 CD1 C:LEU334 5.0 14.8 1.0

R.K.Shrestha, J.A.Ronau, C.W.Davies, R.G.Guenette, E.R.Strieter, L.N.Paul, C.Das. Insights Into the Mechanism of Deubiquitination By Jamm Deubiquitinases From Cocrystal Structures of the Enzyme with the Substrate and Product. Biochemistry V. 53 3199 2014.
ISSN: ISSN 0006-2960
PubMed: 24787148
DOI: 10.1021/BI5003162