Nickel in PDB 5wtq: Crystal Structure of Human Proteasome-Assembling Chaperone PAC4

The structure of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4, PDB code: 5wtq was solved by E.Kurimoto, T.Satoh, Y.Ito, E.Ishihara, K.Tanaka, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	72.548, 152.779, 212.911, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.4

The structure of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 (pdb code 5wtq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4, PDB code: 5wtq:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:28.4 occ:1.00 O A:HOH339 1.9 28.4 1.0 NE2 A:HIS29 2.0 25.5 1.0 NE2 A:HIS27 2.1 34.5 1.0 NE2 A:HIS46 2.1 29.1 1.0 O A:HOH353 2.2 32.2 1.0 O A:HOH340 2.2 29.3 1.0 CD2 A:HIS29 3.0 26.1 1.0 CE1 A:HIS46 3.0 28.0 1.0 CD2 A:HIS27 3.1 32.0 1.0 CE1 A:HIS29 3.1 29.4 1.0 CE1 A:HIS27 3.2 34.1 1.0 CD2 A:HIS46 3.2 26.5 1.0 O A:LEU68 4.1 36.7 1.0 CG A:HIS29 4.2 24.0 1.0 ND1 A:HIS29 4.2 25.1 1.0 O A:HOH367 4.2 34.0 1.0 ND1 A:HIS46 4.2 27.0 1.0 CG A:HIS27 4.2 34.8 1.0 ND1 A:HIS27 4.2 33.5 1.0 CG A:HIS46 4.3 28.0 1.0 O A:HOH370 4.3 44.6 1.0 OG1 A:THR44 4.7 33.1 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:28.7 occ:1.00 NE2 B:HIS29 2.0 27.7 1.0 NE2 B:HIS27 2.1 31.4 1.0 O B:HOH321 2.1 26.0 1.0 NE2 B:HIS46 2.1 28.3 1.0 O B:HOH347 2.2 32.6 1.0 CD2 B:HIS29 3.0 28.6 1.0 CD2 B:HIS27 3.0 31.5 1.0 CE1 B:HIS46 3.1 29.9 1.0 CE1 B:HIS29 3.1 30.7 1.0 CE1 B:HIS27 3.2 31.6 1.0 CD2 B:HIS46 3.2 29.1 1.0 O B:HOH363 4.1 45.0 1.0 CG B:HIS29 4.1 27.0 1.0 O B:LEU68 4.2 30.4 1.0 ND1 B:HIS29 4.2 31.4 1.0 CG B:HIS27 4.2 31.8 1.0 ND1 B:HIS46 4.2 29.4 1.0 ND1 B:HIS27 4.2 31.4 1.0 CG B:HIS46 4.3 28.1 1.0 O B:HOH373 4.4 53.5 1.0 O B:HOH374 4.6 39.5 1.0 OG1 B:THR44 4.7 33.7 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni201 b:26.3 occ:1.00 NE2 C:HIS29 2.1 30.3 1.0 NE2 C:HIS46 2.1 24.0 1.0 NE2 C:HIS27 2.2 31.1 1.0 O C:HOH316 2.3 29.6 1.0 CD2 C:HIS29 3.0 30.4 1.0 CE1 C:HIS46 3.0 27.0 1.0 CE1 C:HIS29 3.1 29.6 1.0 CD2 C:HIS27 3.1 27.1 1.0 CE1 C:HIS27 3.2 26.5 1.0 CD2 C:HIS46 3.2 24.1 1.0 O C:LEU68 4.1 32.1 1.0 ND1 C:HIS29 4.2 29.8 1.0 CG C:HIS29 4.2 28.2 1.0 ND1 C:HIS46 4.2 27.9 1.0 ND1 C:HIS27 4.3 25.8 1.0 CG C:HIS27 4.3 25.2 1.0 CG C:HIS46 4.3 25.2 1.0 NH2 C:ARG48 4.7 48.1 1.0 CB C:ASN16 5.0 28.0 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni201 b:31.8 occ:1.00 NE2 D:HIS29 2.0 29.5 1.0 O D:HOH320 2.1 30.1 1.0 NE2 D:HIS46 2.2 27.9 1.0 O D:HOH345 2.2 33.3 1.0 NE2 D:HIS27 2.2 38.5 1.0 CD2 D:HIS29 2.9 31.7 1.0 CE1 D:HIS29 3.0 31.8 1.0 CE1 D:HIS46 3.1 28.1 1.0 CD2 D:HIS27 3.1 36.3 1.0 CD2 D:HIS46 3.2 27.6 1.0 CE1 D:HIS27 3.3 40.1 1.0 CG D:HIS29 4.1 28.2 1.0 ND1 D:HIS29 4.1 31.8 1.0 O D:LEU68 4.1 32.4 1.0 ND1 D:HIS46 4.2 26.1 1.0 CG D:HIS27 4.3 40.8 1.0 CG D:HIS46 4.3 26.4 1.0 ND1 D:HIS27 4.3 40.3 1.0 O D:HOH371 4.4 49.6 1.0 O D:HOH378 4.4 40.4 1.0 O D:HOH374 4.6 37.8 1.0 OG1 D:THR44 4.7 37.5 1.0 CB D:ASN16 4.9 52.4 1.0 CG D:ASN16 5.0 50.3 1.0

E.Kurimoto, T.Satoh, Y.Ito, E.Ishihara, K.Okamoto, M.Yagi-Utsumi, K.Tanaka, K.Kato. Crystal Structure of Human Proteasome Assembly Chaperone PAC4 Involved in Proteasome Formation Protein Sci. V. 26 1080 2017.
ISSN: ESSN 1469-896X
PubMed: 28263418
DOI: 10.1002/PRO.3153