Nickel in PDB 6asr: REV1 UBM2 Domain Complex with Ubiquitin

The structure of REV1 UBM2 Domain Complex with Ubiquitin, PDB code: 6asr was solved by D.J.Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 2.36
Space group	I 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	164.924, 164.924, 164.924, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.9

The binding sites of Nickel atom in the REV1 UBM2 Domain Complex with Ubiquitin (pdb code 6asr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the REV1 UBM2 Domain Complex with Ubiquitin, PDB code: 6asr:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the REV1 UBM2 Domain Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of REV1 UBM2 Domain Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:33.2 occ:1.00 OD2 A:ASP52 2.0 34.1 1.0 OE1 A:GLU24 2.0 30.3 1.0 O A:HOH204 2.1 29.7 1.0 CG A:ASP52 3.0 32.3 1.0 CD A:GLU24 3.0 34.6 1.0 CB A:ASP52 3.4 29.6 1.0 OE2 A:GLU24 3.4 34.0 1.0 O A:HOH210 3.9 29.1 1.0 OD1 A:ASP39 4.0 35.3 1.0 OD1 A:ASP52 4.1 32.0 1.0 CG A:GLU24 4.4 32.3 1.0 O A:HOH222 4.5 32.0 1.0 CB A:GLU24 4.8 35.2 1.0 CA A:ASP52 4.9 31.9 1.0

Nickel binding site 2 out of 4 in the REV1 UBM2 Domain Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of REV1 UBM2 Domain Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni102 b:28.1 occ:1.00 OE2 A:GLU34 1.9 27.8 1.0 NZ A:LYS11 1.9 24.5 1.0 O A:HOH227 2.1 36.1 1.0 O A:HOH232 3.0 33.7 1.0 CE A:LYS11 3.1 26.9 1.0 CD A:GLU34 3.1 33.2 1.0 CD A:LYS11 3.6 26.1 1.0 OE1 A:GLU34 3.8 34.4 1.0 CG A:GLU34 4.3 27.5 1.0 CB A:GLU34 4.6 28.3 1.0

Nickel binding site 3 out of 4 in the REV1 UBM2 Domain Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of REV1 UBM2 Domain Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1101 b:44.5 occ:1.00 OE1 B:GLU1019 2.0 52.7 1.0 OD2 B:ASP1017 2.0 41.0 1.0 OE2 B:GLU1019 2.0 62.0 1.0 OD2 C:ASP39 2.0 48.7 1.0 OD1 B:ASP1017 2.0 48.4 1.0 CD B:GLU1019 2.0 52.5 1.0 O B:HOH1209 2.1 46.4 1.0 CG B:ASP1017 2.3 38.6 1.0 CG C:ASP39 3.0 47.3 1.0 CG B:GLU1019 3.3 37.8 1.0 CB C:ASP39 3.5 30.2 1.0 O B:HOH1214 3.7 51.7 1.0 CB B:ASP1017 3.8 34.5 1.0 CB B:GLU1019 3.9 40.9 1.0 NH2 C:ARG74 4.0 53.3 1.0 OD1 C:ASP39 4.1 47.1 1.0 NZ A:LYS6 4.3 39.3 1.0 N B:GLU1019 4.6 36.4 1.0 CA B:ASP1017 4.7 39.3 1.0 CE A:LYS6 4.8 45.9 1.0 CA B:GLU1019 4.8 41.3 1.0 CA C:ASP39 4.9 34.9 1.0

Nickel binding site 4 out of 4 in the REV1 UBM2 Domain Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of REV1 UBM2 Domain Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:48.8 occ:1.00 OD2 C:ASP52 2.0 42.0 1.0 OE1 C:GLU24 2.0 40.2 1.0 O C:HOH223 2.2 50.1 1.0 O C:HOH209 2.2 42.0 1.0 CG C:ASP52 2.9 35.6 1.0 CD C:GLU24 3.0 40.4 1.0 CB C:ASP52 3.3 32.0 1.0 OE2 C:GLU24 3.4 44.2 1.0 O C:HOH204 4.0 34.1 1.0 OD1 C:ASP52 4.0 36.9 1.0 CG C:GLU24 4.3 37.4 1.0 OD1 C:ASP39 4.4 47.1 1.0 O C:HOH201 4.4 48.9 1.0 CB C:GLU24 4.6 31.0 1.0 CA C:ASP52 4.8 32.4 1.0 O A:HOH233 4.9 52.0 1.0

M.Vanarotti, C.R.Grace, D.J.Miller, M.L.Actis, A.Inoue, B.J.Evison, S.Vaithiyalingam, A.P.Singh, E.T.Mcdonald, N.Fujii. Structures of REV1 UBM2 Domain Complex with Ubiquitin and with A Small-Molecule That Inhibits the REV1 UBM2-Ubiquitin Interaction. J. Mol. Biol. V. 430 2857 2018.
ISSN: ESSN 1089-8638
PubMed: 29864443
DOI: 10.1016/J.JMB.2018.05.042