Nickel in PDB 5mle: Crystal Structure of Human Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E

The structure of Crystal Structure of Human Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E, PDB code: 5mle was solved by R.Sethi, Y.Zheng, R.Talon, S.Velupillai, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.A.Ahmed, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.98 / 2.48
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	70.900, 185.820, 196.310, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.4

The binding sites of Nickel atom in the Crystal Structure of Human Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E (pdb code 5mle). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E, PDB code: 5mle:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Human Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E


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 Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni608 b:0.8 occ:1.00 OE2 C:GLU277 2.9 27.5 1.0 O C:VAL72 3.0 30.3 1.0 NE2 C:HIS107 3.0 38.1 1.0 NE2 C:GLN196 3.2 28.1 1.0 CB C:HIS73 3.2 27.2 1.0 CE1 C:HIS138 3.3 27.0 1.0 CG C:HIS73 3.3 27.5 1.0 ND1 C:HIS138 3.5 28.0 1.0 CA C:HIS73 3.6 26.8 1.0 ND1 C:HIS73 3.6 26.3 1.0 C C:VAL72 3.7 29.1 1.0 CE1 C:HIS107 3.8 36.1 1.0 CD2 C:HIS73 3.9 28.0 1.0 N C:HIS73 4.0 28.4 1.0 CD C:GLU277 4.0 28.9 1.0 CD2 C:HIS107 4.0 38.2 1.0 CD C:GLN196 4.1 29.8 1.0 OE1 C:GLN196 4.2 32.6 1.0 CG2 C:THR253 4.2 28.6 1.0 OH C:TYR251 4.2 26.9 1.0 CE1 C:HIS73 4.3 27.6 1.0 CE1 C:TYR251 4.3 29.1 1.0 NE2 C:HIS138 4.4 26.1 1.0 OE1 C:GLU277 4.4 25.2 1.0 NE2 C:HIS73 4.5 27.8 1.0 CZ C:TYR251 4.6 29.5 1.0 CB C:VAL72 4.7 28.3 1.0 CG C:HIS138 4.7 29.5 1.0 CA C:VAL72 4.9 28.7 1.0 ND1 C:HIS107 5.0 37.7 1.0 C C:HIS73 5.0 27.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Human Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E


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 Dihydropyrimidinease-Like 2 (DPYSL2A) /Collapsin Response Mediator Protein (CRMP2 13-516) Mutant Y479E/Y499E within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni607 b:0.7 occ:1.00 NE2 A:HIS107 3.0 39.1 1.0 O A:VAL72 3.0 38.4 1.0 OE2 A:GLU277 3.2 27.6 1.0 CG A:HIS73 3.3 35.3 1.0 CB A:HIS73 3.4 33.1 1.0 NE2 A:GLN196 3.4 37.8 1.0 CE1 A:HIS138 3.6 40.4 1.0 CE1 A:HIS107 3.6 39.4 1.0 ND1 A:HIS73 3.6 36.7 1.0 ND1 A:HIS138 3.6 39.8 1.0 CA A:HIS73 3.7 32.5 1.0 CD2 A:HIS73 3.8 34.2 1.0 C A:VAL72 3.8 34.9 1.0 CG2 A:THR253 4.1 27.6 1.0 CD2 A:HIS107 4.1 39.9 1.0 CD A:GLU277 4.1 27.9 1.0 N A:HIS73 4.2 33.6 1.0 OE1 A:GLN196 4.2 37.2 1.0 CD A:GLN196 4.2 37.5 1.0 CE1 A:HIS73 4.2 37.6 1.0 OE1 A:GLU277 4.3 28.8 1.0 NE2 A:HIS73 4.3 36.1 1.0 OH A:TYR251 4.4 26.6 1.0 CE1 A:TYR251 4.5 29.1 1.0 NE2 A:HIS138 4.6 39.3 1.0 CG A:HIS138 4.7 40.0 1.0 CG2 A:VAL72 4.7 36.7 1.0 CB A:VAL72 4.8 36.9 1.0 CZ A:TYR251 4.8 28.0 1.0 ND1 A:HIS107 4.9 40.3 1.0 CA A:VAL72 5.0 35.6 1.0 CB A:THR253 5.0 28.4 1.0

Y.Zheng, R.Sethi, L.S.Mangala, C.Taylor, J.Goldsmith, M.Wang, K.Masuda, M.Karaminejadranjbar, D.Mannion, F.Miranda, S.Herrero-Gonzalez, K.Hellner, F.Chen, A.Alsaadi, A.Albukhari, D.C.Fotso, C.Yau, D.Jiang, S.Pradeep, C.Rodriguez-Aguayo, G.Lopez-Berestein, S.Knapp, N.S.Gray, L.Campo, K.A.Myers, S.Dhar, D.Ferguson, R.C.Bast, A.K.Sood, F.Von Delft, A.A.Ahmed. Tuning Microtubule Dynamics to Enhance Cancer Therapy By Modulating Fer-Mediated CRMP2 Phosphorylation. Nat Commun V. 9 476 2018.
ISSN: ESSN 2041-1723
PubMed: 29396402
DOI: 10.1038/S41467-017-02811-7