Nickel in PDB 4d7y: Crystal Structure of Mouse C1QL1 Globular Domain

The structure of Crystal Structure of Mouse C1QL1 Globular Domain, PDB code: 4d7y was solved by W.Kakegawa, N.Mitakidis, E.Miura, M.Abe, K.Matsuda, Y.Takeo, K.Kohda, J.Motohashi, A.Takahashi, S.Nagao, S.Muramatsu, M.Watanabe, K.Sakimura, A.R.Aricescu, M.Yuzaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.040 / 1.44
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	68.080, 68.080, 65.910, 90.00, 90.00, 120.00
R / Rfree (%)	14.01 / 16.93

The structure of Crystal Structure of Mouse C1QL1 Globular Domain also contains other interesting chemical elements:

Cadmium	(Cd)	2 atoms
Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Nickel atom in the Crystal Structure of Mouse C1QL1 Globular Domain (pdb code 4d7y). 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 Mouse C1QL1 Globular Domain, PDB code: 4d7y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Mouse C1QL1 Globular Domain


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 Mouse C1QL1 Globular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1261 b:8.6 occ:0.36 O A:HOH2063 2.2 12.4 1.0 OD2 A:ASP214 2.2 12.4 1.0 CG A:ASP214 3.2 10.6 1.0 OD1 A:ASP214 3.9 11.7 1.0 CD A:CD1260 4.0 10.3 0.3 OD2 A:ASP208 4.2 14.1 1.0 O A:HOH2065 4.2 11.3 1.0 CB A:ASP214 4.3 10.9 1.0 O A:GLN207 4.5 12.2 1.0 NI A:NI1262 5.0 11.4 0.4

Nickel binding site 2 out of 2 in the Crystal Structure of Mouse C1QL1 Globular Domain


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 Mouse C1QL1 Globular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1262 b:11.4 occ:0.37 O A:HOH2062 2.1 14.7 1.0 OD2 A:ASP208 2.2 14.1 1.0 CG A:ASP208 3.1 14.2 1.0 OD1 A:ASP208 3.5 13.8 1.0 O A:HOH2063 4.2 12.4 1.0 OD2 A:ASP210 4.2 18.2 1.0 CB A:ASP208 4.4 13.4 1.0 ND2 A:ASN212 4.6 15.9 1.0 CA A:ASP208 4.7 12.7 1.0 NI A:NI1261 5.0 8.6 0.4 N A:ALA209 5.0 11.3 1.0

W.Kakegawa, N.Mitakidis, E.Miura, M.Abe, K.Matsuda, Y.Takeo, K.Kohda, J.Motohashi, A.Takahashi, S.Nagao, S.Muramatsu, M.Watanabe, K.Sakimura, A.R.Aricescu, M.Yuzaki. Anterograde C1QL1 Signaling Is Required in Order to Determine and Maintain A Single-Winner Climbing Fiber in the Mouse Cerebellum Neuron V. 85 316 2015.
ISSN: ISSN 0896-6273
PubMed: 25611509
DOI: 10.1016/J.NEURON.2014.12.020