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

Protein crystallography data

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

Other elements in 4d7y:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Mouse C1QL1 Globular Domain (pdb code 4d7y). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Mouse C1QL1 Globular Domain, PDB code: 4d7y:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4d7y

Go back to Cadmium Binding Sites List in 4d7y
Cadmium 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 Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Mouse C1QL1 Globular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1259

b:16.0
occ:0.33
OD2 A:ASP210 2.5 18.2 1.0
CL A:CL1263 2.8 31.8 0.3
OD1 A:ASP210 2.8 19.5 1.0
CG A:ASP210 3.0 15.9 1.0
O A:HOH2062 4.4 14.7 1.0
CB A:ASP210 4.4 15.2 1.0

Cadmium binding site 2 out of 2 in 4d7y

Go back to Cadmium Binding Sites List in 4d7y
Cadmium 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 Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Mouse C1QL1 Globular Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1260

b:10.3
occ:0.33
OD1 A:ASP214 2.4 11.7 1.0
O A:HOH2068 2.5 14.6 1.0
CG A:ASP214 3.2 10.6 1.0
OD2 A:ASP214 3.4 12.4 1.0
NI A:NI1261 4.0 8.6 0.4
O A:HOH2067 4.3 13.2 1.0
N A:TYR215 4.5 10.4 1.0
O A:HOH2065 4.6 11.3 1.0
CB A:ASP214 4.7 10.9 1.0
O A:HOH2070 4.7 42.5 1.0
O A:TYR215 4.7 13.3 1.0

Reference:

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
Page generated: Sun Jan 24 09:56:35 2021

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