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Cadmium in PDB 5wuf: Structural Basis For Conductance Through Tric Cation Channels

Protein crystallography data

The structure of Structural Basis For Conductance Through Tric Cation Channels, PDB code: 5wuf was solved by Y.Mao, F.Gao, M.Su, X.H.Wang, Y.Zeng, R.Bruni, B.Kloss, W.A.Hendrickson, Y.H.Chen, New York Consortium On Membrane Protein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.74 / 2.40
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 91.312, 91.312, 252.799, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 27.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structural Basis For Conductance Through Tric Cation Channels (pdb code 5wuf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structural Basis For Conductance Through Tric Cation Channels, PDB code: 5wuf:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5wuf

Go back to Cadmium Binding Sites List in 5wuf
Cadmium binding site 1 out of 4 in the Structural Basis For Conductance Through Tric Cation Channels


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structural Basis For Conductance Through Tric Cation Channels within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:80.0
occ:1.00
OD1 A:ASP30 2.7 93.1 1.0
OD2 A:ASP30 2.7 0.6 1.0
O A:HOH416 2.8 50.3 1.0
CG A:ASP30 3.0 89.5 1.0
N A:GLY33 3.8 76.6 1.0
CA A:GLY33 4.2 60.1 1.0
CB A:ASP30 4.5 87.3 1.0
CB A:PHE32 4.6 77.6 1.0
C A:PHE32 4.7 77.1 1.0

Cadmium binding site 2 out of 4 in 5wuf

Go back to Cadmium Binding Sites List in 5wuf
Cadmium binding site 2 out of 4 in the Structural Basis For Conductance Through Tric Cation Channels


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structural Basis For Conductance Through Tric Cation Channels within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:80.3
occ:0.94
NE2 A:HIS166 2.9 61.5 1.0
O A:HOH425 3.1 66.4 1.0
CD2 A:HIS166 3.2 52.7 1.0
O A:HOH404 3.7 67.0 1.0
CE1 A:HIS166 4.1 77.4 1.0
CG A:HIS166 4.5 61.0 1.0
CD2 A:LEU111 4.8 77.0 1.0
ND1 A:HIS166 4.9 63.3 1.0

Cadmium binding site 3 out of 4 in 5wuf

Go back to Cadmium Binding Sites List in 5wuf
Cadmium binding site 3 out of 4 in the Structural Basis For Conductance Through Tric Cation Channels


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structural Basis For Conductance Through Tric Cation Channels within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:0.8
occ:1.00
OE2 A:GLU149 2.7 87.9 1.0
OE2 A:GLU148 2.9 0.2 1.0
OE1 A:GLU149 2.9 0.8 1.0
CD A:GLU149 3.1 90.0 1.0
CD A:GLU148 3.2 0.9 1.0
OE1 A:GLU148 3.3 97.4 1.0
CG A:GLU148 4.3 0.2 1.0
O A:HOH403 4.3 0.5 1.0
CG A:GLU149 4.5 82.2 1.0
CD A:ARG147 4.6 66.6 1.0
CB A:ARG147 4.6 69.2 1.0
ND1 A:HIS194 4.7 95.1 1.0
CE1 A:HIS194 4.7 98.1 1.0
N A:GLU148 4.9 82.0 1.0

Cadmium binding site 4 out of 4 in 5wuf

Go back to Cadmium Binding Sites List in 5wuf
Cadmium binding site 4 out of 4 in the Structural Basis For Conductance Through Tric Cation Channels


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structural Basis For Conductance Through Tric Cation Channels within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:0.5
occ:1.00
O A:HOH410 2.6 50.0 1.0
OD1 A:ASP9 3.0 0.6 1.0
NH1 A:ARG49 3.4 70.9 1.0
OD2 A:ASP9 3.4 0.0 1.0
CG A:ASP9 3.5 99.1 1.0
CD A:LYS109 3.7 63.6 1.0
O A:HOH406 3.7 50.0 1.0
NH2 A:ARG49 3.9 52.3 1.0
CZ A:ARG49 3.9 73.5 1.0
NZ A:LYS109 4.4 62.0 1.0
CB A:LYS109 4.5 59.9 1.0
CB A:LEU105 4.5 54.4 1.0
CE A:LYS109 4.6 52.3 1.0
CG A:LYS109 4.6 56.8 1.0
O A:LEU105 4.7 65.3 1.0
CB A:ASP9 4.9 87.5 1.0

Reference:

M.Su, F.Gao, Q.Yuan, Y.Mao, D.L.Li, Y.Guo, C.Yang, X.H.Wang, R.Bruni, B.Kloss, H.Zhao, Y.Zeng, F.B.Zhang, A.R.Marks, W.A.Hendrickson, Y.H.Chen. Structural Basis For Conductance Through Tric Cation Channels. Nat Commun V. 8 15103 2017.
ISSN: ESSN 2041-1723
PubMed: 28524849
DOI: 10.1038/NCOMMS15103
Page generated: Sat Dec 12 08:27:56 2020

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