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Cadmium in PDB 4uto: Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State

Protein crystallography data

The structure of Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State, PDB code: 4uto was solved by Z.Luo, R.M.Counago, M.Maher, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.73 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.737, 59.292, 62.468, 106.86, 104.90, 93.37
R / Rfree (%) 18.1 / 21.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State (pdb code 4uto). 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 Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State, PDB code: 4uto:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4uto

Go back to Cadmium Binding Sites List in 4uto
Cadmium binding site 1 out of 2 in the Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State


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 Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1310

b:13.2
occ:0.21
NE2 A:HIS139 2.6 9.7 1.0
OE2 A:GLU205 2.6 20.1 1.0
OE1 A:GLU205 2.6 21.5 1.0
O A:HOH2037 2.7 45.1 1.0
CD A:GLU205 2.9 23.0 1.0
HE1 A:HIS67 3.0 24.1 0.6
HE1 A:HIS139 3.1 10.9 1.0
CE1 A:HIS139 3.2 10.0 1.0
CE1 A:HIS67 3.4 22.1 0.6
NE2 A:HIS67 3.4 22.1 0.6
HB3 A:ALA207 3.6 10.4 1.0
CD2 A:HIS139 3.7 8.8 1.0
HG12 A:ILE225 3.8 21.0 1.0
HD2 A:HIS139 4.0 11.8 1.0
HB2 A:ALA207 4.1 8.8 1.0
HG21 A:ILE225 4.3 21.9 1.0
CB A:ALA207 4.3 9.3 1.0
CG A:GLU205 4.3 13.7 1.0
ND1 A:HIS139 4.4 8.9 1.0
ND1 A:HIS67 4.4 22.9 0.6
HD21 A:ASN280 4.5 41.7 1.0
HG2 A:GLU205 4.5 15.2 1.0
CD2 A:HIS67 4.5 22.4 0.6
O A:HOH2188 4.6 19.2 1.0
CG A:HIS139 4.7 7.3 1.0
O A:HOH2187 4.7 37.1 1.0
HA A:ILE225 4.8 13.9 1.0
CG1 A:ILE225 4.8 20.1 1.0
HG3 A:GLU205 4.9 16.9 1.0
HB3 A:GLU205 4.9 9.7 1.0
HD1 A:HIS67 4.9 26.0 0.6
HB1 A:ALA207 4.9 6.0 1.0
HA A:ALA207 5.0 8.1 1.0

Cadmium binding site 2 out of 2 in 4uto

Go back to Cadmium Binding Sites List in 4uto
Cadmium binding site 2 out of 2 in the Crystal Structure of Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State


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 Pneumococcal Surface Antigen Psaa D280N in the Cd-Bound, Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1310

b:17.2
occ:0.18
NE2 B:HIS139 2.5 10.2 1.0
HE1 B:HIS67 2.6 24.1 0.5
OE1 B:GLU205 2.7 21.9 1.0
OE2 B:GLU205 2.8 27.6 1.0
CE1 B:HIS67 3.0 23.1 0.5
CD B:GLU205 3.1 28.5 1.0
HE1 B:HIS139 3.2 13.4 1.0
NE2 B:HIS67 3.2 23.8 0.5
CE1 B:HIS139 3.2 9.6 1.0
CD2 B:HIS139 3.7 9.3 1.0
HB3 B:ALA207 3.7 11.4 1.0
HD2 B:HIS139 3.9 11.4 1.0
ND1 B:HIS67 4.1 23.8 0.5
HG12 B:ILE225 4.1 20.4 1.0
HD21 B:ASN280 4.1 28.8 1.0
HG21 B:ILE225 4.2 24.3 1.0
HB2 B:ALA207 4.2 11.2 1.0
CD2 B:HIS67 4.3 24.6 0.5
CB B:ALA207 4.4 10.9 1.0
ND1 B:HIS139 4.4 8.3 1.0
HD1 B:HIS67 4.5 26.1 0.5
CG B:GLU205 4.5 11.9 1.0
O B:HOH2174 4.7 20.3 1.0
CG B:HIS139 4.7 8.2 1.0
HG2 B:GLU205 4.7 10.8 1.0
O B:HOH2204 4.7 27.3 1.0
CG B:HIS67 4.8 23.5 0.5
ND2 B:ASN280 4.8 23.5 1.0
HD2 B:HIS67 4.9 26.3 0.5
HB3 B:GLU205 5.0 7.0 1.0

Reference:

S.L.Begg, B.A.Eijkelkamp, Z.Luo, R.M.Counago, J.R.Morey, M.J.Maher, C.Y.Ong, A.G.Mcewan, B.Kobe, M.L.O'mara, J.C.Paton, C.A.Mcdevitt. Dysregulation of Transition Metal Ion Homeostasis Is the Molecular Basis For Cadmium Toxicity in Streptococcus Pneumoniae. Nat.Commun. V. 6 6418 2015.
ISSN: ISSN 2041-1723
PubMed: 25731976
DOI: 10.1038/NCOMMS7418
Page generated: Sat Dec 12 08:25:53 2020

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