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Cadmium in PDB 4rdr: Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions)

Protein crystallography data

The structure of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions), PDB code: 4rdr was solved by C.Calmettes, T.F.Moraes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.98 / 2.47
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.073, 155.819, 159.607, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.8

Other elements in 4rdr:

The structure of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions) (pdb code 4rdr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions), PDB code: 4rdr:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4rdr

Go back to Cadmium Binding Sites List in 4rdr
Cadmium binding site 1 out of 2 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd801

b:92.7
occ:1.00
OD2 A:ASP251 2.4 84.0 1.0
OD1 A:ASP251 2.5 84.0 1.0
NE2 A:HIS249 2.5 83.5 1.0
CG A:ASP251 2.7 79.2 1.0
CE1 A:HIS249 3.4 77.8 1.0
CD2 A:HIS249 3.5 78.0 1.0
CB A:SER284 4.2 94.2 1.0
CB A:ASP251 4.2 68.0 1.0
OG A:SER284 4.5 0.9 1.0
ND1 A:HIS249 4.5 78.5 1.0
CG A:HIS249 4.6 73.6 1.0
NZ A:LYS558 4.7 94.8 1.0

Cadmium binding site 2 out of 2 in 4rdr

Go back to Cadmium Binding Sites List in 4rdr
Cadmium binding site 2 out of 2 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Locked Conformation Bound to Zinc and Cadmium Ions) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd802

b:0.6
occ:1.00
NE2 A:HIS243 2.3 79.9 1.0
OE1 A:GLU347 2.3 81.5 1.0
CD2 A:HIS243 2.4 65.6 1.0
OD2 A:ASP246 2.4 0.3 1.0
OE2 A:GLU347 2.5 94.9 1.0
OD1 A:ASP246 2.5 0.2 1.0
CD A:GLU347 2.7 81.3 1.0
CG A:ASP246 2.7 0.9 1.0
CE1 A:HIS243 3.5 98.3 1.0
CG A:HIS243 3.6 86.8 1.0
NE2 A:HIS241 3.7 99.8 1.0
ND1 A:HIS243 4.1 99.6 1.0
CB A:ASP246 4.2 92.7 1.0
CG A:GLU347 4.2 77.1 1.0
CE1 A:HIS241 4.5 0.2 1.0
CD2 A:HIS241 4.7 97.9 1.0
CB A:HIS243 4.7 94.3 1.0
CA A:HIS243 4.8 0.5 1.0
CB A:GLU347 4.8 61.9 1.0
CA A:ASP246 4.9 90.7 1.0
ND1 A:HIS298 5.0 0.9 1.0

Reference:

C.Calmettes, C.Ing, C.M.Buckwalter, M.El Bakkouri, C.Chieh-Lin Lai, A.Pogoutse, S.D.Gray-Owen, R.Pomes, T.F.Moraes. The Molecular Mechanism of Zinc Acquisition By the Neisserial Outer-Membrane Transporter Znud. Nat Commun V. 6 7996 2015.
ISSN: ESSN 2041-1723
PubMed: 26282243
DOI: 10.1038/NCOMMS8996
Page generated: Sat Dec 12 08:25:48 2020

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