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Cadmium in PDB 4u9r: Structure of the N-Terminal Extension From Cupriavidus Metallidurans Czcp

Protein crystallography data

The structure of Structure of the N-Terminal Extension From Cupriavidus Metallidurans Czcp, PDB code: 4u9r was solved by A.T.Smith, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.01 / 2.17
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 58.160, 58.160, 72.010, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of the N-Terminal Extension From Cupriavidus Metallidurans Czcp (pdb code 4u9r). 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 N-Terminal Extension From Cupriavidus Metallidurans Czcp, PDB code: 4u9r:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 4u9r

Go back to Cadmium Binding Sites List in 4u9r
Cadmium binding site 1 out of 2 in the Structure of the N-Terminal Extension From Cupriavidus Metallidurans Czcp


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 N-Terminal Extension From Cupriavidus Metallidurans Czcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:49.4
occ:1.00
OD1 A:ASP42 2.1 38.1 1.0
OE2 A:GLU146 2.1 62.2 1.0
NE2 A:HIS105 2.2 63.2 1.0
CD A:GLU146 2.6 68.9 1.0
SG A:CYS44 2.6 36.7 1.0
OE1 A:GLU146 2.7 73.6 1.0
CD2 A:HIS105 2.8 68.7 1.0
OD2 A:ASP42 2.8 63.9 1.0
CG A:ASP42 2.8 57.3 1.0
CB A:CYS44 3.2 33.0 1.0
CE1 A:HIS105 3.4 72.4 1.0
N A:CYS44 3.8 40.1 1.0
CG A:GLU146 3.8 69.1 1.0
CA A:CYS44 4.0 38.8 1.0
CG A:HIS105 4.0 75.0 1.0
CD2 A:LEU37 4.2 50.6 1.0
NH1 A:ARG47 4.2 44.0 1.0
CB A:ASP42 4.3 49.0 1.0
ND1 A:HIS105 4.3 71.3 1.0
CB A:PHE103 4.4 47.8 1.0
O A:HOH408 4.5 45.6 1.0
CD A:PRO43 4.6 51.4 1.0
CG A:PRO43 4.6 49.8 1.0
N A:PRO43 4.7 47.8 1.0
CB A:GLU146 4.7 69.5 1.0
C A:PRO43 4.8 47.5 1.0
C A:ASP42 5.0 49.4 1.0

Cadmium binding site 2 out of 2 in 4u9r

Go back to Cadmium Binding Sites List in 4u9r
Cadmium binding site 2 out of 2 in the Structure of the N-Terminal Extension From Cupriavidus Metallidurans Czcp


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 N-Terminal Extension From Cupriavidus Metallidurans Czcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:37.1
occ:1.00
NE2 A:HIS77 2.2 27.2 1.0
NE2 A:HIS62 2.2 39.0 1.0
SG A:CYS75 2.5 33.1 1.0
P A:TCE303 2.7 64.1 1.0
C1 A:TCE303 2.8 75.0 1.0
CE1 A:HIS62 2.9 45.8 1.0
CD2 A:HIS77 3.1 31.1 1.0
CE1 A:HIS77 3.2 34.3 1.0
CD2 A:HIS62 3.4 42.8 1.0
CB A:CYS75 3.4 31.1 1.0
C3 A:TCE303 3.9 84.9 1.0
C6 A:TCE303 4.1 86.2 1.0
ND1 A:HIS62 4.1 41.1 1.0
ND1 A:HIS77 4.3 35.0 1.0
CG A:HIS77 4.3 31.0 1.0
NH2 A:ARG27 4.3 47.0 1.0
C2 A:TCE303 4.3 81.4 1.0
C4 A:TCE303 4.3 84.2 1.0
CG A:HIS62 4.4 39.0 1.0
CD A:LYS25 4.4 41.3 1.0
CD A:LYS64 4.5 61.6 1.0
CA A:CYS75 4.6 33.3 1.0
C A:CYS75 4.7 31.2 1.0
NZ A:LYS25 4.7 47.1 1.0
O A:CYS75 4.7 28.7 1.0
CE A:LYS25 4.9 46.9 1.0
NE A:ARG27 4.9 45.7 1.0

Reference:

A.T.Smith, D.Barupala, T.L.Stemmler, A.C.Rosenzweig. A New Metal Binding Domain Involved in Cadmium, Cobalt and Zinc Transport. Nat.Chem.Biol. V. 11 678 2015.
ISSN: ESSN 1552-4469
PubMed: 26192600
DOI: 10.1038/NCHEMBIO.1863
Page generated: Sat Dec 12 08:25:50 2020

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