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Cadmium in PDB 3ow2: Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit

Protein crystallography data

The structure of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit, PDB code: 3ow2 was solved by Z.F.Kanyo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.853, 298.000, 574.985, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3ow2:

The structure of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit also contains other interesting chemical elements:

Fluorine (F) 1 atom
Strontium (Sr) 98 atoms
Magnesium (Mg) 61 atoms
Potassium (K) 1 atom
Chlorine (Cl) 13 atoms
Sodium (Na) 26 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit (pdb code 3ow2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit, PDB code: 3ow2:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 3ow2

Go back to Cadmium Binding Sites List in 3ow2
Cadmium binding site 1 out of 4 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


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 Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd8701

b:0.2
occ:1.00
SG T:CYS32 2.3 33.8 1.0
SG T:CYS36 2.3 38.0 1.0
SG T:CYS6 2.4 36.4 1.0
SG T:CYS9 2.5 50.1 1.0
CB T:CYS6 3.3 39.6 1.0
CB T:CYS9 3.4 46.7 1.0
N T:CYS9 3.6 43.3 1.0
CB T:CYS32 3.6 36.1 1.0
CB T:CYS36 3.7 39.5 1.0
CA T:CYS9 4.0 45.5 1.0
N T:CYS32 4.3 37.1 1.0
CB T:TYR8 4.4 39.7 1.0
OG1 T:THR11 4.4 46.3 1.0
CA T:CYS32 4.5 36.4 1.0
N T:GLY10 4.6 47.4 1.0
C T:TYR8 4.7 42.2 1.0
CA T:CYS6 4.7 40.8 1.0
C T:CYS9 4.7 46.7 1.0
OG T:SER33 4.8 42.1 1.0
N T:SER33 4.8 38.6 1.0
CA T:TYR8 4.9 40.9 1.0
O T:CYS6 5.0 40.2 1.0
CD2 T:TYR8 5.0 36.7 1.0
N T:TYR8 5.0 40.5 1.0

Cadmium binding site 2 out of 4 in 3ow2

Go back to Cadmium Binding Sites List in 3ow2
Cadmium binding site 2 out of 4 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


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 Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cd101

b:0.7
occ:1.00
SG Y:CYS60 2.0 29.6 1.0
SG Y:CYS39 2.3 44.7 1.0
SG Y:CYS57 2.6 45.0 1.0
SG Y:CYS42 2.6 61.8 1.0
CB Y:CYS39 2.8 50.9 1.0
CB Y:CYS42 3.1 59.9 1.0
CB Y:CYS60 3.4 38.5 1.0
CB Y:CYS57 3.7 45.1 1.0
N Y:CYS42 3.7 59.5 1.0
N Y:CYS60 3.8 43.0 1.0
CA Y:CYS42 3.9 60.0 1.0
CA Y:CYS60 4.2 39.9 1.0
CA Y:CYS39 4.3 52.3 1.0
CB Y:HIS59 4.3 48.3 1.0
C Y:CYS42 4.4 60.2 1.0
O Y:PHE44 4.5 61.1 1.0
CD2 Y:HIS59 4.6 52.4 1.0
C Y:CYS39 4.8 53.5 1.0
O Y:CYS42 4.8 61.3 1.0
CG Y:HIS59 4.8 51.5 1.0
N Y:GLY43 4.8 59.7 1.0
N Y:PHE44 4.8 61.9 1.0
CB Y:PHE44 4.9 62.7 1.0
C Y:VAL41 4.9 58.8 1.0
C Y:HIS59 4.9 44.8 1.0
CB Y:VAL41 4.9 57.8 1.0
O Y:CYS39 5.0 54.2 1.0

Cadmium binding site 3 out of 4 in 3ow2

Go back to Cadmium Binding Sites List in 3ow2
Cadmium binding site 3 out of 4 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd101

b:0.8
occ:1.00
SG Z:CYS22 2.3 22.1 1.0
SG Z:CYS34 2.3 21.2 1.0
SG Z:CYS37 2.3 21.6 1.0
SG Z:CYS19 2.3 21.8 1.0
CB Z:CYS22 3.0 24.7 1.0
CB Z:CYS19 3.3 26.6 1.0
CB Z:CYS34 3.4 23.1 1.0
CB Z:CYS37 3.4 21.3 1.0
N Z:CYS22 3.4 25.8 1.0
CA Z:CYS22 3.8 25.3 1.0
N Z:CYS37 3.9 23.8 1.0
CB Z:PHE39 4.1 26.9 1.0
CA Z:CYS37 4.2 23.4 1.0
CB Z:ARG21 4.3 24.8 1.0
C Z:ARG21 4.3 26.4 1.0
CD Z:ARG21 4.5 26.4 1.0
CA Z:CYS19 4.6 26.6 1.0
C Z:CYS22 4.7 26.9 1.0
CA Z:ARG21 4.7 26.1 1.0
O Z:CYS19 4.7 29.2 1.0
N Z:GLY23 4.7 27.2 1.0
N Z:PHE39 4.7 26.5 1.0
N Z:ARG21 4.8 27.3 1.0
CG Z:ARG21 4.8 25.7 1.0
CA Z:CYS34 4.8 23.5 1.0
C Z:CYS37 4.8 23.4 1.0
CB Z:SER36 4.8 22.8 1.0
C Z:CYS19 4.9 29.0 1.0
N Z:GLY38 4.9 23.2 1.0

Cadmium binding site 4 out of 4 in 3ow2

Go back to Cadmium Binding Sites List in 3ow2
Cadmium binding site 4 out of 4 in the Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd101

b:87.6
occ:1.00
SG 2:CYS14 2.1 43.4 1.0
SG 2:CYS74 2.4 59.1 1.0
SG 2:CYS11 2.4 40.8 1.0
SG 2:CYS71 2.4 38.7 1.0
CB 2:CYS71 3.1 41.6 1.0
CB 2:CYS11 3.6 41.0 1.0
CB 2:CYS74 3.6 52.2 1.0
CB 2:CYS14 3.6 45.3 1.0
N 2:CYS14 3.9 46.6 1.0
N 2:CYS74 3.9 50.6 1.0
CA 2:CYS14 4.3 46.1 1.0
CA 2:CYS74 4.3 50.9 1.0
CB 2:HIS13 4.5 45.4 1.0
CA 2:CYS71 4.5 41.5 1.0
OE1 2:GLN18 4.7 54.9 1.0
C 2:HIS13 4.9 46.8 1.0
CA 2:CYS11 4.9 41.7 1.0
C 2:CYS74 5.0 50.2 1.0
N 2:GLY75 5.0 48.8 1.0

Reference:

Z.F.Kanyo, N/A. N/A N/A.
Page generated: Wed Oct 28 10:04:09 2020
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