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:
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: Fri Jul 19 16:20:39 2024
|