Cadmium in PDB 3ccm: Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
Protein crystallography data
The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U, PDB code: 3ccm
was solved by
G.Blaha,
G.Gurel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.70 /
2.55
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
211.531,
298.177,
573.367,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.1 /
24
|
Other elements in 3ccm:
The structure of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
(pdb code 3ccm). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the
Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U, PDB code: 3ccm:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
Cadmium binding site 1 out
of 5 in 3ccm
Go back to
Cadmium Binding Sites List in 3ccm
Cadmium binding site 1 out
of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Cd8705
b:88.3
occ:1.00
|
O
|
O:HOH5650
|
2.4
|
46.8
|
1.0
|
ND1
|
O:HIS40
|
2.7
|
29.1
|
1.0
|
O
|
O:HOH5322
|
3.1
|
41.2
|
1.0
|
CG
|
O:HIS40
|
3.6
|
27.9
|
1.0
|
CE1
|
O:HIS40
|
3.6
|
27.7
|
1.0
|
CB
|
O:HIS40
|
3.7
|
30.7
|
1.0
|
CG
|
O:ARG37
|
4.3
|
38.5
|
1.0
|
O
|
O:HOH3002
|
4.5
|
56.6
|
1.0
|
NE2
|
O:HIS40
|
4.7
|
30.3
|
1.0
|
CD2
|
O:HIS40
|
4.7
|
29.4
|
1.0
|
CZ
|
O:ARG37
|
4.7
|
40.7
|
1.0
|
NH1
|
O:ARG37
|
4.8
|
39.5
|
1.0
|
NE
|
O:ARG37
|
4.8
|
40.0
|
1.0
|
O
|
O:ARG37
|
4.9
|
34.2
|
1.0
|
CB
|
O:ARG37
|
4.9
|
37.5
|
1.0
|
CA
|
O:ARG37
|
5.0
|
36.4
|
1.0
|
|
Cadmium binding site 2 out
of 5 in 3ccm
Go back to
Cadmium Binding Sites List in 3ccm
Cadmium binding site 2 out
of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Cd8701
b:62.7
occ:1.00
|
SG
|
U:CYS36
|
2.4
|
44.7
|
1.0
|
SG
|
U:CYS6
|
2.5
|
41.6
|
1.0
|
SG
|
U:CYS9
|
2.5
|
48.6
|
1.0
|
SG
|
U:CYS32
|
2.6
|
30.1
|
1.0
|
CB
|
U:CYS6
|
3.1
|
47.6
|
1.0
|
CB
|
U:CYS9
|
3.3
|
46.8
|
1.0
|
CB
|
U:CYS36
|
3.5
|
42.4
|
1.0
|
CB
|
U:CYS32
|
3.7
|
33.0
|
1.0
|
N
|
U:CYS9
|
3.7
|
45.5
|
1.0
|
CA
|
U:CYS9
|
4.0
|
46.4
|
1.0
|
N
|
U:CYS32
|
4.1
|
33.5
|
1.0
|
OG1
|
U:THR11
|
4.4
|
53.4
|
1.0
|
CA
|
U:CYS32
|
4.5
|
34.0
|
1.0
|
OG
|
U:SER33
|
4.6
|
29.7
|
1.0
|
CA
|
U:CYS6
|
4.6
|
46.6
|
1.0
|
CB
|
U:TYR8
|
4.7
|
41.9
|
1.0
|
N
|
U:GLY10
|
4.8
|
49.2
|
1.0
|
N
|
U:SER33
|
4.8
|
36.7
|
1.0
|
C
|
U:CYS9
|
4.8
|
47.9
|
1.0
|
C
|
U:TYR8
|
4.9
|
45.1
|
1.0
|
CA
|
U:CYS36
|
4.9
|
42.2
|
1.0
|
|
Cadmium binding site 3 out
of 5 in 3ccm
Go back to
Cadmium Binding Sites List in 3ccm
Cadmium binding site 3 out
of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Cd8703
b:67.7
occ:1.00
|
SG
|
Z:CYS84
|
2.2
|
41.2
|
1.0
|
SG
|
Z:CYS63
|
2.4
|
53.4
|
1.0
|
SG
|
Z:CYS66
|
2.5
|
63.2
|
1.0
|
SG
|
Z:CYS81
|
2.5
|
43.5
|
1.0
|
CB
|
Z:CYS81
|
3.2
|
48.4
|
1.0
|
CB
|
Z:CYS63
|
3.3
|
55.8
|
1.0
|
CB
|
Z:CYS84
|
3.4
|
46.4
|
1.0
|
CB
|
Z:CYS66
|
3.6
|
63.5
|
1.0
|
N
|
Z:CYS66
|
3.8
|
63.0
|
1.0
|
N
|
Z:CYS84
|
3.8
|
48.8
|
1.0
|
CA
|
Z:CYS84
|
4.2
|
47.4
|
1.0
|
CA
|
Z:CYS66
|
4.3
|
63.0
|
1.0
|
CB
|
Z:ASN65
|
4.3
|
61.2
|
1.0
|
CB
|
Z:TYR83
|
4.6
|
52.9
|
1.0
|
CB
|
Z:TYR86
|
4.6
|
43.2
|
1.0
|
CD2
|
Z:TYR83
|
4.7
|
56.5
|
1.0
|
CA
|
Z:CYS81
|
4.7
|
47.1
|
1.0
|
CA
|
Z:CYS63
|
4.7
|
56.5
|
1.0
|
C
|
Z:ASN65
|
4.9
|
62.6
|
1.0
|
C
|
Z:CYS66
|
4.9
|
63.0
|
1.0
|
C
|
Z:CYS84
|
4.9
|
47.6
|
1.0
|
C
|
Z:TYR83
|
4.9
|
50.4
|
1.0
|
CA
|
Z:ASN65
|
5.0
|
61.4
|
1.0
|
|
Cadmium binding site 4 out
of 5 in 3ccm
Go back to
Cadmium Binding Sites List in 3ccm
Cadmium binding site 4 out
of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Cd8702
b:54.9
occ:1.00
|
SG
|
1:CYS22
|
2.4
|
20.2
|
1.0
|
SG
|
1:CYS19
|
2.4
|
21.2
|
1.0
|
SG
|
1:CYS34
|
2.5
|
20.7
|
1.0
|
SG
|
1:CYS37
|
2.5
|
17.7
|
1.0
|
CB
|
1:CYS19
|
3.1
|
21.9
|
1.0
|
CB
|
1:CYS34
|
3.2
|
21.4
|
1.0
|
CB
|
1:CYS22
|
3.3
|
23.3
|
1.0
|
CB
|
1:CYS37
|
3.3
|
18.0
|
1.0
|
N
|
1:CYS22
|
3.7
|
26.5
|
1.0
|
N
|
1:CYS37
|
3.7
|
20.7
|
1.0
|
CA
|
1:CYS37
|
4.0
|
20.0
|
1.0
|
CA
|
1:CYS22
|
4.1
|
24.4
|
1.0
|
CB
|
1:PHE39
|
4.3
|
23.9
|
1.0
|
CA
|
1:CYS19
|
4.6
|
23.8
|
1.0
|
CA
|
1:CYS34
|
4.6
|
22.6
|
1.0
|
CB
|
1:ARG21
|
4.7
|
28.9
|
1.0
|
C
|
1:CYS37
|
4.7
|
18.8
|
1.0
|
N
|
1:PHE39
|
4.7
|
22.8
|
1.0
|
N
|
1:GLY38
|
4.7
|
19.5
|
1.0
|
C
|
1:ARG21
|
4.8
|
28.0
|
1.0
|
CB
|
1:SER36
|
4.8
|
21.7
|
1.0
|
O
|
1:HOH1020
|
4.8
|
30.8
|
1.0
|
C
|
1:SER36
|
4.9
|
22.6
|
1.0
|
C
|
1:CYS22
|
4.9
|
23.2
|
1.0
|
N
|
1:GLY23
|
4.9
|
21.4
|
1.0
|
|
Cadmium binding site 5 out
of 5 in 3ccm
Go back to
Cadmium Binding Sites List in 3ccm
Cadmium binding site 5 out
of 5 in the Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Structure of Anisomycin Resistant 50S Ribosomal Subunit: 23S Rrna Mutation G2611U within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Cd8704
b:63.9
occ:1.00
|
SG
|
3:CYS71
|
2.3
|
41.1
|
1.0
|
SG
|
3:CYS74
|
2.4
|
51.1
|
1.0
|
SG
|
3:CYS11
|
2.4
|
41.9
|
1.0
|
O
|
3:HOH9055
|
2.5
|
0.1
|
1.0
|
SG
|
3:CYS14
|
2.6
|
53.8
|
1.0
|
CB
|
3:CYS71
|
3.2
|
47.1
|
1.0
|
CB
|
3:CYS14
|
3.3
|
51.3
|
1.0
|
CB
|
3:CYS11
|
3.5
|
44.0
|
1.0
|
CB
|
3:CYS74
|
3.6
|
53.2
|
1.0
|
N
|
3:CYS14
|
3.8
|
52.7
|
1.0
|
N
|
3:CYS74
|
4.1
|
54.9
|
1.0
|
CA
|
3:CYS14
|
4.1
|
53.4
|
1.0
|
CA
|
3:CYS74
|
4.4
|
54.0
|
1.0
|
OE1
|
3:GLN18
|
4.4
|
55.1
|
1.0
|
CB
|
3:HIS13
|
4.5
|
49.9
|
1.0
|
CA
|
3:CYS71
|
4.6
|
46.5
|
1.0
|
C
|
3:HIS13
|
4.7
|
51.0
|
1.0
|
CG
|
3:GLN18
|
4.9
|
52.3
|
1.0
|
CA
|
3:CYS11
|
4.9
|
44.0
|
1.0
|
CB
|
3:GLN18
|
5.0
|
49.8
|
1.0
|
O
|
3:HOH9033
|
5.0
|
30.2
|
1.0
|
|
Reference:
G.Blaha,
G.Gurel,
S.J.Schroeder,
P.B.Moore,
T.A.Steitz.
Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Fri Jul 19 15:43:09 2024
|