Cadmium in PDB 1mms: Crystal Structure of the Ribosomal Protein L11-Rna Complex
Protein crystallography data
The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms
was solved by
B.T.Wimberly,
R.Guymon,
J.P.Mccutcheon,
S.W.White,
V.Ramakrishnan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.57
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.890,
84.260,
155.510,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.9 /
25.4
|
Other elements in 1mms:
The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
(pdb code 1mms). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the
Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cadmium binding site 1 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 1 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd201
b:77.5
occ:0.91
|
O
|
C:HOH262
|
2.3
|
39.1
|
1.0
|
O
|
C:HOH264
|
2.4
|
49.4
|
1.0
|
N7
|
C:G1071
|
2.6
|
31.3
|
1.0
|
O
|
C:HOH263
|
3.3
|
31.5
|
1.0
|
O
|
C:HOH266
|
3.5
|
54.5
|
1.0
|
O6
|
C:G1071
|
3.5
|
31.9
|
1.0
|
C5
|
C:G1071
|
3.6
|
14.6
|
1.0
|
C8
|
C:G1071
|
3.6
|
20.4
|
1.0
|
C6
|
C:G1071
|
3.9
|
28.2
|
1.0
|
N1
|
C:G1089
|
4.3
|
10.6
|
1.0
|
OP1
|
C:G1071
|
4.3
|
39.0
|
1.0
|
O
|
C:HOH218
|
4.3
|
23.4
|
1.0
|
O6
|
C:G1089
|
4.5
|
38.0
|
1.0
|
O
|
C:HOH267
|
4.6
|
21.2
|
1.0
|
N4
|
C:C1072
|
4.6
|
23.9
|
1.0
|
C6
|
C:G1089
|
4.8
|
23.5
|
1.0
|
C4
|
C:G1071
|
4.8
|
11.2
|
1.0
|
N9
|
C:G1071
|
4.8
|
22.6
|
1.0
|
OP1
|
C:A1098
|
4.8
|
56.4
|
1.0
|
OP2
|
C:A1098
|
4.9
|
22.0
|
1.0
|
|
Cadmium binding site 2 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 2 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd202
b:32.4
occ:0.91
|
O
|
C:HOH445
|
1.9
|
3.6
|
1.0
|
O
|
C:HOH446
|
2.0
|
19.5
|
1.0
|
O
|
C:HOH447
|
2.0
|
12.2
|
1.0
|
N7
|
C:G1087
|
2.1
|
9.4
|
1.0
|
O2'
|
C:A1086
|
2.5
|
37.4
|
1.0
|
C8
|
C:G1087
|
3.1
|
23.9
|
1.0
|
C5
|
C:G1087
|
3.2
|
16.6
|
1.0
|
C2'
|
C:A1086
|
3.5
|
40.9
|
1.0
|
O6
|
C:G1087
|
3.6
|
25.8
|
1.0
|
C6
|
C:G1087
|
3.8
|
25.6
|
1.0
|
O3'
|
C:A1086
|
3.9
|
30.6
|
1.0
|
N1
|
C:A1103
|
4.0
|
23.8
|
1.0
|
OP2
|
C:A1057
|
4.0
|
50.5
|
1.0
|
OP2
|
C:G1087
|
4.1
|
19.3
|
1.0
|
O2'
|
C:G1056
|
4.2
|
36.3
|
1.0
|
N9
|
C:G1087
|
4.3
|
19.6
|
1.0
|
C3'
|
C:A1086
|
4.3
|
38.3
|
1.0
|
C6
|
C:G1089
|
4.3
|
23.5
|
1.0
|
C4
|
C:G1087
|
4.4
|
16.3
|
1.0
|
C5
|
C:G1089
|
4.4
|
14.4
|
1.0
|
O6
|
C:G1089
|
4.4
|
38.0
|
1.0
|
N7
|
C:G1089
|
4.6
|
20.2
|
1.0
|
N7
|
C:A1057
|
4.6
|
16.5
|
1.0
|
P
|
C:G1087
|
4.6
|
31.0
|
1.0
|
C2
|
C:A1103
|
4.6
|
20.5
|
1.0
|
C1'
|
C:A1086
|
4.7
|
29.9
|
1.0
|
N1
|
C:G1089
|
4.8
|
10.6
|
1.0
|
C6
|
C:A1103
|
4.8
|
17.5
|
1.0
|
N6
|
C:A1103
|
4.8
|
18.4
|
1.0
|
O5'
|
C:G1087
|
4.9
|
29.6
|
1.0
|
C4
|
C:G1089
|
4.9
|
10.9
|
1.0
|
|
Cadmium binding site 3 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 3 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd211
b:48.0
occ:0.91
|
O
|
C:HOH254
|
2.2
|
20.4
|
1.0
|
O
|
D:HOH256
|
2.2
|
15.3
|
1.0
|
OP1
|
D:A1095
|
2.3
|
64.6
|
1.0
|
O
|
D:HOH255
|
2.3
|
15.6
|
1.0
|
N7
|
C:A1067
|
2.4
|
21.4
|
1.0
|
C8
|
C:A1067
|
3.3
|
13.3
|
1.0
|
C5
|
C:A1067
|
3.5
|
7.0
|
1.0
|
P
|
D:A1095
|
3.7
|
43.6
|
1.0
|
N6
|
C:A1067
|
3.7
|
26.0
|
1.0
|
O3'
|
D:U1094
|
4.0
|
48.0
|
1.0
|
C6
|
C:A1067
|
4.0
|
18.5
|
1.0
|
O6
|
C:G1068
|
4.0
|
26.9
|
1.0
|
O
|
D:HOH427
|
4.3
|
17.3
|
1.0
|
O2'
|
C:U1066
|
4.4
|
33.4
|
1.0
|
O5'
|
D:A1095
|
4.4
|
28.9
|
1.0
|
N9
|
C:A1067
|
4.5
|
16.6
|
1.0
|
OP1
|
C:A1067
|
4.6
|
52.4
|
1.0
|
C4
|
C:A1067
|
4.6
|
16.3
|
1.0
|
O3'
|
C:U1066
|
4.6
|
45.3
|
1.0
|
C6
|
C:G1068
|
4.8
|
23.5
|
1.0
|
OP2
|
D:A1095
|
4.8
|
36.6
|
1.0
|
C8
|
D:A1095
|
4.9
|
20.4
|
1.0
|
|
Cadmium binding site 4 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 4 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
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 the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd302
b:31.5
occ:0.91
|
O
|
D:HOH461
|
2.0
|
2.0
|
1.0
|
O
|
D:HOH462
|
2.0
|
22.2
|
1.0
|
N7
|
D:G1087
|
2.1
|
6.6
|
1.0
|
O
|
D:HOH463
|
2.2
|
27.4
|
1.0
|
O2'
|
D:A1086
|
2.4
|
53.2
|
1.0
|
O
|
D:HOH460
|
2.4
|
28.4
|
1.0
|
C8
|
D:G1087
|
3.0
|
13.2
|
1.0
|
C5
|
D:G1087
|
3.2
|
11.8
|
1.0
|
C2'
|
D:A1086
|
3.4
|
42.6
|
1.0
|
O6
|
D:G1087
|
3.7
|
28.3
|
1.0
|
C6
|
D:G1087
|
3.8
|
26.4
|
1.0
|
O3'
|
D:A1086
|
3.8
|
33.2
|
1.0
|
N1
|
D:A1103
|
4.0
|
26.2
|
1.0
|
OP2
|
D:G1087
|
4.0
|
28.8
|
1.0
|
OP2
|
D:A1057
|
4.1
|
40.3
|
1.0
|
O2'
|
D:G1056
|
4.1
|
28.7
|
1.0
|
C3'
|
D:A1086
|
4.2
|
36.9
|
1.0
|
N9
|
D:G1087
|
4.2
|
24.4
|
1.0
|
C4
|
D:G1087
|
4.3
|
16.4
|
1.0
|
C6
|
D:G1089
|
4.4
|
26.6
|
1.0
|
C5
|
D:G1089
|
4.5
|
20.6
|
1.0
|
P
|
D:G1087
|
4.5
|
31.8
|
1.0
|
O6
|
D:G1089
|
4.5
|
34.4
|
1.0
|
C2
|
D:A1103
|
4.6
|
23.0
|
1.0
|
O
|
D:HOH372
|
4.7
|
29.1
|
1.0
|
N7
|
D:A1057
|
4.7
|
23.7
|
1.0
|
C1'
|
D:A1086
|
4.7
|
38.4
|
1.0
|
N7
|
D:G1089
|
4.8
|
20.2
|
1.0
|
O5'
|
D:G1087
|
4.8
|
32.9
|
1.0
|
C6
|
D:A1103
|
4.8
|
19.9
|
1.0
|
N1
|
D:G1089
|
4.8
|
18.2
|
1.0
|
N6
|
D:A1103
|
4.8
|
16.8
|
1.0
|
C4
|
D:G1089
|
5.0
|
15.8
|
1.0
|
|
Cadmium binding site 5 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 5 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd311
b:76.3
occ:0.91
|
N7
|
D:A1067
|
2.5
|
23.2
|
1.0
|
OP1
|
C:A1095
|
3.1
|
62.5
|
1.0
|
C8
|
D:A1067
|
3.4
|
19.0
|
1.0
|
C5
|
D:A1067
|
3.6
|
12.6
|
1.0
|
N6
|
D:A1067
|
3.8
|
21.1
|
1.0
|
C6
|
D:A1067
|
4.2
|
16.3
|
1.0
|
O6
|
D:G1068
|
4.2
|
32.9
|
1.0
|
P
|
C:A1095
|
4.3
|
56.2
|
1.0
|
O2'
|
D:U1066
|
4.3
|
47.2
|
1.0
|
O3'
|
C:U1094
|
4.5
|
56.8
|
1.0
|
N9
|
D:A1067
|
4.7
|
18.5
|
1.0
|
O3'
|
D:U1066
|
4.7
|
47.2
|
1.0
|
C8
|
C:A1095
|
4.7
|
21.4
|
1.0
|
OP1
|
D:A1067
|
4.8
|
61.4
|
1.0
|
C4
|
D:A1067
|
4.8
|
22.3
|
1.0
|
O5'
|
C:A1095
|
4.8
|
37.3
|
1.0
|
N7
|
C:A1095
|
4.8
|
21.3
|
1.0
|
C6
|
D:G1068
|
5.0
|
18.6
|
1.0
|
|
Cadmium binding site 6 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 6 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd390
b:66.3
occ:1.00
|
O
|
D:HOH392
|
2.4
|
74.8
|
1.0
|
N7
|
D:G1071
|
2.5
|
24.2
|
1.0
|
O
|
D:HOH394
|
2.6
|
55.7
|
1.0
|
O
|
D:HOH396
|
2.7
|
38.7
|
1.0
|
O
|
D:HOH391
|
3.1
|
26.1
|
1.0
|
O6
|
D:G1071
|
3.4
|
34.1
|
1.0
|
C5
|
D:G1071
|
3.4
|
13.4
|
1.0
|
C8
|
D:G1071
|
3.5
|
17.7
|
1.0
|
C6
|
D:G1071
|
3.7
|
24.4
|
1.0
|
N1
|
D:G1089
|
4.1
|
18.2
|
1.0
|
OP1
|
D:G1071
|
4.4
|
43.0
|
1.0
|
O6
|
D:G1089
|
4.4
|
34.4
|
1.0
|
O
|
D:HOH395
|
4.6
|
23.2
|
1.0
|
N4
|
D:C1072
|
4.6
|
21.6
|
1.0
|
C6
|
D:G1089
|
4.6
|
26.6
|
1.0
|
C4
|
D:G1071
|
4.6
|
12.7
|
1.0
|
MG
|
D:MG318
|
4.6
|
17.5
|
1.0
|
N9
|
D:G1071
|
4.7
|
20.7
|
1.0
|
O
|
D:HOH452
|
4.8
|
47.9
|
1.0
|
OP1
|
D:A1098
|
4.9
|
56.5
|
1.0
|
N2
|
D:G1089
|
4.9
|
24.0
|
1.0
|
C2
|
D:G1089
|
4.9
|
22.5
|
1.0
|
|
Cadmium binding site 7 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 7 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd413
b:33.4
occ:0.10
|
O
|
A:ALA118
|
2.9
|
45.8
|
1.0
|
SD
|
A:MET113
|
3.0
|
47.3
|
1.0
|
CE
|
A:MET113
|
3.5
|
49.6
|
1.0
|
N
|
A:SER120
|
3.8
|
48.4
|
1.0
|
CG
|
A:MET113
|
3.8
|
45.8
|
1.0
|
C
|
A:ALA118
|
3.9
|
43.8
|
1.0
|
C
|
A:ASN119
|
3.9
|
48.1
|
1.0
|
C
|
A:SER120
|
4.0
|
45.9
|
1.0
|
CA
|
A:SER120
|
4.2
|
43.9
|
1.0
|
O
|
A:SER120
|
4.2
|
53.7
|
1.0
|
O
|
A:ASN119
|
4.3
|
53.1
|
1.0
|
N
|
A:LEU121
|
4.4
|
47.0
|
1.0
|
CA
|
A:ASN119
|
4.4
|
42.4
|
1.0
|
N
|
A:ASN119
|
4.5
|
42.1
|
1.0
|
CB
|
A:ALA118
|
4.8
|
41.3
|
1.0
|
CA
|
A:ALA118
|
4.9
|
41.2
|
1.0
|
CA
|
A:LEU121
|
5.0
|
44.8
|
1.0
|
|
Cadmium binding site 8 out
of 8 in 1mms
Go back to
Cadmium Binding Sites List in 1mms
Cadmium binding site 8 out
of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd414
b:14.1
occ:0.10
|
NZ
|
A:LYS112
|
2.2
|
28.6
|
1.0
|
OP2
|
C:U1060
|
2.8
|
31.4
|
1.0
|
O
|
A:THR72
|
3.1
|
51.4
|
1.0
|
OD2
|
A:ASP115
|
3.2
|
58.2
|
1.0
|
OG1
|
A:THR72
|
3.3
|
56.8
|
1.0
|
CE
|
A:LYS112
|
3.3
|
31.0
|
1.0
|
CB
|
A:ASP115
|
3.5
|
48.7
|
1.0
|
CG
|
A:ASP115
|
3.5
|
57.4
|
1.0
|
O3'
|
C:G1059
|
3.6
|
34.1
|
1.0
|
P
|
C:U1060
|
3.8
|
31.4
|
1.0
|
C
|
A:THR72
|
4.1
|
47.2
|
1.0
|
CB
|
A:LYS71
|
4.1
|
41.2
|
1.0
|
N
|
A:THR72
|
4.2
|
51.6
|
1.0
|
CG
|
A:PRO55
|
4.5
|
66.7
|
1.0
|
OD1
|
A:ASP115
|
4.5
|
51.5
|
1.0
|
CB
|
A:THR72
|
4.5
|
49.4
|
1.0
|
CA
|
A:THR72
|
4.5
|
48.5
|
1.0
|
CD
|
A:LYS71
|
4.5
|
47.8
|
1.0
|
O
|
A:PRO73
|
4.6
|
41.4
|
1.0
|
C5'
|
C:G1059
|
4.6
|
22.7
|
1.0
|
CD
|
A:LYS112
|
4.6
|
35.7
|
1.0
|
C3'
|
C:G1059
|
4.7
|
26.7
|
1.0
|
O5'
|
C:U1060
|
4.8
|
22.6
|
1.0
|
C4'
|
C:G1059
|
4.8
|
24.8
|
1.0
|
C
|
A:PRO73
|
4.9
|
38.4
|
1.0
|
|
Reference:
B.T.Wimberly,
R.Guymon,
J.P.Mccutcheon,
S.W.White,
V.Ramakrishnan.
A Detailed View of A Ribosomal Active Site: the Structure of the L11-Rna Complex. Cell(Cambridge,Mass.) V. 97 491 1999.
ISSN: ISSN 0092-8674
PubMed: 10338213
DOI: 10.1016/S0092-8674(00)80759-X
Page generated: Fri Jul 19 13:53:35 2024
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