Mercury 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:
Mercury Binding Sites:
The binding sites of Mercury 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 Mercury atom.
In total 8 binding sites of Mercury where determined in the
Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Mercury binding site 1 out
of 8 in 1mms
Go back to
Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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:Hg227
b:21.1
occ:0.10
|
N3
|
C:U1078
|
2.5
|
24.7
|
1.0
|
O2
|
C:U1078
|
3.0
|
29.6
|
1.0
|
OP1
|
C:G1089
|
3.0
|
30.8
|
1.0
|
C2
|
C:U1078
|
3.1
|
27.0
|
1.0
|
N6
|
C:A1077
|
3.4
|
32.9
|
1.0
|
C4
|
C:U1078
|
3.5
|
26.7
|
1.0
|
C5'
|
C:G1089
|
3.6
|
29.5
|
1.0
|
O4
|
C:U1078
|
3.6
|
44.0
|
1.0
|
P
|
C:G1089
|
4.2
|
26.5
|
1.0
|
O5'
|
C:G1089
|
4.2
|
14.9
|
1.0
|
C6
|
C:A1077
|
4.3
|
29.0
|
1.0
|
N1
|
C:U1078
|
4.5
|
21.7
|
1.0
|
C3'
|
C:A1088
|
4.6
|
27.8
|
1.0
|
C4'
|
C:G1089
|
4.8
|
26.2
|
1.0
|
C5
|
C:U1078
|
4.8
|
18.5
|
1.0
|
O3'
|
C:A1088
|
4.8
|
19.4
|
1.0
|
N1
|
C:A1077
|
5.0
|
23.4
|
1.0
|
|
Mercury binding site 2 out
of 8 in 1mms
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Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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:Hg230
b:65.0
occ:0.41
|
N3
|
C:U1061
|
2.2
|
73.7
|
1.0
|
O4
|
C:U1061
|
3.0
|
68.7
|
1.0
|
C4
|
C:U1061
|
3.0
|
67.1
|
1.0
|
C6
|
C:A1070
|
3.1
|
59.8
|
1.0
|
C2
|
C:U1061
|
3.2
|
62.3
|
1.0
|
N6
|
C:A1070
|
3.3
|
69.0
|
1.0
|
O2
|
C:U1061
|
3.3
|
62.3
|
1.0
|
C5
|
C:A1070
|
3.3
|
55.3
|
1.0
|
OP1
|
C:A1069
|
3.4
|
34.7
|
1.0
|
N1
|
C:A1070
|
3.6
|
56.3
|
1.0
|
N7
|
C:A1070
|
3.8
|
50.9
|
1.0
|
C4
|
C:A1070
|
4.0
|
46.6
|
1.0
|
C2
|
C:A1070
|
4.2
|
41.8
|
1.0
|
C5
|
C:U1061
|
4.4
|
54.5
|
1.0
|
N1
|
C:U1061
|
4.4
|
50.5
|
1.0
|
N3
|
C:A1070
|
4.5
|
44.2
|
1.0
|
C8
|
C:A1070
|
4.5
|
49.9
|
1.0
|
O3'
|
C:G1068
|
4.6
|
40.5
|
1.0
|
P
|
C:A1069
|
4.6
|
35.9
|
1.0
|
N9
|
C:A1070
|
4.7
|
42.7
|
1.0
|
C6
|
C:U1061
|
4.9
|
45.7
|
1.0
|
|
Mercury binding site 3 out
of 8 in 1mms
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Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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
|
D:Hg332
b:82.4
occ:0.60
|
N3
|
D:U1061
|
1.9
|
60.8
|
1.0
|
O4
|
D:U1061
|
2.6
|
48.6
|
1.0
|
C4
|
D:U1061
|
2.6
|
51.8
|
1.0
|
C2
|
D:U1061
|
3.0
|
53.5
|
1.0
|
C6
|
D:A1070
|
3.0
|
50.9
|
1.0
|
N6
|
D:A1070
|
3.2
|
62.3
|
1.0
|
C5
|
D:A1070
|
3.3
|
44.5
|
1.0
|
O2
|
D:U1061
|
3.3
|
44.6
|
1.0
|
N1
|
D:A1070
|
3.4
|
49.0
|
1.0
|
OP1
|
D:A1069
|
3.5
|
29.0
|
1.0
|
N7
|
D:A1070
|
3.8
|
45.9
|
1.0
|
C4
|
D:A1070
|
3.9
|
42.2
|
1.0
|
C5
|
D:U1061
|
4.0
|
40.8
|
1.0
|
C2
|
D:A1070
|
4.0
|
37.7
|
1.0
|
N1
|
D:U1061
|
4.2
|
45.0
|
1.0
|
N3
|
D:A1070
|
4.3
|
40.3
|
1.0
|
C8
|
D:A1070
|
4.5
|
43.8
|
1.0
|
C6
|
D:U1061
|
4.5
|
43.4
|
1.0
|
N9
|
D:A1070
|
4.6
|
42.6
|
1.0
|
P
|
D:A1069
|
4.7
|
27.2
|
1.0
|
O3'
|
D:G1068
|
4.8
|
38.7
|
1.0
|
|
Mercury binding site 4 out
of 8 in 1mms
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Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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:Hg347
b:54.2
occ:0.20
|
N3
|
D:U1078
|
2.5
|
28.6
|
1.0
|
O2
|
D:U1078
|
3.1
|
30.9
|
1.0
|
C2
|
D:U1078
|
3.2
|
35.3
|
1.0
|
OP1
|
D:G1089
|
3.2
|
28.3
|
1.0
|
O
|
D:HOH346
|
3.4
|
40.4
|
1.0
|
C4
|
D:U1078
|
3.5
|
30.3
|
1.0
|
N6
|
D:A1077
|
3.6
|
25.1
|
1.0
|
C5'
|
D:G1089
|
3.6
|
30.9
|
1.0
|
O4
|
D:U1078
|
3.6
|
39.1
|
1.0
|
O5'
|
D:G1089
|
4.3
|
22.5
|
1.0
|
P
|
D:G1089
|
4.4
|
27.7
|
1.0
|
C6
|
D:A1077
|
4.5
|
24.3
|
1.0
|
N1
|
D:U1078
|
4.6
|
25.9
|
1.0
|
C4'
|
D:G1089
|
4.7
|
24.7
|
1.0
|
C3'
|
D:A1088
|
4.8
|
28.6
|
1.0
|
C5
|
D:U1078
|
4.8
|
25.9
|
1.0
|
O3'
|
D:A1088
|
5.0
|
22.0
|
1.0
|
|
Mercury binding site 5 out
of 8 in 1mms
Go back to
Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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:Hg451
b:26.2
occ:0.10
|
N3
|
D:C1097
|
2.5
|
31.0
|
1.0
|
O2
|
D:C1097
|
2.6
|
29.2
|
1.0
|
C2
|
D:C1097
|
2.9
|
27.9
|
1.0
|
C4
|
D:C1097
|
3.6
|
45.0
|
1.0
|
N4
|
D:C1097
|
4.0
|
50.6
|
1.0
|
N1
|
D:C1097
|
4.3
|
31.4
|
1.0
|
O4'
|
D:A1098
|
4.4
|
47.7
|
1.0
|
C1'
|
D:A1098
|
4.5
|
36.9
|
1.0
|
N6
|
D:A1096
|
4.5
|
30.6
|
1.0
|
N1
|
D:A1096
|
4.6
|
23.8
|
1.0
|
C5
|
D:C1097
|
4.9
|
39.1
|
1.0
|
C6
|
D:A1096
|
4.9
|
23.5
|
1.0
|
|
Mercury binding site 6 out
of 8 in 1mms
Go back to
Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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
|
A:Hg415
b:35.2
occ:0.10
|
OG1
|
A:THR19
|
2.5
|
0.0
|
1.0
|
CB
|
A:CYS39
|
2.6
|
93.9
|
1.0
|
C
|
A:CYS39
|
3.7
|
96.3
|
1.0
|
CA
|
A:CYS39
|
3.8
|
95.6
|
1.0
|
N
|
A:LYS40
|
3.8
|
96.8
|
1.0
|
SG
|
A:CYS39
|
3.8
|
0.0
|
1.0
|
CB
|
A:THR19
|
3.9
|
0.0
|
1.0
|
O
|
A:ALA18
|
4.1
|
98.4
|
1.0
|
ND2
|
A:ASN43
|
4.2
|
99.1
|
1.0
|
CG
|
A:LYS40
|
4.2
|
97.7
|
1.0
|
O
|
A:CYS39
|
4.3
|
95.5
|
1.0
|
C
|
A:ALA18
|
4.4
|
96.6
|
1.0
|
CG2
|
A:THR19
|
4.5
|
99.8
|
1.0
|
CA
|
A:LYS40
|
4.5
|
96.2
|
1.0
|
CB
|
A:ALA18
|
4.7
|
95.0
|
1.0
|
N
|
A:THR19
|
4.8
|
96.2
|
1.0
|
O
|
A:MET36
|
4.8
|
95.1
|
1.0
|
CA
|
A:THR19
|
4.9
|
98.6
|
1.0
|
N
|
A:CYS39
|
4.9
|
94.4
|
1.0
|
CB
|
A:LYS40
|
5.0
|
95.7
|
1.0
|
|
Mercury binding site 7 out
of 8 in 1mms
Go back to
Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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:Hg416
b:45.0
occ:0.10
|
N
|
A:THR19
|
2.5
|
96.2
|
1.0
|
CG2
|
A:VAL24
|
2.6
|
91.8
|
1.0
|
CB
|
A:VAL24
|
2.6
|
92.9
|
1.0
|
CG1
|
A:VAL24
|
2.9
|
90.9
|
1.0
|
CA
|
A:THR19
|
2.9
|
98.6
|
1.0
|
SG
|
A:CYS39
|
3.1
|
0.0
|
1.0
|
CG2
|
A:ILE35
|
3.5
|
87.7
|
1.0
|
C
|
A:THR19
|
3.6
|
98.3
|
1.0
|
C
|
A:ALA18
|
3.6
|
96.6
|
1.0
|
CB
|
A:ALA18
|
3.9
|
95.0
|
1.0
|
CA
|
A:ALA18
|
4.0
|
96.8
|
1.0
|
N
|
A:GLY25
|
4.1
|
95.4
|
1.0
|
CA
|
A:VAL24
|
4.1
|
96.0
|
1.0
|
N
|
A:PRO20
|
4.1
|
0.0
|
1.0
|
O
|
A:THR19
|
4.2
|
94.3
|
1.0
|
CB
|
A:THR19
|
4.3
|
0.0
|
1.0
|
CD
|
A:PRO20
|
4.4
|
0.0
|
1.0
|
O
|
A:PRO20
|
4.5
|
0.0
|
1.0
|
CB
|
A:CYS39
|
4.5
|
93.9
|
1.0
|
OG1
|
A:THR19
|
4.5
|
0.0
|
1.0
|
C
|
A:VAL24
|
4.6
|
94.5
|
1.0
|
O
|
A:ALA18
|
4.7
|
98.4
|
1.0
|
N
|
A:VAL24
|
4.8
|
0.0
|
1.0
|
CA
|
A:CYS39
|
4.9
|
95.6
|
1.0
|
CB
|
A:ILE35
|
4.9
|
95.2
|
1.0
|
|
Mercury binding site 8 out
of 8 in 1mms
Go back to
Mercury Binding Sites List in 1mms
Mercury 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 Mercury with other atoms in the Hg 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:Hg448
b:21.0
occ:0.10
|
NE2
|
A:HIS31
|
2.1
|
84.8
|
1.0
|
O2
|
C:C1097
|
2.5
|
30.7
|
1.0
|
CE1
|
A:HIS31
|
2.5
|
81.3
|
1.0
|
CD2
|
A:HIS31
|
3.4
|
86.0
|
1.0
|
C2
|
C:C1097
|
3.5
|
31.3
|
1.0
|
ND1
|
A:HIS31
|
3.8
|
88.1
|
1.0
|
N3
|
C:C1097
|
3.9
|
27.5
|
1.0
|
CG
|
A:HIS31
|
4.2
|
90.3
|
1.0
|
N1
|
C:A1096
|
4.5
|
19.5
|
1.0
|
N1
|
C:C1097
|
4.8
|
29.8
|
1.0
|
CG2
|
A:ILE9
|
4.8
|
74.1
|
1.0
|
C2
|
C:A1096
|
4.9
|
19.8
|
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: Sun Aug 11 00:35:04 2024
|