Cadmium in PDB 1s72: Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Protein crystallography data
The structure of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72
was solved by
D.J.Klein,
T.M.Schmeing,
P.B.Moore,
T.A.Steitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.40
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
211.660,
299.670,
573.770,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.8 /
22.2
|
Other elements in 1s72:
The structure of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
(pdb code 1s72). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the
Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
Cadmium binding site 1 out
of 5 in 1s72
Go back to
Cadmium Binding Sites List in 1s72
Cadmium binding site 1 out
of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Cd8405
b:73.6
occ:1.00
|
ND1
|
O:HIS40
|
2.6
|
27.1
|
1.0
|
O
|
O:HOH5650
|
2.6
|
35.8
|
1.0
|
O
|
0:HOH5541
|
3.0
|
30.6
|
1.0
|
CE1
|
O:HIS40
|
3.5
|
30.9
|
1.0
|
CG
|
O:HIS40
|
3.5
|
28.2
|
1.0
|
CB
|
O:HIS40
|
3.8
|
29.4
|
1.0
|
CG
|
O:ARG37
|
4.3
|
39.8
|
1.0
|
NE2
|
O:HIS40
|
4.6
|
33.4
|
1.0
|
CD2
|
O:HIS40
|
4.6
|
31.0
|
1.0
|
O
|
0:HOH3866
|
4.7
|
44.5
|
1.0
|
CZ
|
O:ARG37
|
4.8
|
41.7
|
1.0
|
NH1
|
O:ARG37
|
4.8
|
41.2
|
1.0
|
NE
|
O:ARG37
|
4.9
|
41.0
|
1.0
|
CB
|
O:ARG37
|
4.9
|
36.5
|
1.0
|
CA
|
O:ARG37
|
4.9
|
35.2
|
1.0
|
O
|
O:ARG37
|
5.0
|
36.2
|
1.0
|
|
Cadmium binding site 2 out
of 5 in 1s72
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Cadmium Binding Sites List in 1s72
Cadmium binding site 2 out
of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Cd8401
b:52.1
occ:1.00
|
SG
|
U:CYS32
|
2.5
|
30.0
|
1.0
|
SG
|
U:CYS36
|
2.5
|
47.0
|
1.0
|
SG
|
U:CYS6
|
2.6
|
48.3
|
1.0
|
SG
|
U:CYS9
|
2.7
|
44.1
|
1.0
|
CB
|
U:CYS6
|
3.3
|
48.0
|
1.0
|
CB
|
U:CYS9
|
3.3
|
45.1
|
1.0
|
CB
|
U:CYS36
|
3.5
|
45.8
|
1.0
|
CB
|
U:CYS32
|
3.7
|
34.7
|
1.0
|
N
|
U:CYS9
|
3.8
|
47.2
|
1.0
|
N
|
U:CYS32
|
4.1
|
36.2
|
1.0
|
CA
|
U:CYS9
|
4.1
|
46.5
|
1.0
|
OG
|
U:SER33
|
4.4
|
37.7
|
1.0
|
CA
|
U:CYS32
|
4.5
|
37.0
|
1.0
|
OG1
|
U:THR11
|
4.5
|
52.2
|
1.0
|
CB
|
U:TYR8
|
4.6
|
45.1
|
1.0
|
N
|
U:SER33
|
4.8
|
40.0
|
1.0
|
CA
|
U:CYS6
|
4.8
|
49.4
|
1.0
|
N
|
U:GLY10
|
4.8
|
48.0
|
1.0
|
C
|
U:TYR8
|
4.9
|
47.4
|
1.0
|
C
|
U:CYS9
|
4.9
|
47.5
|
1.0
|
CA
|
U:CYS36
|
4.9
|
45.0
|
1.0
|
C
|
U:CYS32
|
5.0
|
39.1
|
1.0
|
|
Cadmium binding site 3 out
of 5 in 1s72
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Cadmium Binding Sites List in 1s72
Cadmium binding site 3 out
of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Cd8403
b:48.6
occ:1.00
|
SG
|
Z:CYS60
|
2.3
|
47.7
|
1.0
|
SG
|
Z:CYS57
|
2.5
|
44.0
|
1.0
|
SG
|
Z:CYS39
|
2.5
|
52.4
|
1.0
|
SG
|
Z:CYS42
|
2.8
|
60.7
|
1.0
|
CB
|
Z:CYS39
|
3.2
|
53.9
|
1.0
|
CB
|
Z:CYS57
|
3.2
|
46.6
|
1.0
|
CB
|
Z:CYS60
|
3.5
|
49.0
|
1.0
|
CB
|
Z:CYS42
|
3.7
|
58.1
|
1.0
|
N
|
Z:CYS42
|
3.8
|
58.7
|
1.0
|
N
|
Z:CYS60
|
3.9
|
50.8
|
1.0
|
CA
|
Z:CYS60
|
4.3
|
49.5
|
1.0
|
CB
|
Z:ASN41
|
4.3
|
60.7
|
1.0
|
CA
|
Z:CYS42
|
4.3
|
58.0
|
1.0
|
CB
|
Z:TYR62
|
4.6
|
45.5
|
1.0
|
CD2
|
Z:TYR59
|
4.6
|
56.0
|
1.0
|
CB
|
Z:TYR59
|
4.7
|
53.1
|
1.0
|
CA
|
Z:CYS39
|
4.7
|
54.2
|
1.0
|
CA
|
Z:CYS57
|
4.7
|
45.2
|
1.0
|
C
|
Z:CYS42
|
4.9
|
57.5
|
1.0
|
C
|
Z:ASN41
|
4.9
|
59.4
|
1.0
|
C
|
Z:CYS60
|
5.0
|
49.4
|
1.0
|
|
Cadmium binding site 4 out
of 5 in 1s72
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Cadmium Binding Sites List in 1s72
Cadmium binding site 4 out
of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Cd8402
b:44.2
occ:1.00
|
SG
|
1:CYS37
|
2.4
|
26.8
|
1.0
|
SG
|
1:CYS22
|
2.5
|
25.0
|
1.0
|
SG
|
1:CYS34
|
2.5
|
24.8
|
1.0
|
SG
|
1:CYS19
|
2.5
|
22.9
|
1.0
|
CB
|
1:CYS19
|
3.1
|
21.3
|
1.0
|
CB
|
1:CYS34
|
3.2
|
19.8
|
1.0
|
CB
|
1:CYS37
|
3.2
|
23.7
|
1.0
|
CB
|
1:CYS22
|
3.3
|
23.2
|
1.0
|
N
|
1:CYS22
|
3.7
|
27.0
|
1.0
|
N
|
1:CYS37
|
3.8
|
24.8
|
1.0
|
CA
|
1:CYS37
|
4.0
|
23.8
|
1.0
|
CA
|
1:CYS22
|
4.0
|
25.2
|
1.0
|
CB
|
1:PHE39
|
4.3
|
25.2
|
1.0
|
CA
|
1:CYS19
|
4.6
|
25.0
|
1.0
|
CA
|
1:CYS34
|
4.6
|
21.9
|
1.0
|
CB
|
1:ARG21
|
4.7
|
29.0
|
1.0
|
C
|
1:ARG21
|
4.7
|
28.0
|
1.0
|
C
|
1:CYS37
|
4.7
|
24.4
|
1.0
|
CB
|
1:SER36
|
4.8
|
24.6
|
1.0
|
O
|
1:HOH8418
|
4.8
|
24.5
|
1.0
|
C
|
1:CYS22
|
4.8
|
24.7
|
1.0
|
N
|
1:PHE39
|
4.9
|
23.8
|
1.0
|
C
|
1:SER36
|
4.9
|
26.5
|
1.0
|
N
|
1:GLY38
|
4.9
|
23.9
|
1.0
|
N
|
1:GLY23
|
4.9
|
25.2
|
1.0
|
|
Cadmium binding site 5 out
of 5 in 1s72
Go back to
Cadmium Binding Sites List in 1s72
Cadmium binding site 5 out
of 5 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Cd8404
b:49.5
occ:1.00
|
SG
|
3:CYS71
|
2.4
|
50.2
|
1.0
|
SG
|
3:CYS11
|
2.5
|
43.2
|
1.0
|
SG
|
3:CYS74
|
2.6
|
54.2
|
1.0
|
SG
|
3:CYS14
|
2.9
|
56.1
|
1.0
|
CB
|
3:CYS14
|
3.1
|
53.9
|
1.0
|
CB
|
3:CYS71
|
3.1
|
50.9
|
1.0
|
O
|
3:HOH8559
|
3.2
|
97.1
|
1.0
|
CB
|
3:CYS74
|
3.3
|
52.2
|
1.0
|
CB
|
3:CYS11
|
3.6
|
44.3
|
1.0
|
N
|
3:CYS14
|
3.7
|
53.7
|
1.0
|
CA
|
3:CYS14
|
3.9
|
54.6
|
1.0
|
N
|
3:CYS74
|
4.1
|
53.4
|
1.0
|
CA
|
3:CYS74
|
4.3
|
52.2
|
1.0
|
CB
|
3:HIS13
|
4.6
|
51.2
|
1.0
|
CA
|
3:CYS71
|
4.6
|
50.4
|
1.0
|
OE1
|
3:GLN18
|
4.6
|
62.0
|
1.0
|
C
|
3:HIS13
|
4.8
|
52.3
|
1.0
|
CD
|
3:GLN18
|
5.0
|
58.0
|
1.0
|
C
|
3:CYS74
|
5.0
|
51.3
|
1.0
|
|
Reference:
D.J.Klein,
P.B.Moore,
T.A.Steitz.
The Roles of Ribosomal Proteins in the Structure, Assembly and Evolution of the Large Ribosomal Subunit J.Mol.Biol. V. 340 141 2004.
ISSN: ISSN 0022-2836
PubMed: 15184028
DOI: 10.1016/J.JMB.2004.03.076
Page generated: Fri Jul 19 14:13:44 2024
|