Cadmium in PDB 1jj2: Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
Protein crystallography data
The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2
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 (%)
|
18.9 /
22.2
|
Other elements in 1jj2:
The structure of Fully 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 Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution
(pdb code 1jj2). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the
Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
Cadmium binding site 1 out
of 5 in 1jj2
Go back to
Cadmium Binding Sites List in 1jj2
Cadmium binding site 1 out
of 5 in the Fully 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 Fully 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
|
N:Cd8405
b:72.0
occ:1.00
|
ND1
|
N:HIS40
|
2.6
|
25.6
|
1.0
|
O
|
N:HOH5650
|
2.7
|
34.4
|
1.0
|
O
|
0:HOH5558
|
2.9
|
29.2
|
1.0
|
CE1
|
N:HIS40
|
3.5
|
29.7
|
1.0
|
CG
|
N:HIS40
|
3.5
|
27.0
|
1.0
|
CB
|
N:HIS40
|
3.8
|
28.4
|
1.0
|
CG
|
N:ARG37
|
4.3
|
38.3
|
1.0
|
NE2
|
N:HIS40
|
4.6
|
32.1
|
1.0
|
CD2
|
N:HIS40
|
4.6
|
29.5
|
1.0
|
O
|
0:HOH3869
|
4.7
|
41.4
|
1.0
|
NH1
|
N:ARG37
|
4.8
|
39.8
|
1.0
|
CZ
|
N:ARG37
|
4.8
|
40.1
|
1.0
|
NE
|
N:ARG37
|
4.9
|
39.5
|
1.0
|
CB
|
N:ARG37
|
4.9
|
35.5
|
1.0
|
CA
|
N:ARG37
|
5.0
|
33.9
|
1.0
|
O
|
N:ARG37
|
5.0
|
35.2
|
1.0
|
|
Cadmium binding site 2 out
of 5 in 1jj2
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Cadmium Binding Sites List in 1jj2
Cadmium binding site 2 out
of 5 in the Fully 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 Fully 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
|
T:Cd8401
b:49.6
occ:1.00
|
SG
|
T:CYS36
|
2.5
|
46.1
|
1.0
|
SG
|
T:CYS32
|
2.5
|
29.1
|
1.0
|
SG
|
T:CYS6
|
2.6
|
47.6
|
1.0
|
SG
|
T:CYS9
|
2.7
|
43.3
|
1.0
|
CB
|
T:CYS6
|
3.3
|
47.8
|
1.0
|
CB
|
T:CYS9
|
3.4
|
44.4
|
1.0
|
CB
|
T:CYS36
|
3.5
|
44.9
|
1.0
|
CB
|
T:CYS32
|
3.7
|
33.8
|
1.0
|
N
|
T:CYS9
|
3.8
|
46.7
|
1.0
|
N
|
T:CYS32
|
4.1
|
35.2
|
1.0
|
CA
|
T:CYS9
|
4.2
|
45.9
|
1.0
|
OG
|
T:SER33
|
4.4
|
37.3
|
1.0
|
CA
|
T:CYS32
|
4.4
|
36.4
|
1.0
|
OG1
|
T:THR11
|
4.5
|
51.6
|
1.0
|
CB
|
T:TYR8
|
4.6
|
44.7
|
1.0
|
N
|
T:SER33
|
4.7
|
39.3
|
1.0
|
CA
|
T:CYS6
|
4.8
|
49.5
|
1.0
|
N
|
T:GLY10
|
4.8
|
47.2
|
1.0
|
CA
|
T:CYS36
|
4.9
|
44.2
|
1.0
|
C
|
T:CYS9
|
4.9
|
46.7
|
1.0
|
C
|
T:TYR8
|
4.9
|
47.1
|
1.0
|
C
|
T:CYS32
|
5.0
|
38.3
|
1.0
|
|
Cadmium binding site 3 out
of 5 in 1jj2
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Cadmium Binding Sites List in 1jj2
Cadmium binding site 3 out
of 5 in the Fully 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 Fully 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
|
Y:Cd8403
b:50.0
occ:1.00
|
SG
|
Y:CYS60
|
2.4
|
48.4
|
1.0
|
SG
|
Y:CYS57
|
2.5
|
44.3
|
1.0
|
SG
|
Y:CYS39
|
2.5
|
53.2
|
1.0
|
SG
|
Y:CYS42
|
2.8
|
60.7
|
1.0
|
CB
|
Y:CYS57
|
3.2
|
46.4
|
1.0
|
CB
|
Y:CYS39
|
3.3
|
55.0
|
1.0
|
CB
|
Y:CYS42
|
3.6
|
57.9
|
1.0
|
CB
|
Y:CYS60
|
3.6
|
48.6
|
1.0
|
N
|
Y:CYS42
|
3.8
|
58.4
|
1.0
|
N
|
Y:CYS60
|
4.0
|
51.1
|
1.0
|
CA
|
Y:CYS42
|
4.3
|
58.0
|
1.0
|
CA
|
Y:CYS60
|
4.4
|
49.8
|
1.0
|
CB
|
Y:HIS59
|
4.6
|
53.8
|
1.0
|
CB
|
Y:TYR62
|
4.7
|
45.8
|
1.0
|
CB
|
Y:VAL41
|
4.7
|
58.7
|
1.0
|
CD2
|
Y:HIS59
|
4.7
|
55.8
|
1.0
|
CA
|
Y:CYS57
|
4.7
|
46.3
|
1.0
|
CA
|
Y:CYS39
|
4.8
|
55.9
|
1.0
|
C
|
Y:CYS42
|
4.8
|
57.6
|
1.0
|
CG1
|
Y:VAL41
|
4.8
|
60.0
|
1.0
|
C
|
Y:VAL41
|
5.0
|
58.6
|
1.0
|
|
Cadmium binding site 4 out
of 5 in 1jj2
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Cadmium Binding Sites List in 1jj2
Cadmium binding site 4 out
of 5 in the Fully 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 Fully 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:Cd8402
b:37.9
occ:1.00
|
SG
|
Z:CYS37
|
2.4
|
24.7
|
1.0
|
SG
|
Z:CYS22
|
2.5
|
23.3
|
1.0
|
SG
|
Z:CYS34
|
2.5
|
23.0
|
1.0
|
SG
|
Z:CYS19
|
2.5
|
21.7
|
1.0
|
CB
|
Z:CYS19
|
3.1
|
20.5
|
1.0
|
CB
|
Z:CYS34
|
3.2
|
20.0
|
1.0
|
CB
|
Z:CYS37
|
3.2
|
23.4
|
1.0
|
CB
|
Z:CYS22
|
3.3
|
22.9
|
1.0
|
N
|
Z:CYS22
|
3.7
|
27.0
|
1.0
|
N
|
Z:CYS37
|
3.8
|
24.4
|
1.0
|
CA
|
Z:CYS37
|
4.0
|
22.5
|
1.0
|
CA
|
Z:CYS22
|
4.1
|
23.6
|
1.0
|
CB
|
Z:PHE39
|
4.3
|
24.1
|
1.0
|
CA
|
Z:CYS19
|
4.6
|
22.7
|
1.0
|
CA
|
Z:CYS34
|
4.6
|
20.7
|
1.0
|
CB
|
Z:ARG21
|
4.7
|
28.6
|
1.0
|
C
|
Z:ARG21
|
4.7
|
27.0
|
1.0
|
C
|
Z:CYS37
|
4.7
|
23.7
|
1.0
|
CB
|
Z:SER36
|
4.8
|
24.0
|
1.0
|
O
|
Z:HOH8418
|
4.8
|
24.6
|
1.0
|
C
|
Z:CYS22
|
4.9
|
23.9
|
1.0
|
N
|
Z:PHE39
|
4.9
|
22.7
|
1.0
|
C
|
Z:SER36
|
4.9
|
25.5
|
1.0
|
N
|
Z:GLY38
|
4.9
|
23.1
|
1.0
|
N
|
Z:GLY23
|
4.9
|
24.8
|
1.0
|
|
Cadmium binding site 5 out
of 5 in 1jj2
Go back to
Cadmium Binding Sites List in 1jj2
Cadmium binding site 5 out
of 5 in the Fully 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 Fully 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
|
2:Cd8404
b:47.8
occ:1.00
|
SG
|
2:CYS71
|
2.4
|
49.7
|
1.0
|
SG
|
2:CYS11
|
2.5
|
42.0
|
1.0
|
SG
|
2:CYS74
|
2.6
|
53.7
|
1.0
|
SG
|
2:CYS14
|
2.9
|
56.3
|
1.0
|
CB
|
2:CYS14
|
3.0
|
53.6
|
1.0
|
CB
|
2:CYS71
|
3.2
|
50.4
|
1.0
|
O
|
2:HOH8560
|
3.2
|
96.3
|
1.0
|
CB
|
2:CYS74
|
3.3
|
51.8
|
1.0
|
CB
|
2:CYS11
|
3.6
|
43.0
|
1.0
|
N
|
2:CYS14
|
3.7
|
52.9
|
1.0
|
CA
|
2:CYS14
|
3.9
|
54.0
|
1.0
|
N
|
2:CYS74
|
4.1
|
52.9
|
1.0
|
CA
|
2:CYS74
|
4.3
|
51.6
|
1.0
|
CB
|
2:HIS13
|
4.6
|
49.8
|
1.0
|
CA
|
2:CYS71
|
4.6
|
49.9
|
1.0
|
OE1
|
2:GLN18
|
4.7
|
60.8
|
1.0
|
C
|
2:HIS13
|
4.8
|
51.1
|
1.0
|
CA
|
2:CYS11
|
5.0
|
43.7
|
1.0
|
|
Reference:
D.J.Klein,
T.M.Schmeing,
P.B.Moore,
T.A.Steitz.
The Kink-Turn: A New Rna Secondary Structure Motif. Embo J. V. 20 4214 2001.
ISSN: ISSN 0261-4189
PubMed: 11483524
DOI: 10.1093/EMBOJ/20.15.4214
Page generated: Fri Jul 19 13:39:35 2024
|