Cadmium in PDB 1m1k: Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Protein crystallography data
The structure of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k
was solved by
J.L.Hansen,
J.A.Ippolito,
N.Ban,
P.Nissen,
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)
|
20.00 /
3.20
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
213.751,
301.566,
574.436,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.4 /
25
|
Other elements in 1m1k:
The structure of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
(pdb code 1m1k). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the
Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1m1k:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
Cadmium binding site 1 out
of 5 in 1m1k
Go back to
Cadmium Binding Sites List in 1m1k
Cadmium binding site 1 out
of 5 in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_01.jpg) Mono view
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Cd8405
b:0.6
occ:1.00
|
ND1
|
P:HIS40
|
2.8
|
56.4
|
1.0
|
O
|
P:HOH5322
|
2.9
|
27.7
|
1.0
|
O
|
P:HOH5650
|
2.9
|
50.2
|
1.0
|
CG
|
P:HIS40
|
3.6
|
54.9
|
1.0
|
CE1
|
P:HIS40
|
3.7
|
55.7
|
1.0
|
CB
|
P:HIS40
|
3.8
|
53.3
|
1.0
|
CG
|
P:ARG37
|
4.3
|
63.7
|
1.0
|
NH1
|
P:ARG37
|
4.7
|
67.2
|
1.0
|
O
|
A:HOH3935
|
4.7
|
47.6
|
1.0
|
CZ
|
P:ARG37
|
4.7
|
67.0
|
1.0
|
O
|
P:ARG37
|
4.7
|
59.0
|
1.0
|
CD2
|
P:HIS40
|
4.7
|
54.7
|
1.0
|
NE2
|
P:HIS40
|
4.8
|
55.5
|
1.0
|
CA
|
P:ARG37
|
4.8
|
59.9
|
1.0
|
CB
|
P:ARG37
|
4.8
|
61.8
|
1.0
|
NE
|
P:ARG37
|
4.9
|
67.3
|
1.0
|
|
Cadmium binding site 2 out
of 5 in 1m1k
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Cadmium Binding Sites List in 1m1k
Cadmium binding site 2 out
of 5 in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_02.jpg) Mono view
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Cd8401
b:75.8
occ:1.00
|
SG
|
V:CYS32
|
2.2
|
46.8
|
1.0
|
SG
|
V:CYS36
|
2.3
|
57.2
|
1.0
|
SG
|
V:CYS6
|
2.4
|
61.1
|
1.0
|
SG
|
V:CYS9
|
2.6
|
62.7
|
1.0
|
CB
|
V:CYS6
|
3.3
|
63.6
|
1.0
|
CB
|
V:CYS9
|
3.4
|
63.1
|
1.0
|
CB
|
V:CYS36
|
3.5
|
57.8
|
1.0
|
CB
|
V:CYS32
|
3.6
|
52.8
|
1.0
|
N
|
V:CYS9
|
3.8
|
63.4
|
1.0
|
N
|
V:CYS32
|
4.1
|
54.1
|
1.0
|
CA
|
V:CYS9
|
4.2
|
62.6
|
1.0
|
OG1
|
V:THR11
|
4.4
|
69.8
|
1.0
|
OG
|
V:SER33
|
4.4
|
60.1
|
1.0
|
CA
|
V:CYS32
|
4.4
|
54.5
|
1.0
|
CB
|
V:TYR8
|
4.6
|
63.4
|
1.0
|
N
|
V:SER33
|
4.7
|
58.4
|
1.0
|
CA
|
V:CYS6
|
4.8
|
63.5
|
1.0
|
N
|
V:GLY10
|
4.8
|
63.2
|
1.0
|
CA
|
V:CYS36
|
4.9
|
58.1
|
1.0
|
C
|
V:TYR8
|
4.9
|
64.1
|
1.0
|
C
|
V:CYS9
|
4.9
|
62.7
|
1.0
|
C
|
V:CYS32
|
5.0
|
56.2
|
1.0
|
CD2
|
V:TYR8
|
5.0
|
62.0
|
1.0
|
|
Cadmium binding site 3 out
of 5 in 1m1k
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Cadmium Binding Sites List in 1m1k
Cadmium binding site 3 out
of 5 in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_03.jpg) Mono view
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Cd8403
b:77.5
occ:1.00
|
SG
|
1:CYS60
|
2.3
|
68.5
|
1.0
|
SG
|
1:CYS39
|
2.4
|
64.0
|
1.0
|
SG
|
1:CYS57
|
2.5
|
75.7
|
1.0
|
SG
|
1:CYS42
|
2.8
|
80.1
|
1.0
|
CB
|
1:CYS39
|
3.3
|
67.3
|
1.0
|
CB
|
1:CYS57
|
3.3
|
75.7
|
1.0
|
CB
|
1:CYS60
|
3.4
|
68.3
|
1.0
|
CB
|
1:CYS42
|
3.5
|
80.4
|
1.0
|
N
|
1:CYS42
|
3.7
|
81.2
|
1.0
|
N
|
1:CYS60
|
3.9
|
70.4
|
1.0
|
CA
|
1:CYS42
|
4.2
|
81.1
|
1.0
|
CA
|
1:CYS60
|
4.3
|
68.6
|
1.0
|
CB
|
1:VAL41
|
4.6
|
80.9
|
1.0
|
CB
|
1:TYR62
|
4.6
|
69.8
|
1.0
|
CB
|
1:HIS59
|
4.6
|
79.8
|
1.0
|
CD2
|
1:HIS59
|
4.7
|
84.1
|
1.0
|
CA
|
1:CYS39
|
4.7
|
71.3
|
1.0
|
CG1
|
1:VAL41
|
4.8
|
80.8
|
1.0
|
CA
|
1:CYS57
|
4.8
|
74.9
|
1.0
|
C
|
1:CYS42
|
4.9
|
81.3
|
1.0
|
C
|
1:VAL41
|
4.9
|
80.7
|
1.0
|
|
Cadmium binding site 4 out
of 5 in 1m1k
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Cadmium Binding Sites List in 1m1k
Cadmium binding site 4 out
of 5 in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_04.jpg) Mono view
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Cd8402
b:70.2
occ:1.00
|
SG
|
2:CYS37
|
2.4
|
49.8
|
1.0
|
SG
|
2:CYS19
|
2.5
|
54.4
|
1.0
|
SG
|
2:CYS34
|
2.6
|
49.0
|
1.0
|
SG
|
2:CYS22
|
2.6
|
48.3
|
1.0
|
CB
|
2:CYS19
|
3.0
|
50.4
|
1.0
|
CB
|
2:CYS22
|
3.2
|
47.3
|
1.0
|
CB
|
2:CYS34
|
3.2
|
45.7
|
1.0
|
CB
|
2:CYS37
|
3.3
|
44.4
|
1.0
|
N
|
2:CYS22
|
3.6
|
46.6
|
1.0
|
N
|
2:CYS37
|
3.8
|
44.7
|
1.0
|
CA
|
2:CYS22
|
4.0
|
48.4
|
1.0
|
CA
|
2:CYS37
|
4.2
|
45.0
|
1.0
|
CB
|
2:PHE39
|
4.3
|
49.2
|
1.0
|
CA
|
2:CYS19
|
4.5
|
50.0
|
1.0
|
CB
|
2:ARG21
|
4.6
|
46.9
|
1.0
|
C
|
2:CYS22
|
4.7
|
47.2
|
1.0
|
CA
|
2:CYS34
|
4.7
|
47.2
|
1.0
|
C
|
2:ARG21
|
4.7
|
47.6
|
1.0
|
O
|
2:HOH8420
|
4.7
|
36.1
|
1.0
|
CB
|
2:SER36
|
4.7
|
43.9
|
1.0
|
N
|
2:GLY23
|
4.8
|
47.6
|
1.0
|
N
|
2:PHE39
|
4.8
|
46.8
|
1.0
|
C
|
2:CYS37
|
4.9
|
43.4
|
1.0
|
C
|
2:SER36
|
4.9
|
43.6
|
1.0
|
N
|
2:GLY38
|
4.9
|
43.9
|
1.0
|
C
|
2:CYS19
|
5.0
|
49.2
|
1.0
|
N
|
2:GLU24
|
5.0
|
49.2
|
1.0
|
|
Cadmium binding site 5 out
of 5 in 1m1k
Go back to
Cadmium Binding Sites List in 1m1k
Cadmium binding site 5 out
of 5 in the Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_05.jpg) Mono view
![](/pictures/CD/pdb/m1/1m1k-CD-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Co-Crystal Structure of Azithromycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Cd8404
b:75.5
occ:1.00
|
SG
|
4:CYS71
|
2.3
|
54.0
|
1.0
|
SG
|
4:CYS74
|
2.5
|
72.7
|
1.0
|
SG
|
4:CYS14
|
2.5
|
79.9
|
1.0
|
SG
|
4:CYS11
|
2.6
|
72.2
|
1.0
|
CB
|
4:CYS14
|
3.0
|
76.7
|
1.0
|
CB
|
4:CYS71
|
3.1
|
59.3
|
1.0
|
O
|
4:HOH8561
|
3.1
|
0.8
|
1.0
|
CB
|
4:CYS74
|
3.5
|
71.5
|
1.0
|
CB
|
4:CYS11
|
3.5
|
70.4
|
1.0
|
N
|
4:CYS14
|
3.7
|
75.1
|
1.0
|
CA
|
4:CYS14
|
3.9
|
75.6
|
1.0
|
N
|
4:CYS74
|
4.1
|
73.2
|
1.0
|
CA
|
4:CYS74
|
4.3
|
72.0
|
1.0
|
CA
|
4:CYS71
|
4.5
|
62.6
|
1.0
|
OE1
|
4:GLN18
|
4.6
|
79.8
|
1.0
|
CB
|
4:HIS13
|
4.7
|
73.3
|
1.0
|
C
|
4:HIS13
|
4.9
|
75.8
|
1.0
|
CD
|
4:GLN18
|
5.0
|
77.7
|
1.0
|
CA
|
4:CYS11
|
5.0
|
70.7
|
1.0
|
|
Reference:
J.L.Hansen,
J.A.Ippolito,
N.Ban,
P.Nissen,
P.B.Moore,
T.A.Steitz.
The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit. Mol.Cell V. 10 117 2002.
ISSN: ISSN 1097-2765
PubMed: 12150912
DOI: 10.1016/S1097-2765(02)00570-1
Page generated: Fri Jul 19 13:50:43 2024
|