Cadmium in PDB 1kd1: Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Protein crystallography data
The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1
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)
|
19.99 /
3.00
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
212.902,
300.474,
575.176,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22 /
26.9
|
Other elements in 1kd1:
The structure of Co-Crystal Structure of Spiramycin 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
(pdb code 1kd1). 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
Cadmium binding site 1 out
of 5 in 1kd1
Go back to
Cadmium Binding Sites List in 1kd1
Cadmium binding site 1 out
of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Cd8405
b:0.7
occ:1.00
|
O
|
P:HOH5650
|
2.7
|
82.3
|
1.0
|
ND1
|
P:HIS40
|
2.9
|
47.5
|
1.0
|
O
|
P:HOH5322
|
3.7
|
36.1
|
1.0
|
CE1
|
P:HIS40
|
3.7
|
48.1
|
1.0
|
CG
|
P:HIS40
|
4.0
|
47.6
|
1.0
|
CB
|
P:HIS40
|
4.3
|
47.9
|
1.0
|
CG
|
P:ARG37
|
4.4
|
57.3
|
1.0
|
NH1
|
P:ARG37
|
4.6
|
59.2
|
1.0
|
O
|
A:HOH4332
|
4.7
|
70.7
|
1.0
|
CZ
|
P:ARG37
|
4.8
|
59.7
|
1.0
|
CD2
|
P:LEU7
|
4.9
|
55.1
|
1.0
|
NE2
|
P:HIS40
|
4.9
|
48.8
|
1.0
|
CG1
|
P:VAL79
|
4.9
|
54.5
|
1.0
|
CD1
|
P:LEU7
|
5.0
|
51.7
|
1.0
|
|
Cadmium binding site 2 out
of 5 in 1kd1
Go back to
Cadmium Binding Sites List in 1kd1
Cadmium binding site 2 out
of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Cd8401
b:0.0
occ:1.00
|
CB
|
V:CYS9
|
2.8
|
95.8
|
1.0
|
SG
|
V:CYS36
|
3.0
|
0.4
|
1.0
|
N
|
V:CYS9
|
3.0
|
95.5
|
1.0
|
SG
|
V:CYS6
|
3.1
|
0.7
|
1.0
|
CB
|
V:CYS36
|
3.4
|
95.5
|
1.0
|
CA
|
V:CYS9
|
3.5
|
95.3
|
1.0
|
SG
|
V:CYS9
|
3.5
|
96.8
|
1.0
|
CB
|
V:CYS6
|
3.5
|
0.2
|
1.0
|
CB
|
V:TYR8
|
3.9
|
95.4
|
1.0
|
SG
|
V:CYS32
|
4.0
|
95.5
|
1.0
|
C
|
V:TYR8
|
4.2
|
95.5
|
1.0
|
CD2
|
V:TYR8
|
4.2
|
95.7
|
1.0
|
N
|
V:GLY10
|
4.3
|
94.3
|
1.0
|
C
|
V:CYS9
|
4.4
|
94.9
|
1.0
|
CA
|
V:TYR8
|
4.5
|
95.8
|
1.0
|
CG
|
V:TYR8
|
4.6
|
95.6
|
1.0
|
CB
|
V:CYS32
|
4.6
|
93.7
|
1.0
|
N
|
V:CYS32
|
4.7
|
91.8
|
1.0
|
N
|
V:TYR8
|
4.7
|
96.0
|
1.0
|
OG1
|
V:THR11
|
4.8
|
95.5
|
1.0
|
CA
|
V:CYS36
|
4.9
|
94.6
|
1.0
|
CA
|
V:CYS6
|
5.0
|
0.1
|
1.0
|
|
Cadmium binding site 3 out
of 5 in 1kd1
Go back to
Cadmium Binding Sites List in 1kd1
Cadmium binding site 3 out
of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Cd8403
b:0.9
occ:1.00
|
CB
|
1:CYS42
|
2.9
|
0.3
|
1.0
|
N
|
1:CYS42
|
3.1
|
0.5
|
1.0
|
SG
|
1:CYS42
|
3.4
|
0.3
|
1.0
|
SG
|
1:CYS39
|
3.5
|
0.1
|
1.0
|
SG
|
1:CYS60
|
3.5
|
0.2
|
1.0
|
CA
|
1:CYS42
|
3.6
|
0.1
|
1.0
|
CB
|
1:CYS60
|
3.6
|
98.5
|
1.0
|
CB
|
1:CYS39
|
3.7
|
0.3
|
1.0
|
SG
|
1:CYS57
|
4.1
|
0.8
|
1.0
|
CB
|
1:VAL41
|
4.1
|
0.2
|
1.0
|
CB
|
1:CYS57
|
4.2
|
0.7
|
1.0
|
CG1
|
1:VAL41
|
4.2
|
0.6
|
1.0
|
C
|
1:VAL41
|
4.3
|
0.3
|
1.0
|
C
|
1:CYS42
|
4.3
|
0.6
|
1.0
|
N
|
1:CYS60
|
4.4
|
99.0
|
1.0
|
CA
|
1:CYS60
|
4.6
|
97.9
|
1.0
|
CD2
|
1:HIS59
|
4.6
|
0.8
|
1.0
|
CA
|
1:VAL41
|
4.7
|
0.1
|
1.0
|
O
|
1:CYS42
|
4.7
|
0.3
|
1.0
|
CB
|
1:TYR62
|
4.9
|
91.3
|
1.0
|
N
|
1:VAL41
|
4.9
|
0.8
|
1.0
|
|
Cadmium binding site 4 out
of 5 in 1kd1
Go back to
Cadmium Binding Sites List in 1kd1
Cadmium binding site 4 out
of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Cd8402
b:59.9
occ:1.00
|
SG
|
2:CYS34
|
2.5
|
42.6
|
1.0
|
SG
|
2:CYS37
|
2.5
|
41.4
|
1.0
|
SG
|
2:CYS19
|
2.6
|
44.5
|
1.0
|
SG
|
2:CYS22
|
2.7
|
37.0
|
1.0
|
CB
|
2:CYS19
|
3.0
|
40.0
|
1.0
|
CB
|
2:CYS22
|
3.2
|
38.6
|
1.0
|
CB
|
2:CYS37
|
3.2
|
35.0
|
1.0
|
CB
|
2:CYS34
|
3.2
|
38.9
|
1.0
|
N
|
2:CYS22
|
3.6
|
40.3
|
1.0
|
N
|
2:CYS37
|
3.9
|
34.7
|
1.0
|
CA
|
2:CYS22
|
4.0
|
39.7
|
1.0
|
CA
|
2:CYS37
|
4.1
|
35.2
|
1.0
|
CB
|
2:PHE39
|
4.3
|
43.6
|
1.0
|
CA
|
2:CYS19
|
4.5
|
39.9
|
1.0
|
O
|
2:HOH8421
|
4.5
|
35.2
|
1.0
|
CB
|
2:ARG21
|
4.6
|
42.1
|
1.0
|
C
|
2:ARG21
|
4.6
|
39.7
|
1.0
|
CA
|
2:CYS34
|
4.7
|
37.9
|
1.0
|
C
|
2:CYS22
|
4.7
|
39.9
|
1.0
|
C
|
2:CYS37
|
4.8
|
35.3
|
1.0
|
N
|
2:GLY23
|
4.8
|
40.0
|
1.0
|
N
|
2:PHE39
|
4.9
|
40.6
|
1.0
|
CA
|
2:ARG21
|
4.9
|
41.6
|
1.0
|
CD
|
2:ARG21
|
5.0
|
40.8
|
1.0
|
C
|
2:SER36
|
5.0
|
34.2
|
1.0
|
C
|
2:CYS19
|
5.0
|
40.9
|
1.0
|
CB
|
2:SER36
|
5.0
|
34.6
|
1.0
|
|
Cadmium binding site 5 out
of 5 in 1kd1
Go back to
Cadmium Binding Sites List in 1kd1
Cadmium binding site 5 out
of 5 in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Cd8404
b:0.9
occ:1.00
|
CB
|
4:CYS14
|
2.7
|
0.0
|
1.0
|
SG
|
4:CYS71
|
3.1
|
0.1
|
1.0
|
CB
|
4:CYS11
|
3.2
|
0.1
|
1.0
|
SG
|
4:CYS11
|
3.2
|
0.7
|
1.0
|
O
|
4:HOH8564
|
3.4
|
0.8
|
1.0
|
CB
|
4:CYS71
|
3.5
|
0.5
|
1.0
|
SG
|
4:CYS14
|
3.5
|
0.8
|
1.0
|
N
|
4:CYS14
|
3.7
|
0.9
|
1.0
|
CA
|
4:CYS14
|
3.8
|
0.4
|
1.0
|
OE1
|
4:GLN18
|
4.0
|
0.3
|
1.0
|
CD
|
4:GLN18
|
4.1
|
0.9
|
1.0
|
NE2
|
4:GLN18
|
4.1
|
0.4
|
1.0
|
CB
|
4:CYS74
|
4.2
|
0.4
|
1.0
|
SG
|
4:CYS74
|
4.4
|
0.6
|
1.0
|
CB
|
4:GLN18
|
4.6
|
0.2
|
1.0
|
O
|
4:GLU16
|
4.6
|
0.9
|
1.0
|
CA
|
4:CYS11
|
4.6
|
0.4
|
1.0
|
N
|
4:CYS74
|
4.7
|
0.8
|
1.0
|
C
|
4:CYS14
|
4.9
|
0.3
|
1.0
|
CG
|
4:GLN18
|
4.9
|
1.0
|
1.0
|
C
|
4:HIS13
|
4.9
|
0.3
|
1.0
|
O
|
4:CYS11
|
4.9
|
0.7
|
1.0
|
CA
|
4:CYS71
|
5.0
|
0.3
|
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 13:44:28 2024
|