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Cadmium in PDB 3cpw: The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cpw was solved by J.A.Ippolito, Z.K.Kanyo, D.Wang, F.J.Franceschi, P.B.Moore, T.A.Steitz, E.M.Duffy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.730, 298.580, 575.290, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cpw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cpw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cpw

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Cadmium binding site 1 out of 5 in the The Structure of the Antibiotic Linezolid Bound to the Large 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 The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cd8705

b:0.7
occ:1.00
ND1 N:HIS40 2.5 45.0 1.0
O N:HOH5650 3.1 78.6 1.0
CE1 N:HIS40 3.4 46.5 1.0
CG N:HIS40 3.6 44.1 1.0
O N:HOH5322 3.8 49.4 1.0
CB N:HIS40 4.0 46.2 1.0
O N:HOH3002 4.5 61.3 1.0
CG N:ARG37 4.6 56.5 1.0
NE2 N:HIS40 4.6 46.3 1.0
CD2 N:LEU7 4.7 53.6 1.0
CD2 N:HIS40 4.7 45.9 1.0
CD1 N:LEU7 4.9 52.5 1.0
CG1 N:VAL79 5.0 59.1 1.0

Cadmium binding site 2 out of 5 in 3cpw

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Cadmium binding site 2 out of 5 in the The Structure of the Antibiotic Linezolid Bound to the Large 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 The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd8701

b:64.4
occ:1.00
SG T:CYS36 2.4 54.9 1.0
SG T:CYS9 2.5 58.4 1.0
SG T:CYS6 2.5 59.4 1.0
SG T:CYS32 2.5 47.1 1.0
CB T:CYS6 3.2 60.1 1.0
CB T:CYS9 3.5 57.3 1.0
CB T:CYS36 3.5 55.8 1.0
CB T:CYS32 3.6 50.8 1.0
N T:CYS9 3.9 56.6 1.0
N T:CYS32 4.0 50.2 1.0
CA T:CYS9 4.3 57.3 1.0
OG1 T:THR11 4.4 65.3 1.0
CA T:CYS32 4.4 51.3 1.0
OG T:SER33 4.5 53.3 1.0
N T:SER33 4.7 53.2 1.0
CA T:CYS6 4.7 60.5 1.0
CB T:TYR8 4.8 56.3 1.0
N T:GLY10 4.9 58.8 1.0
C T:CYS32 4.9 52.6 1.0
CA T:CYS36 4.9 54.7 1.0
C T:CYS9 5.0 58.2 1.0

Cadmium binding site 3 out of 5 in 3cpw

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Cadmium binding site 3 out of 5 in the The Structure of the Antibiotic Linezolid Bound to the Large 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 The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cd8703

b:59.7
occ:1.00
SG Y:CYS60 2.2 47.0 1.0
SG Y:CYS39 2.5 54.0 1.0
SG Y:CYS57 2.6 57.1 1.0
SG Y:CYS42 2.8 66.7 1.0
CB Y:CYS39 3.2 55.0 1.0
CB Y:CYS57 3.3 54.5 1.0
CB Y:CYS60 3.4 50.1 1.0
CB Y:CYS42 3.6 63.5 1.0
N Y:CYS60 3.8 53.3 1.0
N Y:CYS42 3.8 63.0 1.0
CA Y:CYS60 4.1 51.9 1.0
CB Y:ASN41 4.2 59.2 1.0
CA Y:CYS42 4.3 63.1 1.0
CD2 Y:TYR59 4.5 60.2 1.0
CB Y:TYR62 4.6 47.5 1.0
CB Y:TYR59 4.6 56.3 1.0
CA Y:CYS39 4.7 56.0 1.0
CA Y:CYS57 4.8 53.1 1.0
C Y:CYS60 4.8 52.2 1.0
C Y:CYS42 4.8 63.5 1.0
ND2 Y:ASN41 4.9 59.0 1.0
C Y:ASN41 4.9 62.1 1.0
C Y:TYR59 4.9 54.3 1.0
N Y:TYR62 5.0 50.7 1.0

Cadmium binding site 4 out of 5 in 3cpw

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Cadmium binding site 4 out of 5 in the The Structure of the Antibiotic Linezolid Bound to the Large 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 The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8702

b:67.3
occ:1.00
SG Z:CYS22 2.3 35.6 1.0
SG Z:CYS34 2.4 38.8 1.0
SG Z:CYS19 2.4 37.6 1.0
SG Z:CYS37 2.5 39.4 1.0
CB Z:CYS19 3.1 38.3 1.0
CB Z:CYS22 3.2 38.7 1.0
CB Z:CYS34 3.2 36.0 1.0
CB Z:CYS37 3.4 38.7 1.0
N Z:CYS22 3.6 41.6 1.0
N Z:CYS37 3.8 40.0 1.0
CA Z:CYS22 4.0 39.5 1.0
CA Z:CYS37 4.1 38.1 1.0
CB Z:PHE39 4.3 40.4 1.0
CB Z:ARG21 4.6 40.2 1.0
CA Z:CYS19 4.6 40.3 1.0
CA Z:CYS34 4.7 37.5 1.0
CB Z:SER36 4.7 37.4 1.0
C Z:ARG21 4.7 41.6 1.0
C Z:CYS37 4.8 36.7 1.0
C Z:CYS22 4.8 38.5 1.0
N Z:PHE39 4.8 37.2 1.0
N Z:GLY23 4.9 39.6 1.0
N Z:GLY38 4.9 37.1 1.0
C Z:SER36 4.9 40.4 1.0
O Z:HOH8970 5.0 37.9 1.0
CA Z:ARG21 5.0 40.6 1.0

Cadmium binding site 5 out of 5 in 3cpw

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Cadmium binding site 5 out of 5 in the The Structure of the Antibiotic Linezolid Bound to the Large 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 The Structure of the Antibiotic Linezolid Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8704

b:65.7
occ:1.00
SG 2:CYS11 2.3 61.7 1.0
SG 2:CYS74 2.3 70.7 1.0
SG 2:CYS71 2.4 65.0 1.0
SG 2:CYS14 2.7 74.5 1.0
O 2:HOH8990 2.9 0.8 1.0
CB 2:CYS71 3.1 65.0 1.0
CB 2:CYS14 3.2 70.2 1.0
CB 2:CYS74 3.5 68.6 1.0
CB 2:CYS11 3.7 62.2 1.0
N 2:CYS14 3.8 69.3 1.0
CA 2:CYS14 4.0 69.5 1.0
N 2:CYS74 4.1 69.3 1.0
CA 2:CYS74 4.4 68.9 1.0
CA 2:CYS71 4.6 63.5 1.0
CB 2:HIS13 4.7 68.2 1.0
OE1 2:GLN18 4.7 72.4 1.0
C 2:HIS13 4.9 69.1 1.0
NE2 2:GLN18 4.9 71.2 1.0
CD 2:GLN18 4.9 70.4 1.0
CA 2:CYS11 5.0 63.4 1.0

Reference:

J.A.Ippolito, Z.K.Kanyo, D.Wang, F.J.Franceschi, P.B.Moore, T.A.Steitz, E.M.Duffy. Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit J.Med.Chem. V. 51 3353 2008.
ISSN: ISSN 0022-2623
PubMed: 18494460
DOI: 10.1021/JM800379D
Page generated: Fri Aug 28 13:32:04 2020
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