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Cadmium in PDB 1k8a: Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k8a was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 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 (%) 22.7 / 26.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1k8a). 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 Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k8a:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1k8a

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Cadmium binding site 1 out of 5 in the Co-Crystal Structure of Carbomycin A 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 Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd8405

b:0.8
occ:1.00
O P:HOH5650 2.8 52.6 1.0
ND1 P:HIS40 2.8 38.0 1.0
O A:HOH5585 3.0 42.0 1.0
CG P:HIS40 3.7 38.0 1.0
CE1 P:HIS40 3.8 38.0 1.0
CB P:HIS40 3.9 40.1 1.0
CG P:ARG37 4.1 54.4 1.0
CZ P:ARG37 4.4 54.0 1.0
NE P:ARG37 4.5 53.3 1.0
NH1 P:ARG37 4.6 52.9 1.0
CB P:ARG37 4.6 52.4 1.0
CA P:ARG37 4.7 51.8 1.0
O P:ARG37 4.7 49.9 1.0
NH2 P:ARG37 4.7 54.3 1.0
O A:HOH9677 4.8 68.8 1.0
O A:HOH3923 4.8 73.0 1.0
CD P:ARG37 4.9 53.8 1.0
CD2 P:HIS40 4.9 37.1 1.0
NE2 P:HIS40 4.9 38.2 1.0

Cadmium binding site 2 out of 5 in 1k8a

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Cadmium binding site 2 out of 5 in the Co-Crystal Structure of Carbomycin A 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 Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cd8401

b:0.6
occ:1.00
SG V:CYS6 2.4 0.7 1.0
SG V:CYS36 2.8 0.1 1.0
CB V:CYS36 3.1 96.6 1.0
CB V:CYS6 3.3 0.3 1.0
N V:CYS9 3.5 96.5 1.0
SG V:CYS32 3.5 98.0 1.0
CB V:CYS9 3.6 96.6 1.0
SG V:CYS9 3.7 96.5 1.0
CB V:TYR8 3.8 95.8 1.0
N V:CYS32 3.9 94.6 1.0
CA V:CYS9 4.1 96.4 1.0
CB V:CYS32 4.2 96.7 1.0
CD2 V:TYR8 4.4 95.3 1.0
C V:TYR8 4.4 96.5 1.0
CA V:TYR8 4.5 96.6 1.0
CA V:CYS36 4.6 95.5 1.0
N V:TYR8 4.6 97.0 1.0
CA V:CYS32 4.6 96.5 1.0
CG V:TYR8 4.6 95.4 1.0
CA V:CYS6 4.7 0.8 1.0
N V:SER33 4.8 97.6 1.0
OG V:SER33 4.8 96.3 1.0
CA V:PHE31 4.8 93.3 1.0
N V:GLY10 4.9 96.3 1.0
C V:PHE31 4.9 93.5 1.0

Cadmium binding site 3 out of 5 in 1k8a

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Cadmium binding site 3 out of 5 in the Co-Crystal Structure of Carbomycin A 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 Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8403

b:0.3
occ:1.00
SG 1:CYS42 2.8 0.5 1.0
CB 1:CYS42 3.1 0.5 1.0
SG 1:CYS57 3.3 0.8 1.0
SG 1:CYS39 3.3 0.3 1.0
SG 1:CYS60 3.3 0.1 1.0
CB 1:CYS39 3.5 0.3 1.0
N 1:CYS42 3.6 0.9 1.0
CB 1:CYS60 3.6 99.4 1.0
CB 1:CYS57 3.7 0.3 1.0
CA 1:CYS42 3.9 0.1 1.0
N 1:CYS60 4.1 99.3 1.0
CD2 1:HIS59 4.4 0.4 1.0
CA 1:CYS60 4.5 98.3 1.0
CB 1:HIS59 4.6 0.9 1.0
C 1:CYS42 4.6 0.6 1.0
CB 1:VAL41 4.6 0.3 1.0
CG1 1:VAL41 4.7 0.3 1.0
C 1:VAL41 4.8 0.6 1.0
CG 1:HIS59 4.9 0.8 1.0

Cadmium binding site 4 out of 5 in 1k8a

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Cadmium binding site 4 out of 5 in the Co-Crystal Structure of Carbomycin A 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 Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8402

b:60.4
occ:1.00
SG 2:CYS34 2.3 40.3 1.0
SG 2:CYS37 2.4 41.2 1.0
SG 2:CYS22 2.5 36.7 1.0
SG 2:CYS19 2.5 43.2 1.0
CB 2:CYS19 3.0 38.0 1.0
CB 2:CYS34 3.2 38.7 1.0
CB 2:CYS22 3.3 37.0 1.0
CB 2:CYS37 3.4 36.5 1.0
N 2:CYS22 3.7 38.0 1.0
N 2:CYS37 3.9 36.7 1.0
CA 2:CYS22 4.0 37.9 1.0
CA 2:CYS37 4.2 36.7 1.0
CB 2:PHE39 4.4 46.8 1.0
CA 2:CYS19 4.5 37.9 1.0
O 2:HOH8422 4.6 42.8 1.0
CA 2:CYS34 4.7 38.7 1.0
C 2:ARG21 4.7 37.1 1.0
CB 2:ARG21 4.7 39.9 1.0
C 2:CYS22 4.7 38.1 1.0
C 2:CYS37 4.9 36.2 1.0
N 2:GLY23 4.9 37.7 1.0
CB 2:SER36 4.9 34.8 1.0
N 2:GLU24 5.0 39.8 1.0
N 2:PHE39 5.0 41.7 1.0

Cadmium binding site 5 out of 5 in 1k8a

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Cadmium binding site 5 out of 5 in the Co-Crystal Structure of Carbomycin A 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 Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Cd8404

b:0.6
occ:1.00
CB 4:CYS14 2.7 0.7 1.0
SG 4:CYS71 2.7 0.1 1.0
CB 4:CYS11 3.2 0.7 1.0
SG 4:CYS11 3.3 0.9 1.0
SG 4:CYS14 3.4 0.7 1.0
O 4:HOH8559 3.5 0.4 1.0
OE1 4:GLN18 3.7 0.4 1.0
CB 4:CYS71 3.7 0.5 1.0
CD 4:GLN18 3.7 0.2 1.0
NE2 4:GLN18 3.8 0.9 1.0
CA 4:CYS14 4.0 0.6 1.0
CB 4:GLN18 4.1 1.0 1.0
N 4:CYS14 4.1 0.7 1.0
O 4:GLU16 4.3 0.7 1.0
CG 4:GLN18 4.4 1.0 1.0
SG 4:CYS74 4.4 0.8 1.0
CB 4:CYS74 4.5 0.5 1.0
CA 4:CYS11 4.7 0.4 1.0
N 4:CYS74 4.8 0.0 1.0
CE1 4:HIS20 4.8 0.4 1.0
CA 4:CYS71 5.0 0.1 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 Aug 28 12:04:00 2020
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