Atomistry » Cadmium » PDB 1jv4-1mwr » 1k8a
Atomistry »
  Cadmium »
    PDB 1jv4-1mwr »
      1k8a »

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

Other elements in 1k8a:

The structure of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 119 atoms
Potassium (K) 3 atoms
Chlorine (Cl) 23 atoms
Sodium (Na) 83 atoms

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

Go back to Cadmium Binding Sites List in 1k8a
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

Go back to Cadmium Binding Sites List in 1k8a
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

Go back to Cadmium Binding Sites List in 1k8a
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

Go back to Cadmium Binding Sites List in 1k8a
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

Go back to Cadmium Binding Sites List in 1k8a
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: Sun Jan 24 09:42:07 2021

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy