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Cadmium in PDB 3cma: The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.79 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.316, 297.905, 573.138, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.5

Other elements in 3cma:

The structure of The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium (Sr) 107 atoms
Magnesium (Mg) 93 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structure of Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cma). 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cma:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cma

Go back to Cadmium Binding Sites List in 3cma
Cadmium binding site 1 out of 5 in the The Structure of Cca and Cca-Phe-Cap-Bio 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:0.5
occ:1.00
 ND1 O:HIS40 2.6 30.2 1.0
O O:HOH5650 2.9 39.3 1.0
O O:HOH5322 3.2 38.1 1.0
CE1 O:HIS40 3.5 28.4 1.0
CG O:HIS40 3.6 30.1 1.0
CB O:HIS40 3.9 33.9 1.0
O 0:HOH5224 4.0 51.5 1.0
CG O:ARG37 4.4 45.9 1.0
CZ O:ARG37 4.7 47.5 1.0
NH1 O:ARG37 4.7 46.9 1.0
NE2 O:HIS40 4.7 29.6 1.0
CD2 O:HIS40 4.8 29.9 1.0
NE O:ARG37 4.9 46.5 1.0
CB O:ARG37 4.9 44.3 1.0
CA O:ARG37 5.0 42.2 1.0
NH2 O:ARG37 5.0 48.1 1.0

Cadmium binding site 2 out of 5 in 3cma

Go back to Cadmium Binding Sites List in 3cma
Cadmium binding site 2 out of 5 in the The Structure of Cca and Cca-Phe-Cap-Bio 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:50.9
occ:1.00
 SG U:CYS9 2.5 40.8 1.0
SG U:CYS36 2.5 39.3 1.0
SG U:CYS32 2.6 36.0 1.0
SG U:CYS6 2.6 45.0 1.0
CB U:CYS6 3.3 47.9 1.0
CB U:CYS9 3.5 44.4 1.0
CB U:CYS36 3.5 40.4 1.0
CB U:CYS32 3.6 40.0 1.0
N U:CYS9 3.7 42.7 1.0
N U:CYS32 4.0 38.3 1.0
CA U:CYS9 4.2 45.2 1.0
CA U:CYS32 4.4 41.2 1.0
OG U:SER33 4.4 42.1 1.0
CB U:TYR8 4.5 43.1 1.0
N U:SER33 4.6 43.3 1.0
CA U:CYS6 4.8 50.1 1.0
OG1 U:THR11 4.8 55.0 1.0
C U:TYR8 4.8 43.1 1.0
C U:CYS32 4.9 42.0 1.0
CA U:CYS36 4.9 42.8 1.0
C U:CYS9 4.9 45.9 1.0
CD2 U:TYR8 4.9 39.6 1.0
N U:GLY10 4.9 47.9 1.0

Cadmium binding site 3 out of 5 in 3cma

Go back to Cadmium Binding Sites List in 3cma
Cadmium binding site 3 out of 5 in the The Structure of Cca and Cca-Phe-Cap-Bio 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:62.5
occ:1.00
 SG Z:CYS84 2.5 61.6 1.0
SG Z:CYS63 2.6 79.3 1.0
SG Z:CYS66 2.7 88.1 1.0
SG Z:CYS81 2.7 75.3 1.0
CB Z:CYS81 3.2 71.9 1.0
CB Z:CYS84 3.3 63.5 1.0
CB Z:CYS63 3.3 83.0 1.0
CB Z:CYS66 3.7 84.7 1.0
N Z:CYS84 3.7 65.9 1.0
N Z:CYS66 3.9 84.3 1.0
CA Z:CYS84 4.0 64.7 1.0
CB Z:ASN65 4.2 81.9 1.0
CA Z:CYS66 4.4 84.3 1.0
CD2 Z:TYR83 4.4 74.1 1.0
ND2 Z:ASN65 4.5 81.8 1.0
CB Z:TYR83 4.5 70.9 1.0
CB Z:TYR86 4.6 53.8 1.0
C Z:CYS84 4.7 64.8 1.0
CA Z:CYS81 4.7 70.5 1.0
CA Z:CYS63 4.8 83.9 1.0
C Z:TYR83 4.8 67.9 1.0
C Z:ASN65 4.8 83.9 1.0
CG Z:ASN65 4.9 81.2 1.0
CA Z:ASN65 5.0 83.0 1.0
CG Z:TYR83 5.0 73.0 1.0

Cadmium binding site 4 out of 5 in 3cma

Go back to Cadmium Binding Sites List in 3cma
Cadmium binding site 4 out of 5 in the The Structure of Cca and Cca-Phe-Cap-Bio 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:50.6
occ:1.00
 SG 1:CYS22 2.5 32.1 1.0
SG 1:CYS19 2.6 25.8 1.0
SG 1:CYS37 2.6 27.1 1.0
SG 1:CYS34 2.6 29.0 1.0
CB 1:CYS19 3.1 26.1 1.0
CB 1:CYS22 3.3 30.9 1.0
CB 1:CYS34 3.3 24.9 1.0
CB 1:CYS37 3.5 25.7 1.0
N 1:CYS22 3.6 29.9 1.0
N 1:CYS37 3.8 26.4 1.0
CA 1:CYS22 4.0 29.3 1.0
CA 1:CYS37 4.2 25.6 1.0
CB 1:PHE39 4.3 31.9 1.0
CB 1:ARG21 4.5 27.2 1.0
CA 1:CYS19 4.6 27.0 1.0
CB 1:SER36 4.6 23.5 1.0
C 1:ARG21 4.7 30.4 1.0
CA 1:CYS34 4.8 26.2 1.0
N 1:PHE39 4.8 28.2 1.0
C 1:CYS37 4.8 24.7 1.0
N 1:GLY38 4.8 24.0 1.0
C 1:CYS22 4.8 28.3 1.0
N 1:GLY23 4.8 27.4 1.0
C 1:SER36 4.9 26.8 1.0
CD 1:ARG21 4.9 26.7 1.0
CA 1:ARG21 5.0 29.4 1.0
N 1:ARG21 5.0 29.8 1.0

Cadmium binding site 5 out of 5 in 3cma

Go back to Cadmium Binding Sites List in 3cma
Cadmium binding site 5 out of 5 in the The Structure of Cca and Cca-Phe-Cap-Bio 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 Cca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:54.8
occ:1.00
 SG 3:CYS71 2.5 49.5 1.0
SG 3:CYS11 2.5 44.8 1.0
SG 3:CYS74 2.5 57.5 1.0
O 3:HOH9053 2.6 0.2 1.0
SG 3:CYS14 3.0 62.5 1.0
CB 3:CYS14 3.2 58.2 1.0
CB 3:CYS71 3.2 51.0 1.0
N 3:CYS14 3.6 57.7 1.0
CB 3:CYS11 3.6 49.1 1.0
CB 3:CYS74 3.7 59.9 1.0
CA 3:CYS14 3.9 57.8 1.0
N 3:CYS74 4.2 60.8 1.0
OE1 3:GLN18 4.2 65.6 1.0
CB 3:HIS13 4.3 56.9 1.0
C 3:HIS13 4.5 57.1 1.0
CA 3:CYS74 4.5 60.5 1.0
CA 3:CYS71 4.7 51.1 1.0
CD 3:GLN18 4.8 62.6 1.0
CA 3:HIS13 4.9 56.1 1.0
O 3:HOH9030 4.9 50.7 1.0

Reference:

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908
Page generated: Thu Jul 10 12:28:07 2025

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