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

Protein crystallography data

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme 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) 49.82 / 2.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 210.786, 297.778, 572.588, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 3cme:

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

Strontium (Sr) 108 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cme). 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cme

Go back to Cadmium Binding Sites List in 3cme
Cadmium binding site 1 out of 5 in the The Structure of Ca 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 Ca 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:0.6
occ:1.00
ND1 O:HIS40 2.7 36.9 1.0
O O:HOH5650 3.1 64.1 1.0
O O:HOH5322 3.4 73.7 1.0
CG O:HIS40 3.7 36.5 1.0
CE1 O:HIS40 3.7 36.9 1.0
CB O:HIS40 3.8 38.3 1.0
O 0:HOH5228 4.3 56.1 1.0
CG O:ARG37 4.5 46.3 1.0
CZ O:ARG37 4.8 42.4 1.0
NE2 O:HIS40 4.8 37.5 1.0
CD2 O:HIS40 4.8 37.2 1.0
NE O:ARG37 4.9 42.7 1.0
O O:HOH1390 4.9 76.2 1.0
CB O:ARG37 5.0 45.7 1.0
NH2 O:ARG37 5.0 41.9 1.0

Cadmium binding site 2 out of 5 in 3cme

Go back to Cadmium Binding Sites List in 3cme
Cadmium binding site 2 out of 5 in the The Structure of Ca 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 Ca 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:57.1
occ:1.00
SG U:CYS9 2.5 49.5 1.0
SG U:CYS32 2.5 35.7 1.0
SG U:CYS36 2.6 44.7 1.0
SG U:CYS6 2.6 52.3 1.0
CB U:CYS9 3.4 52.5 1.0
CB U:CYS32 3.4 38.9 1.0
CB U:CYS6 3.5 51.0 1.0
CB U:CYS36 3.5 43.9 1.0
N U:CYS9 3.6 51.9 1.0
N U:CYS32 4.0 38.6 1.0
CA U:CYS9 4.1 52.7 1.0
CA U:CYS32 4.3 38.9 1.0
CB U:TYR8 4.4 49.8 1.0
OG U:SER33 4.6 36.9 1.0
N U:GLY10 4.6 53.2 1.0
N U:SER33 4.7 39.1 1.0
C U:TYR8 4.7 50.2 1.0
C U:CYS9 4.8 52.9 1.0
C U:CYS32 4.8 39.5 1.0
CA U:CYS6 4.9 51.2 1.0
CD2 U:TYR8 4.9 46.6 1.0
CA U:TYR8 4.9 50.4 1.0
CA U:CYS36 4.9 45.5 1.0
N U:TYR8 5.0 51.0 1.0

Cadmium binding site 3 out of 5 in 3cme

Go back to Cadmium Binding Sites List in 3cme
Cadmium binding site 3 out of 5 in the The Structure of Ca 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 Ca 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:55.5
occ:1.00
SG Z:CYS84 2.5 51.1 1.0
SG Z:CYS63 2.5 58.8 1.0
SG Z:CYS66 2.7 71.1 1.0
SG Z:CYS81 2.7 65.9 1.0
CB Z:CYS84 3.2 53.0 1.0
CB Z:CYS81 3.2 63.7 1.0
CB Z:CYS63 3.3 62.6 1.0
N Z:CYS84 3.5 56.2 1.0
CB Z:CYS66 3.5 68.4 1.0
N Z:CYS66 3.8 67.2 1.0
CA Z:CYS84 3.9 54.5 1.0
CA Z:CYS66 4.3 67.3 1.0
CB Z:TYR83 4.4 61.6 1.0
CD2 Z:TYR83 4.4 65.6 1.0
CB Z:ASN65 4.5 63.4 1.0
C Z:CYS84 4.6 53.9 1.0
CB Z:TYR86 4.6 51.5 1.0
C Z:TYR83 4.6 58.2 1.0
CA Z:CYS81 4.7 61.8 1.0
CA Z:CYS63 4.8 63.7 1.0
ND2 Z:ASN65 4.8 61.4 1.0
N Z:ASP85 4.8 53.4 1.0
C Z:ASN65 4.9 66.1 1.0
CG Z:TYR83 4.9 64.4 1.0
N Z:TYR86 4.9 52.8 1.0
CA Z:TYR83 5.0 60.8 1.0

Cadmium binding site 4 out of 5 in 3cme

Go back to Cadmium Binding Sites List in 3cme
Cadmium binding site 4 out of 5 in the The Structure of Ca 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 Ca 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:57.2
occ:1.00
SG 1:CYS37 2.5 29.6 1.0
SG 1:CYS34 2.6 34.4 1.0
SG 1:CYS22 2.6 36.1 1.0
SG 1:CYS19 2.6 38.0 1.0
CB 1:CYS34 3.2 30.3 1.0
CB 1:CYS19 3.2 34.8 1.0
CB 1:CYS37 3.5 31.2 1.0
CB 1:CYS22 3.6 33.8 1.0
N 1:CYS37 3.7 32.4 1.0
N 1:CYS22 3.9 32.0 1.0
CB 1:PHE39 4.0 35.8 1.0
CA 1:CYS37 4.2 31.1 1.0
CA 1:CYS22 4.4 31.6 1.0
CB 1:SER36 4.4 26.7 1.0
N 1:PHE39 4.5 29.6 1.0
CB 1:ARG21 4.5 30.1 1.0
N 1:GLY38 4.6 28.1 1.0
CA 1:CYS34 4.6 30.4 1.0
CA 1:CYS19 4.7 32.9 1.0
C 1:CYS37 4.7 29.4 1.0
O 1:HOH1020 4.8 24.9 1.0
C 1:SER36 4.8 30.8 1.0
C 1:ARG21 4.9 31.9 1.0
CD 1:ARG21 4.9 26.9 1.0
CA 1:PHE39 4.9 33.2 1.0
O 1:GLU24 5.0 35.7 1.0
CA 1:SER36 5.0 30.1 1.0

Cadmium binding site 5 out of 5 in 3cme

Go back to Cadmium Binding Sites List in 3cme
Cadmium binding site 5 out of 5 in the The Structure of Ca 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 Ca 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:52.2
occ:1.00
SG 3:CYS71 2.5 47.0 1.0
SG 3:CYS11 2.5 58.3 1.0
SG 3:CYS74 2.5 56.0 1.0
O 3:HOH9050 2.7 0.9 1.0
SG 3:CYS14 2.8 65.4 1.0
CB 3:CYS71 3.1 50.9 1.0
CB 3:CYS14 3.4 60.0 1.0
CB 3:CYS11 3.6 57.4 1.0
N 3:CYS14 3.7 60.0 1.0
CB 3:CYS74 3.9 57.4 1.0
CA 3:CYS14 4.1 60.5 1.0
CB 3:HIS13 4.2 58.3 1.0
N 3:CYS74 4.3 57.8 1.0
OE1 3:GLN18 4.4 69.5 1.0
C 3:HIS13 4.5 58.7 1.0
CA 3:CYS71 4.6 50.8 1.0
CA 3:CYS74 4.7 58.0 1.0
CA 3:HIS13 4.7 58.5 1.0
N 3:HIS13 5.0 56.9 1.0
CA 3:CYS11 5.0 57.5 1.0
O 3:CYS11 5.0 56.3 1.0
CD 3:GLN18 5.0 67.6 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: Wed Oct 28 10:02:32 2020
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