Cadmium in PDB 1q81: Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.

The structure of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit., PDB code: 1q81 was solved by J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.163, 301.288, 575.397, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.9

The structure of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	2 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Cadmium atom in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. (pdb code 1q81). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit., PDB code: 1q81:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ P:Cd8405 b:0.0 occ:1.00 ND1 P:HIS40 3.0 45.8 1.0 O P:HOH5650 3.2 82.7 1.0 CG P:ARG37 3.6 55.6 1.0 CE1 P:HIS40 3.6 44.1 1.0 O P:HOH3002 3.7 83.3 1.0 CG P:HIS40 3.8 44.8 1.0 CB P:ARG37 4.0 53.8 1.0 CZ P:ARG37 4.0 55.1 1.0 CA P:ARG37 4.1 53.2 1.0 NE P:ARG37 4.1 55.4 1.0 NH1 P:ARG37 4.1 53.2 1.0 CB P:HIS40 4.2 47.2 1.0 O A:HOH5529 4.2 58.2 1.0 CD P:ARG37 4.3 55.5 1.0 NH2 P:ARG37 4.5 53.1 1.0 OP2 A:G656 4.5 48.2 1.0 NE2 P:HIS40 4.6 43.3 1.0 CD2 P:LEU7 4.6 58.6 1.0 O P:ARG37 4.6 54.0 1.0 CD2 P:HIS40 4.7 43.6 1.0 C P:ARG37 4.9 53.2 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ V:Cd8401 b:0.0 occ:1.00 SG V:CYS36 2.8 77.9 1.0 N V:CYS9 2.8 94.3 1.0 CB V:CYS9 2.9 95.6 1.0 SG V:CYS6 3.1 0.8 1.0 SG V:CYS9 3.1 99.8 1.0 CB V:CYS36 3.2 76.6 1.0 CA V:CYS9 3.4 94.5 1.0 CB V:TYR8 3.5 90.5 1.0 SG V:CYS32 3.6 85.6 1.0 CB V:CYS6 3.7 0.7 1.0 CD2 V:TYR8 3.8 86.3 1.0 C V:TYR8 3.9 93.7 1.0 CA V:TYR8 4.1 93.2 1.0 CG V:TYR8 4.2 87.5 1.0 N V:GLY10 4.2 93.2 1.0 C V:CYS9 4.4 93.8 1.0 N V:TYR8 4.4 94.8 1.0 CA V:CYS36 4.7 76.2 1.0 OG1 V:THR11 4.7 90.6 1.0 N V:CYS32 4.7 79.7 1.0 CB V:CYS32 4.7 82.2 1.0 O V:TYR8 4.9 93.7 1.0 O V:CYS6 5.0 0.5 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ 1:Cd8403 b:0.5 occ:1.00 SG 1:CYS60 2.7 0.9 1.0 CB 1:CYS60 2.9 0.7 1.0 SG 1:CYS42 3.4 0.9 1.0 CB 1:CYS42 3.4 0.4 1.0 N 1:CYS60 3.6 0.3 1.0 CA 1:CYS60 3.8 0.9 1.0 SG 1:CYS57 3.9 0.3 1.0 CD2 1:HIS59 3.9 0.1 1.0 SG 1:CYS39 4.0 0.9 1.0 CB 1:CYS57 4.0 0.0 1.0 N 1:CYS42 4.1 0.1 1.0 CB 1:HIS59 4.2 0.2 1.0 CB 1:CYS39 4.3 0.3 1.0 CG 1:HIS59 4.4 0.6 1.0 CA 1:CYS42 4.4 0.0 1.0 CG1 1:VAL41 4.4 0.9 1.0 C 1:HIS59 4.6 0.5 1.0 C 1:CYS60 4.6 0.2 1.0 CB 1:VAL41 4.7 0.1 1.0 CB 1:TYR62 4.9 93.2 1.0 N 1:GLY61 4.9 0.6 1.0 CA 1:HIS59 5.0 0.3 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ 2:Cd8402 b:67.4 occ:1.00 SG 2:CYS34 2.2 42.3 1.0 SG 2:CYS22 2.4 35.6 1.0 SG 2:CYS37 2.6 32.0 1.0 SG 2:CYS19 2.6 42.3 1.0 CB 2:CYS34 3.2 36.5 1.0 CB 2:CYS19 3.2 40.0 1.0 CB 2:CYS37 3.3 33.7 1.0 CB 2:CYS22 3.3 35.9 1.0 N 2:CYS37 3.6 35.5 1.0 N 2:CYS22 3.8 37.3 1.0 CA 2:CYS37 4.0 34.0 1.0 CA 2:CYS22 4.1 37.1 1.0 CB 2:PHE39 4.5 39.2 1.0 O 2:HOH1020 4.5 38.1 1.0 CB 2:SER36 4.5 36.0 1.0 CA 2:CYS34 4.6 34.9 1.0 C 2:SER36 4.6 36.3 1.0 CA 2:CYS19 4.7 39.0 1.0 C 2:CYS37 4.7 34.5 1.0 N 2:GLY38 4.7 33.8 1.0 CB 2:ARG21 4.8 37.8 1.0 N 2:PHE39 4.8 37.1 1.0 N 2:SER36 4.9 35.3 1.0 CA 2:SER36 4.9 36.5 1.0 C 2:CYS22 4.9 37.5 1.0 N 2:GLY23 4.9 38.4 1.0 C 2:ARG21 5.0 38.2 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Minihelix with 3' Puromycin Bound to A-Site of the 50S Ribosomal Subunit. within 5.0Å range: probe atom residue distance (Å) B Occ 4:Cd8404 b:0.0 occ:1.00 SG 4:CYS11 3.0 0.1 1.0 N 4:CYS14 3.0 0.7 1.0 CB 4:CYS14 3.2 1.0 1.0 SG 4:CYS74 3.3 0.8 1.0 CB 4:CYS74 3.4 0.7 1.0 CB 4:HIS13 3.6 0.8 1.0 CA 4:CYS14 3.6 0.8 1.0 SG 4:CYS71 3.8 0.5 1.0 CB 4:CYS71 3.8 0.9 1.0 CB 4:CYS11 3.9 0.4 1.0 C 4:HIS13 4.0 0.2 1.0 CA 4:HIS13 4.2 0.9 1.0 O 4:HOH8561 4.2 0.9 1.0 SG 4:CYS14 4.4 0.2 1.0 CG 4:HIS13 4.4 0.8 1.0 CD2 4:HIS13 4.4 0.9 1.0 N 4:HIS13 4.5 0.4 1.0 O 4:LYS76 4.7 0.9 1.0 CB 4:LYS76 4.7 0.9 1.0 CA 4:CYS74 4.7 0.1 1.0 O 4:HOH8538 4.9 91.1 1.0 N 4:CYS74 4.9 0.3 1.0 C 4:CYS14 5.0 0.9 1.0

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099