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Cadmium in PDB 1q7y: Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit

Protein crystallography data

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y 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) 19.99 / 3.20
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 (%) 22.5 / 28

Other elements in 1q7y:

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center 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

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit (pdb code 1q7y). 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1q7y

Go back to Cadmium Binding Sites List in 1q7y
Cadmium binding site 1 out of 5 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd8405

b:0.6
occ:1.00
 ND1 P:HIS40 2.4 47.4 1.0
CG P:HIS40 3.1 47.4 1.0
CE1 P:HIS40 3.3 47.3 1.0
CB P:HIS40 3.4 47.8 1.0
O P:HOH5650 3.6 64.7 1.0
O P:HOH5322 3.8 0.8 1.0
CG P:ARG37 4.1 57.0 1.0
CD2 P:HIS40 4.2 47.5 1.0
O P:ARG37 4.2 52.0 1.0
CA P:ARG37 4.2 52.1 1.0
NE2 P:HIS40 4.2 47.6 1.0
O P:HOH3002 4.4 29.1 1.0
CB P:ARG37 4.6 53.7 1.0
C P:ARG37 4.7 52.4 1.0
CZ P:ARG37 4.7 57.9 1.0
NE P:ARG37 4.8 58.4 1.0
NH1 P:ARG37 4.9 56.8 1.0
CA P:HIS40 4.9 48.8 1.0

Cadmium binding site 2 out of 5 in 1q7y

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Cadmium binding site 2 out of 5 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cd8401

b:70.3
occ:1.00
 SG V:CYS32 2.2 35.5 1.0
SG V:CYS36 2.3 46.0 1.0
SG V:CYS9 2.5 59.8 1.0
SG V:CYS6 2.6 58.7 1.0
CB V:CYS36 3.3 46.7 1.0
CB V:CYS6 3.3 61.8 1.0
CB V:CYS32 3.4 42.2 1.0
CB V:CYS9 3.5 60.5 1.0
N V:CYS9 3.9 59.9 1.0
N V:CYS32 3.9 44.5 1.0
CA V:CYS32 4.2 44.6 1.0
CA V:CYS9 4.3 60.5 1.0
OG V:SER33 4.4 49.3 1.0
OG1 V:THR11 4.5 58.3 1.0
N V:SER33 4.5 47.5 1.0
CB V:TYR8 4.6 58.2 1.0
CA V:CYS36 4.7 47.5 1.0
C V:CYS32 4.7 47.0 1.0
CA V:CYS6 4.8 61.9 1.0
CD2 V:TYR8 4.9 55.4 1.0
N V:GLY10 4.9 60.8 1.0

Cadmium binding site 3 out of 5 in 1q7y

Go back to Cadmium Binding Sites List in 1q7y
Cadmium binding site 3 out of 5 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8403

b:88.9
occ:1.00
 SG 1:CYS57 2.4 61.3 1.0
SG 1:CYS60 2.5 67.5 1.0
CB 1:CYS60 3.0 65.6 1.0
SG 1:CYS42 3.0 74.9 1.0
SG 1:CYS39 3.2 68.8 1.0
CB 1:CYS57 3.2 65.5 1.0
CB 1:CYS42 3.3 78.0 1.0
N 1:CYS60 3.6 67.2 1.0
CB 1:CYS39 3.8 70.0 1.0
CA 1:CYS60 3.8 65.7 1.0
N 1:CYS42 3.9 79.6 1.0
CA 1:CYS42 4.2 79.5 1.0
C 1:CYS60 4.5 64.9 1.0
CB 1:TYR62 4.6 67.6 1.0
CB 1:HIS59 4.6 74.6 1.0
CB 1:VAL41 4.6 79.7 1.0
CD2 1:HIS59 4.6 78.8 1.0
CG1 1:VAL41 4.7 79.5 1.0
CA 1:CYS57 4.7 66.7 1.0
C 1:HIS59 4.8 69.0 1.0
N 1:GLY61 4.9 64.6 1.0
N 1:TYR62 5.0 66.3 1.0
CG 1:HIS59 5.0 78.0 1.0

Cadmium binding site 4 out of 5 in 1q7y

Go back to Cadmium Binding Sites List in 1q7y
Cadmium binding site 4 out of 5 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8402

b:72.8
occ:1.00
 SG 2:CYS22 2.1 32.0 1.0
SG 2:CYS37 2.5 34.6 1.0
SG 2:CYS19 2.5 40.1 1.0
SG 2:CYS34 2.7 38.5 1.0
CB 2:CYS19 2.9 40.8 1.0
CB 2:CYS22 3.1 34.8 1.0
CB 2:CYS37 3.2 34.3 1.0
N 2:CYS22 3.3 37.3 1.0
CB 2:CYS34 3.5 36.4 1.0
CA 2:CYS22 3.7 36.1 1.0
N 2:CYS37 3.9 37.2 1.0
CA 2:CYS37 4.1 35.9 1.0
O 2:HOH1020 4.4 13.6 1.0
CA 2:CYS19 4.4 40.8 1.0
CB 2:ARG21 4.4 39.1 1.0
C 2:CYS22 4.4 37.4 1.0
C 2:ARG21 4.5 38.0 1.0
N 2:GLY23 4.5 38.1 1.0
CB 2:SER36 4.7 37.3 1.0
CB 2:PHE39 4.7 39.4 1.0
N 2:GLU24 4.8 42.2 1.0
CB 2:GLU24 4.8 44.3 1.0
O 2:GLU24 4.8 42.9 1.0
CA 2:ARG21 4.9 39.4 1.0
O 2:CYS19 4.9 42.2 1.0
C 2:CYS19 4.9 41.5 1.0
CA 2:CYS34 4.9 36.4 1.0
C 2:SER36 4.9 37.6 1.0
C 2:CYS37 4.9 34.5 1.0

Cadmium binding site 5 out of 5 in 1q7y

Go back to Cadmium Binding Sites List in 1q7y
Cadmium binding site 5 out of 5 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Cd8404

b:67.1
occ:1.00
 SG 4:CYS71 2.1 58.2 1.0
SG 4:CYS74 2.3 71.0 1.0
SG 4:CYS11 2.7 61.5 1.0
SG 4:CYS14 2.9 69.0 1.0
CB 4:CYS71 3.0 62.3 1.0
CB 4:CYS74 3.1 72.0 1.0
CB 4:CYS14 3.2 66.8 1.0
O 4:HOH8561 3.4 0.2 1.0
N 4:CYS14 3.5 67.0 1.0
CB 4:CYS11 3.6 63.6 1.0
CA 4:CYS14 3.9 66.5 1.0
N 4:CYS74 4.2 73.9 1.0
CA 4:CYS74 4.2 72.2 1.0
CB 4:HIS13 4.2 66.7 1.0
CA 4:CYS71 4.4 64.5 1.0
C 4:HIS13 4.6 67.1 1.0
O 4:HOH8536 4.8 62.3 1.0
C 4:CYS74 4.9 71.7 1.0
CA 4:HIS13 4.9 67.3 1.0
C 4:CYS71 4.9 67.7 1.0
N 4:GLY75 5.0 71.7 1.0

Reference:

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
Page generated: Thu Jul 10 11:14:58 2025

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