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Cadmium in PDB 1q86: Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit.

Protein crystallography data

The structure of Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit., PDB code: 1q86 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 / 3.00
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 (%) 23.4 / 26.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit. (pdb code 1q86). 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 Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit., PDB code: 1q86:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1q86

Go back to Cadmium Binding Sites List in 1q86
Cadmium binding site 1 out of 5 in the Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the 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 Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd8405

b:0.2
occ:1.00
ND1 P:HIS40 2.6 33.3 1.0
O A:HOH5772 2.9 63.2 1.0
CE1 P:HIS40 3.5 32.9 1.0
CG P:HIS40 3.5 33.2 1.0
O A:HOH5532 3.5 24.8 1.0
CB P:HIS40 3.8 35.3 1.0
NE2 P:HIS40 4.6 33.0 1.0
CD2 P:HIS40 4.7 33.2 1.0
CG P:ARG37 4.7 49.6 1.0
O P:HOH3002 4.7 43.7 1.0
CB P:ARG37 4.9 47.7 1.0
NE P:ARG37 5.0 48.9 1.0
CA P:ARG37 5.0 46.5 1.0
CZ P:ARG37 5.0 48.1 1.0

Cadmium binding site 2 out of 5 in 1q86

Go back to Cadmium Binding Sites List in 1q86
Cadmium binding site 2 out of 5 in the Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the 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 Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Cd8401

b:69.2
occ:1.00
SG V:CYS32 2.3 31.4 1.0
SG V:CYS36 2.3 51.5 1.0
SG V:CYS6 2.4 49.6 1.0
SG V:CYS9 2.6 51.9 1.0
CB V:CYS6 3.1 52.6 1.0
CB V:CYS9 3.4 51.4 1.0
CB V:CYS32 3.6 42.0 1.0
CB V:CYS36 3.7 51.1 1.0
N V:CYS9 3.8 51.2 1.0
N V:CYS32 4.0 44.4 1.0
CA V:CYS9 4.2 51.5 1.0
OG1 V:THR11 4.3 61.4 1.0
CA V:CYS32 4.4 44.3 1.0
OG V:SER33 4.4 51.0 1.0
CB V:TYR8 4.5 49.5 1.0
N V:SER33 4.6 47.9 1.0
CA V:CYS6 4.6 53.3 1.0
N V:GLY10 4.8 53.2 1.0
C V:TYR8 4.9 51.1 1.0
C V:CYS32 4.9 46.4 1.0
C V:CYS9 5.0 52.5 1.0

Cadmium binding site 3 out of 5 in 1q86

Go back to Cadmium Binding Sites List in 1q86
Cadmium binding site 3 out of 5 in the Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the 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 Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8403

b:60.6
occ:1.00
SG 1:CYS60 2.2 52.5 1.0
SG 1:CYS39 2.3 59.8 1.0
SG 1:CYS57 2.4 67.5 1.0
SG 1:CYS42 2.9 69.4 1.0
CB 1:CYS39 3.2 63.0 1.0
CB 1:CYS57 3.3 68.1 1.0
CB 1:CYS42 3.5 69.7 1.0
CB 1:CYS60 3.5 57.1 1.0
N 1:CYS42 3.7 70.9 1.0
N 1:CYS60 3.9 61.6 1.0
CA 1:CYS42 4.2 70.4 1.0
CA 1:CYS60 4.3 59.8 1.0
CB 1:HIS59 4.5 70.0 1.0
CB 1:VAL41 4.6 70.4 1.0
CA 1:CYS39 4.7 65.4 1.0
CG1 1:VAL41 4.7 71.1 1.0
CD2 1:HIS59 4.7 74.7 1.0
CB 1:TYR62 4.7 60.6 1.0
CA 1:CYS57 4.8 67.6 1.0
C 1:CYS42 4.8 70.6 1.0
C 1:VAL41 4.9 70.7 1.0

Cadmium binding site 4 out of 5 in 1q86

Go back to Cadmium Binding Sites List in 1q86
Cadmium binding site 4 out of 5 in the Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the 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 Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8402

b:64.8
occ:1.00
SG 2:CYS37 2.4 37.1 1.0
SG 2:CYS22 2.4 38.8 1.0
SG 2:CYS34 2.4 37.9 1.0
SG 2:CYS19 2.6 37.4 1.0
CB 2:CYS19 3.1 32.2 1.0
CB 2:CYS22 3.2 36.2 1.0
CB 2:CYS34 3.3 34.0 1.0
CB 2:CYS37 3.3 33.1 1.0
N 2:CYS22 3.6 36.1 1.0
N 2:CYS37 3.8 33.4 1.0
CA 2:CYS22 3.9 35.8 1.0
CA 2:CYS37 4.1 32.5 1.0
CB 2:PHE39 4.3 35.5 1.0
CA 2:CYS19 4.6 31.9 1.0
CB 2:ARG21 4.6 35.4 1.0
C 2:CYS22 4.6 34.5 1.0
C 2:ARG21 4.7 36.4 1.0
CB 2:SER36 4.7 33.2 1.0
CA 2:CYS34 4.7 34.1 1.0
O 2:HOH8420 4.7 40.4 1.0
N 2:GLY23 4.7 33.9 1.0
C 2:CYS37 4.9 30.5 1.0
O 2:GLU24 4.9 35.9 1.0
CD 2:ARG21 4.9 35.6 1.0
C 2:SER36 4.9 33.4 1.0
N 2:GLU24 4.9 35.7 1.0
N 2:PHE39 5.0 33.9 1.0
CA 2:ARG21 5.0 35.8 1.0

Cadmium binding site 5 out of 5 in 1q86

Go back to Cadmium Binding Sites List in 1q86
Cadmium binding site 5 out of 5 in the Crystal Structure of Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the 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 Cca-Phe-Cap-Biotin Bound Simultaneously at Half Occupancy to Both the A-Site and P-Site of the the 50S Ribosomal Subunit. within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Cd8404

b:63.7
occ:1.00
SG 4:CYS71 2.2 41.8 1.0
SG 4:CYS74 2.3 65.7 1.0
SG 4:CYS14 2.4 72.0 1.0
SG 4:CYS11 2.4 58.0 1.0
O 4:HOH8558 3.0 1.0 1.0
CB 4:CYS71 3.1 48.5 1.0
CB 4:CYS14 3.1 68.1 1.0
CB 4:CYS74 3.4 63.4 1.0
CB 4:CYS11 3.5 56.7 1.0
N 4:CYS14 3.5 66.8 1.0
CA 4:CYS14 3.8 67.6 1.0
N 4:CYS74 4.1 64.1 1.0
CA 4:CYS74 4.4 63.5 1.0
CB 4:HIS13 4.5 64.6 1.0
CA 4:CYS71 4.5 51.3 1.0
O 4:HOH8535 4.5 30.5 1.0
C 4:HIS13 4.7 65.8 1.0
OE1 4:GLN18 4.8 76.6 1.0
CA 4:CYS11 4.9 57.4 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: Fri Aug 28 12:21:51 2020
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