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Cadmium in PDB 3cd6: Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin

Protein crystallography data

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6 was solved by G.Blaha, G.Gurel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.95 / 2.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.805, 299.997, 576.002, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 3cd6:

The structure of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin 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 Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin (pdb code 3cd6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin, PDB code: 3cd6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3cd6

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Cadmium binding site 1 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:88.6
occ:1.00
ND1 O:HIS40 2.5 36.7 1.0
O 0:HOH6297 2.6 52.7 1.0
O 0:HOH6064 2.9 41.5 1.0
CE1 O:HIS40 3.4 35.9 1.0
CG O:HIS40 3.6 36.2 1.0
CB O:HIS40 3.8 39.5 1.0
NE2 O:HIS40 4.5 37.0 1.0
O 0:HOH4384 4.6 65.4 1.0
CD2 O:HIS40 4.7 36.4 1.0
CG O:ARG37 4.7 46.2 1.0
CZ O:ARG37 4.8 42.2 1.0
NE O:ARG37 4.9 44.7 1.0
NH1 O:ARG37 5.0 41.7 1.0
CB O:ARG37 5.0 44.9 1.0

Cadmium binding site 2 out of 5 in 3cd6

Go back to Cadmium Binding Sites List in 3cd6
Cadmium binding site 2 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:78.0
occ:1.00
SG U:CYS36 2.6 73.7 1.0
SG U:CYS32 2.7 63.8 1.0
SG U:CYS6 2.8 80.7 1.0
SG U:CYS9 2.8 78.1 1.0
CB U:CYS9 3.3 77.6 1.0
CB U:CYS6 3.5 80.4 1.0
CB U:CYS32 3.5 63.9 1.0
CB U:CYS36 3.6 71.1 1.0
N U:CYS9 3.9 77.0 1.0
N U:CYS32 3.9 63.5 1.0
CA U:CYS9 4.2 77.3 1.0
CA U:CYS32 4.2 64.6 1.0
OG1 U:THR11 4.3 83.0 1.0
OG U:SER33 4.4 68.6 1.0
N U:SER33 4.6 66.2 1.0
CB U:TYR8 4.8 73.5 1.0
C U:CYS32 4.8 65.6 1.0
N U:GLY10 4.8 78.7 1.0
C U:CYS9 5.0 77.7 1.0
CA U:CYS6 5.0 80.3 1.0

Cadmium binding site 3 out of 5 in 3cd6

Go back to Cadmium Binding Sites List in 3cd6
Cadmium binding site 3 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:0.0
occ:1.00
SG Z:CYS84 2.9 0.0 1.0
SG Z:CYS66 3.2 0.7 1.0
CB Z:ASN65 3.4 0.6 1.0
SG Z:CYS81 3.4 0.2 1.0
N Z:CYS66 3.5 0.9 1.0
CB Z:CYS66 3.6 0.2 1.0
CB Z:CYS84 3.9 0.9 1.0
CD2 Z:TYR83 4.0 0.7 1.0
C Z:ASN65 4.2 0.8 1.0
CA Z:CYS66 4.2 0.8 1.0
CA Z:ASN65 4.2 0.7 1.0
N Z:CYS84 4.3 0.4 1.0
CG Z:ASN65 4.5 0.8 1.0
CB Z:CYS81 4.5 0.4 1.0
CB Z:CYS63 4.5 0.3 1.0
SG Z:CYS63 4.5 1.0 1.0
CB Z:TYR83 4.6 0.5 1.0
N Z:ASN65 4.6 0.3 1.0
ND2 Z:ASN65 4.7 0.5 1.0
CA Z:CYS84 4.7 0.8 1.0
CG Z:TYR83 4.8 0.2 1.0
CE2 Z:TYR83 4.8 0.8 1.0
CB Z:TYR86 5.0 0.2 1.0

Cadmium binding site 4 out of 5 in 3cd6

Go back to Cadmium Binding Sites List in 3cd6
Cadmium binding site 4 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:54.2
occ:1.00
SG 1:CYS37 2.4 33.7 1.0
SG 1:CYS34 2.5 34.2 1.0
SG 1:CYS22 2.5 34.6 1.0
SG 1:CYS19 2.6 32.5 1.0
CB 1:CYS19 3.1 30.2 1.0
CB 1:CYS22 3.2 31.7 1.0
CB 1:CYS37 3.3 31.0 1.0
CB 1:CYS34 3.3 31.6 1.0
N 1:CYS22 3.7 33.0 1.0
N 1:CYS37 3.9 30.5 1.0
CA 1:CYS22 4.0 31.8 1.0
CA 1:CYS37 4.1 29.5 1.0
CB 1:PHE39 4.4 32.9 1.0
CB 1:ARG21 4.6 29.9 1.0
CA 1:CYS19 4.6 33.5 1.0
CA 1:CYS34 4.7 31.6 1.0
C 1:ARG21 4.7 32.2 1.0
C 1:CYS37 4.8 28.7 1.0
C 1:CYS22 4.8 30.4 1.0
N 1:GLY38 4.8 29.3 1.0
N 1:PHE39 4.9 31.8 1.0
CB 1:SER36 4.9 31.2 1.0
N 1:GLY23 4.9 31.1 1.0
C 1:SER36 4.9 30.9 1.0
CD 1:ARG21 5.0 28.2 1.0

Cadmium binding site 5 out of 5 in 3cd6

Go back to Cadmium Binding Sites List in 3cd6
Cadmium binding site 5 out of 5 in the Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Co-Cystal of Large Ribosomal Subunit Mutant G2616A with Cc-Puromycin within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:0.0
occ:1.00
CB 3:CYS11 3.1 0.3 1.0
CB 3:CYS14 3.2 0.8 1.0
CB 3:GLN18 3.3 0.8 1.0
SG 3:CYS71 3.5 0.3 1.0
SG 3:CYS11 3.5 0.3 1.0
SG 3:CYS14 3.7 0.1 1.0
CG 3:GLN18 3.7 0.3 1.0
NE2 3:GLN18 3.8 0.0 1.0
CD 3:GLN18 3.9 0.3 1.0
O 3:GLU16 4.0 0.7 1.0
N 3:GLN18 4.3 0.2 1.0
CA 3:GLN18 4.3 0.4 1.0
CG 3:GLU16 4.4 0.2 1.0
CA 3:CYS11 4.6 0.6 1.0
OE1 3:GLN18 4.6 1.0 1.0
CA 3:CYS14 4.6 0.5 1.0
SG 3:CYS74 4.6 0.6 1.0
C 3:GLU16 4.7 0.7 1.0
CB 3:CYS71 4.8 0.1 1.0
CE1 3:HIS20 4.9 0.7 1.0
N 3:CYS11 4.9 0.4 1.0
N 3:CYS14 5.0 0.1 1.0
C 3:HIS17 5.0 0.1 1.0

Reference:

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075
Page generated: Wed Oct 28 10:02:23 2020
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