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Cadmium in PDB 2qex: Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

Protein crystallography data

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex was solved by S.J.Schroeder, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.92 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 214.620, 304.048, 578.647, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.1

Other elements in 2qex:

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium (Mg) 116 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit (pdb code 2qex). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2qex

Go back to Cadmium Binding Sites List in 2qex
Cadmium binding site 1 out of 5 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8705

b:0.1
occ:1.00
 ND1 O:HIS40 2.8 34.7 1.0
CE1 O:HIS40 3.5 35.2 1.0
CG O:ARG37 3.8 46.7 1.0
O O:HOH5650 4.0 59.0 1.0
CG O:HIS40 4.0 36.3 1.0
O O:HOH3002 4.1 64.0 1.0
NE O:ARG37 4.4 47.7 1.0
CD O:ARG37 4.4 47.4 1.0
CB O:HIS40 4.5 37.9 1.0
O O:HOH5322 4.5 37.1 1.0
NE2 O:HIS40 4.7 36.6 1.0
CD2 O:LEU7 4.7 45.1 1.0
CB O:ARG37 4.8 44.7 1.0
CZ O:ARG37 4.8 47.7 1.0
CA O:ARG37 4.9 44.2 1.0
CD2 O:HIS40 5.0 37.6 1.0
CD1 O:LEU7 5.0 44.7 1.0

Cadmium binding site 2 out of 5 in 2qex

Go back to Cadmium Binding Sites List in 2qex
Cadmium binding site 2 out of 5 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8701

b:63.5
occ:1.00
 SG U:CYS9 2.4 50.9 1.0
SG U:CYS36 2.5 46.9 1.0
SG U:CYS32 2.5 42.9 1.0
SG U:CYS6 2.5 47.4 1.0
CB U:CYS9 3.1 48.8 1.0
CB U:CYS6 3.2 49.4 1.0
CB U:CYS32 3.4 43.3 1.0
CB U:CYS36 3.5 45.6 1.0
N U:CYS9 3.6 48.5 1.0
CA U:CYS9 4.0 49.3 1.0
N U:CYS32 4.0 43.0 1.0
CA U:CYS32 4.3 44.0 1.0
OG U:SER33 4.4 50.1 1.0
N U:SER33 4.5 45.5 1.0
CB U:TYR8 4.5 46.2 1.0
OG1 U:THR11 4.5 56.8 1.0
CA U:CYS6 4.7 50.5 1.0
N U:GLY10 4.7 50.6 1.0
C U:TYR8 4.8 47.5 1.0
C U:CYS9 4.8 50.1 1.0
C U:CYS32 4.8 45.4 1.0
CA U:CYS36 4.9 46.3 1.0

Cadmium binding site 3 out of 5 in 2qex

Go back to Cadmium Binding Sites List in 2qex
Cadmium binding site 3 out of 5 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8703

b:63.0
occ:1.00
 SG Z:CYS60 2.2 55.7 1.0
SG Z:CYS39 2.3 57.9 1.0
SG Z:CYS57 2.5 55.4 1.0
SG Z:CYS42 2.6 66.0 1.0
CB Z:CYS39 3.0 57.5 1.0
CB Z:CYS60 3.2 54.6 1.0
CB Z:CYS57 3.2 57.0 1.0
CB Z:CYS42 3.6 63.2 1.0
N Z:CYS60 3.6 56.8 1.0
N Z:CYS42 3.7 63.1 1.0
CA Z:CYS60 4.0 55.3 1.0
CB Z:ASN41 4.0 62.9 1.0
CA Z:CYS42 4.2 63.1 1.0
CB Z:TYR59 4.4 62.4 1.0
CA Z:CYS39 4.5 58.5 1.0
CB Z:TYR62 4.5 48.9 1.0
CD2 Z:TYR59 4.5 66.2 1.0
C Z:CYS60 4.7 54.9 1.0
CA Z:CYS57 4.7 55.3 1.0
C Z:ASN41 4.7 62.7 1.0
C Z:TYR59 4.8 58.3 1.0
CA Z:ASN41 4.8 62.5 1.0
C Z:CYS42 4.9 63.4 1.0
N Z:ASP61 4.9 54.7 1.0
N Z:ASN41 4.9 62.1 1.0
N Z:TYR62 4.9 52.9 1.0
CG Z:TYR59 5.0 64.8 1.0
C Z:CYS39 5.0 60.0 1.0
N Z:GLY43 5.0 63.2 1.0

Cadmium binding site 4 out of 5 in 2qex

Go back to Cadmium Binding Sites List in 2qex
Cadmium binding site 4 out of 5 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8702

b:55.4
occ:1.00
 SG 1:CYS34 2.4 29.2 1.0
SG 1:CYS22 2.4 30.1 1.0
SG 1:CYS37 2.4 33.7 1.0
SG 1:CYS19 2.7 26.8 1.0
CB 1:CYS22 3.1 31.9 1.0
CB 1:CYS37 3.2 29.5 1.0
CB 1:CYS19 3.3 28.5 1.0
CB 1:CYS34 3.3 26.8 1.0
N 1:CYS37 3.7 30.5 1.0
N 1:CYS22 3.7 33.7 1.0
CA 1:CYS22 4.0 33.2 1.0
CA 1:CYS37 4.0 30.5 1.0
CB 1:PHE39 4.4 28.8 1.0
CB 1:SER36 4.6 30.9 1.0
C 1:CYS22 4.7 33.4 1.0
CA 1:CYS34 4.8 28.9 1.0
C 1:SER36 4.8 30.6 1.0
C 1:CYS37 4.8 29.0 1.0
CA 1:CYS19 4.8 29.9 1.0
CB 1:ARG21 4.8 30.5 1.0
C 1:ARG21 4.8 33.5 1.0
N 1:GLY23 4.8 33.6 1.0
O 1:HOH1020 5.0 37.3 1.0
N 1:GLY38 5.0 28.6 1.0
N 1:PHE39 5.0 28.1 1.0

Cadmium binding site 5 out of 5 in 2qex

Go back to Cadmium Binding Sites List in 2qex
Cadmium binding site 5 out of 5 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel 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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8704

b:53.5
occ:1.00
 SG 3:CYS74 2.0 53.6 1.0
SG 3:CYS14 2.1 63.9 1.0
SG 3:CYS11 2.4 48.7 1.0
SG 3:CYS71 2.4 51.6 1.0
O 3:HOH8863 2.5 0.3 1.0
CB 3:CYS71 3.3 53.0 1.0
CB 3:CYS74 3.3 52.9 1.0
CB 3:CYS14 3.3 59.3 1.0
CB 3:CYS11 3.5 47.4 1.0
N 3:CYS14 3.8 60.0 1.0
N 3:CYS74 4.0 55.6 1.0
CA 3:CYS14 4.1 59.7 1.0
CA 3:CYS74 4.2 54.3 1.0
NE2 3:GLN18 4.3 67.6 1.0
CB 3:HIS13 4.5 58.6 1.0
C 3:HIS13 4.8 59.3 1.0
CA 3:CYS71 4.8 53.1 1.0
CD 3:GLN18 4.8 66.2 1.0
O 3:HOH8837 4.9 51.8 1.0
CA 3:CYS11 4.9 48.2 1.0
C 3:CYS74 5.0 54.2 1.0

Reference:

S.J.Schroeder, G.Blaha, P.B.Moore. Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit. Antimicrob.Agents Chemother. V. 51 4462 2007.
ISSN: ISSN 0066-4804
PubMed: 17664317
DOI: 10.1128/AAC.00455-07
Page generated: Thu Jul 10 12:00:26 2025

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