Atomistry » Cadmium » PDB 2mpa-2w5f » 2otl
Atomistry »
  Cadmium »
    PDB 2mpa-2w5f »
      2otl »

Cadmium in PDB 2otl: Girodazole Bound to the Large Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Girodazole Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otl was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.36 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 213.077, 300.598, 575.055, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24.8

Other elements in 2otl:

The structure of Girodazole Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 116 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 23 atoms
Sodium (Na) 85 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2otl

Go back to Cadmium Binding Sites List in 2otl
Cadmium binding site 1 out of 5 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd8605

b:93.4
occ:1.00
ND1 O:HIS40 2.6 37.6 1.0
O O:HOH5650 2.7 42.1 1.0
O O:HOH5322 2.8 39.4 1.0
CE1 O:HIS40 3.5 38.0 1.0
CG O:HIS40 3.6 38.1 1.0
CB O:HIS40 3.9 40.9 1.0
CG O:ARG37 4.3 51.5 1.0
NE2 O:HIS40 4.6 38.2 1.0
CZ O:ARG37 4.7 50.0 1.0
CB O:ARG37 4.7 49.4 1.0
CD2 O:HIS40 4.7 37.6 1.0
NH1 O:ARG37 4.7 49.5 1.0
O O:HOH3002 4.7 50.3 1.0
CA O:ARG37 4.8 48.2 1.0
NE O:ARG37 4.8 51.8 1.0
O O:ARG37 4.8 48.4 1.0

Cadmium binding site 2 out of 5 in 2otl

Go back to Cadmium Binding Sites List in 2otl
Cadmium binding site 2 out of 5 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd8601

b:62.1
occ:1.00
SG U:CYS36 2.3 57.8 1.0
SG U:CYS6 2.5 58.5 1.0
SG U:CYS32 2.5 43.1 1.0
SG U:CYS9 2.6 61.2 1.0
CB U:CYS6 3.2 60.6 1.0
CB U:CYS9 3.5 60.2 1.0
CB U:CYS36 3.5 56.7 1.0
CB U:CYS32 3.5 46.7 1.0
N U:CYS9 3.8 59.7 1.0
N U:CYS32 4.0 46.5 1.0
CA U:CYS9 4.2 60.4 1.0
CA U:CYS32 4.3 47.6 1.0
OG1 U:THR11 4.4 68.2 1.0
OG U:SER33 4.4 51.6 1.0
CB U:TYR8 4.5 57.1 1.0
N U:SER33 4.6 50.1 1.0
CA U:CYS6 4.7 61.0 1.0
C U:CYS32 4.8 49.7 1.0
N U:GLY10 4.8 62.4 1.0
CA U:CYS36 4.9 55.2 1.0
C U:TYR8 4.9 59.4 1.0

Cadmium binding site 3 out of 5 in 2otl

Go back to Cadmium Binding Sites List in 2otl
Cadmium binding site 3 out of 5 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8603

b:98.8
occ:1.00
SG Z:CYS60 2.5 90.2 1.0
SG Z:CYS39 2.6 80.1 1.0
SG Z:CYS57 2.7 87.1 1.0
CB Z:CYS60 2.9 89.7 1.0
SG Z:CYS42 3.0 0.7 1.0
C Z:ASN41 3.0 97.8 1.0
CB Z:CYS42 3.1 0.9 1.0
O Z:ASN41 3.1 97.8 1.0
N Z:CYS42 3.2 99.5 1.0
CB Z:ASN41 3.2 94.9 1.0
CB Z:CYS57 3.3 89.1 1.0
N Z:CYS60 3.5 91.4 1.0
CA Z:ASN41 3.5 96.2 1.0
CA Z:CYS60 3.7 89.1 1.0
CA Z:CYS42 3.7 0.1 1.0
CB Z:CYS39 3.9 87.9 1.0
N Z:ASN41 3.9 95.9 1.0
ND2 Z:ASN41 4.3 92.9 1.0
CG Z:ASN41 4.3 93.6 1.0
O Z:CYS42 4.4 0.9 1.0
CB Z:TYR62 4.4 77.2 1.0
C Z:CYS60 4.5 87.8 1.0
CD2 Z:TYR59 4.5 0.3 1.0
CB Z:TYR59 4.5 98.7 1.0
C Z:CYS42 4.6 0.7 1.0
C Z:TYR59 4.7 94.2 1.0
CA Z:CYS57 4.8 88.5 1.0
CG Z:TYR59 4.9 0.6 1.0
O Z:CYS57 4.9 90.0 1.0
N Z:ASP61 4.9 86.6 1.0
C Z:PRO40 5.0 95.7 1.0
N Z:TYR62 5.0 82.0 1.0

Cadmium binding site 4 out of 5 in 2otl

Go back to Cadmium Binding Sites List in 2otl
Cadmium binding site 4 out of 5 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd8602

b:63.6
occ:1.00
SG 1:CYS37 2.3 38.0 1.0
SG 1:CYS34 2.4 38.5 1.0
SG 1:CYS22 2.4 36.4 1.0
SG 1:CYS19 2.5 42.4 1.0
CB 1:CYS19 3.0 38.2 1.0
CB 1:CYS34 3.1 33.4 1.0
CB 1:CYS22 3.1 34.1 1.0
CB 1:CYS37 3.4 32.6 1.0
N 1:CYS22 3.6 36.2 1.0
N 1:CYS37 3.8 32.8 1.0
CA 1:CYS22 3.9 35.3 1.0
CA 1:CYS37 4.1 31.9 1.0
CB 1:PHE39 4.3 38.0 1.0
CA 1:CYS19 4.5 40.4 1.0
CA 1:CYS34 4.6 33.6 1.0
CB 1:ARG21 4.7 35.0 1.0
C 1:ARG21 4.7 37.0 1.0
CB 1:SER36 4.8 34.3 1.0
O 1:HOH1020 4.8 37.6 1.0
C 1:CYS22 4.8 36.1 1.0
C 1:CYS37 4.8 32.4 1.0
C 1:SER36 4.9 34.8 1.0
N 1:PHE39 4.9 36.8 1.0
N 1:GLY23 5.0 35.9 1.0
N 1:GLY38 5.0 34.2 1.0

Cadmium binding site 5 out of 5 in 2otl

Go back to Cadmium Binding Sites List in 2otl
Cadmium binding site 5 out of 5 in the Girodazole Bound to the Large Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Girodazole Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd8604

b:68.2
occ:1.00
SG 3:CYS71 2.3 53.2 1.0
O 3:HOH8757 2.3 0.9 1.0
SG 3:CYS11 2.5 68.3 1.0
SG 3:CYS74 2.5 68.9 1.0
CB 3:CYS14 2.9 73.4 1.0
SG 3:CYS14 3.1 77.1 1.0
CB 3:CYS71 3.3 59.3 1.0
CB 3:CYS74 3.6 70.6 1.0
CB 3:CYS11 3.6 65.7 1.0
N 3:CYS14 3.8 73.3 1.0
CA 3:CYS14 3.9 73.3 1.0
N 3:CYS74 4.0 71.9 1.0
CA 3:CYS74 4.3 71.0 1.0
CA 3:CYS71 4.7 60.9 1.0
CB 3:HIS13 4.8 71.1 1.0
O 3:HOH8733 4.8 50.9 1.0
C 3:HIS13 4.9 72.6 1.0
NE2 3:GLN18 5.0 78.9 1.0
CA 3:CYS11 5.0 65.3 1.0

Reference:

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081
Page generated: Thu Jul 10 11:57:46 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy