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Cadmium in PDB 2qa4: A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit

Protein crystallography data

The structure of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit, PDB code: 2qa4 was solved by T.A.Steitz, J.M.Kavran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 214.490, 302.432, 578.056, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 28.8

Other elements in 2qa4:

The structure of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit (pdb code 2qa4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit, PDB code: 2qa4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 2qa4

Go back to Cadmium Binding Sites List in 2qa4
Cadmium binding site 1 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd67

b:0.3
occ:1.00
SG U:CYS36 2.7 0.7 1.0
CB U:CYS9 2.8 0.2 1.0
SG U:CYS6 3.0 0.2 1.0
SG U:CYS32 3.0 0.4 1.0
CB U:CYS6 3.6 0.1 1.0
N U:CYS9 3.7 0.1 1.0
CB U:CYS36 3.8 0.4 1.0
CA U:CYS9 3.8 0.5 1.0
SG U:CYS9 4.0 0.5 1.0
OG1 U:THR11 4.0 0.8 1.0
CB U:CYS32 4.2 0.6 1.0
N U:CYS32 4.3 0.4 1.0
C U:CYS9 4.7 0.1 1.0
N U:GLY10 4.7 0.1 1.0
CB U:TYR8 4.7 0.4 1.0
OG U:SER33 4.8 0.5 1.0
CD2 U:TYR8 4.8 0.9 1.0
CA U:CYS32 4.8 0.3 1.0
C U:TYR8 4.9 0.8 1.0

Cadmium binding site 2 out of 5 in 2qa4

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Cadmium binding site 2 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd57

b:76.1
occ:1.00
SG 1:CYS22 2.1 43.9 1.0
SG 1:CYS19 2.2 54.9 1.0
SG 1:CYS37 2.5 44.6 1.0
SG 1:CYS34 2.7 50.8 1.0
CB 1:CYS19 2.7 47.6 1.0
CB 1:CYS22 3.1 42.9 1.0
CB 1:CYS37 3.1 39.3 1.0
N 1:CYS22 3.4 43.6 1.0
CB 1:CYS34 3.4 44.1 1.0
CA 1:CYS22 3.7 43.5 1.0
N 1:CYS37 3.9 38.9 1.0
CA 1:CYS37 4.1 39.1 1.0
CA 1:CYS19 4.2 45.2 1.0
N 1:GLY23 4.4 43.6 1.0
CB 1:PHE39 4.4 54.0 1.0
C 1:CYS22 4.5 43.7 1.0
C 1:ARG21 4.5 44.4 1.0
CB 1:ARG21 4.6 44.9 1.0
C 1:CYS19 4.6 46.5 1.0
O 1:CYS19 4.6 47.4 1.0
C 1:CYS37 4.8 38.8 1.0
N 1:GLU24 4.8 45.8 1.0
CA 1:ARG21 4.8 44.0 1.0
N 1:ARG21 4.8 44.3 1.0
CA 1:CYS34 4.9 42.4 1.0
N 1:GLY38 4.9 40.2 1.0
CB 1:SER36 4.9 38.6 1.0
N 1:PHE39 5.0 46.6 1.0
CB 1:GLU24 5.0 47.4 1.0
CD 1:ARG21 5.0 45.4 1.0

Cadmium binding site 3 out of 5 in 2qa4

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Cadmium binding site 3 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd93

b:0.0
occ:1.00
SG Z:CYS42 3.1 0.1 1.0
CB Z:CYS60 3.4 0.3 1.0
SG Z:CYS39 3.6 0.9 1.0
CB Z:CYS39 3.9 0.2 1.0
SG Z:CYS57 3.9 0.5 1.0
CB Z:CYS57 4.1 0.3 1.0
N Z:CYS60 4.2 0.7 1.0
N Z:CYS42 4.2 0.2 1.0
CB Z:CYS42 4.2 0.9 1.0
CD2 Z:TYR59 4.2 0.5 1.0
CB Z:ASN41 4.3 0.5 1.0
CA Z:CYS60 4.4 0.1 1.0
SG Z:CYS60 4.6 0.3 1.0
CB Z:TYR62 4.7 0.2 1.0
CA Z:CYS42 4.7 0.9 1.0
CB Z:TYR59 4.8 0.3 1.0
CB Z:GLU44 4.8 0.3 1.0
N Z:GLU44 5.0 0.8 1.0

Cadmium binding site 4 out of 5 in 2qa4

Go back to Cadmium Binding Sites List in 2qa4
Cadmium binding site 4 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd94

b:0.0
occ:1.00
CB 3:CYS74 3.5 0.4 1.0
SG 3:CYS11 3.8 0.6 1.0
CB 3:CYS71 3.8 0.9 1.0
N 3:CYS14 3.9 0.6 1.0
CB 3:CYS14 3.9 0.9 1.0
CB 3:HIS13 3.9 0.9 1.0
CB 3:CYS11 4.1 0.7 1.0
SG 3:CYS71 4.3 0.3 1.0
CA 3:CYS14 4.5 0.1 1.0
SG 3:CYS74 4.6 1.0 1.0
N 3:CYS74 4.6 0.5 1.0
CA 3:CYS74 4.6 0.7 1.0
CG 3:HIS13 4.7 0.7 1.0
CB 3:LYS76 4.7 0.0 1.0
C 3:HIS13 4.7 0.1 1.0
CA 3:HIS13 4.8 0.8 1.0
CD2 3:HIS13 4.8 0.1 1.0
O 3:LYS76 4.8 0.4 1.0
N 3:LYS76 4.9 0.6 1.0

Cadmium binding site 5 out of 5 in 2qa4

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Cadmium binding site 5 out of 5 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd116

b:0.0
occ:1.00
ND1 O:HIS40 3.0 45.2 1.0
CG O:HIS40 3.9 46.8 1.0
CB O:HIS40 3.9 49.3 1.0
CE1 O:HIS40 4.0 44.6 1.0
CG O:ARG37 4.3 61.7 1.0
NE O:ARG37 4.5 65.6 1.0
CB O:ARG37 4.8 60.1 1.0
CZ O:ARG37 4.8 66.9 1.0
O O:ARG37 4.8 59.5 1.0
CD O:ARG37 4.9 64.4 1.0

Reference:

J.M.Kavran, T.A.Steitz. Structure of the Base of the L7/L12 Stalk of the Haloarcula Marismortui Large Ribosomal Subunit: Analysis of L11 Movements J.Mol.Biol. V. 371 1047 2007.
ISSN: ISSN 0022-2836
PubMed: 17599351
DOI: 10.1016/J.JMB.2007.05.091
Page generated: Fri Jul 19 15:08:36 2024

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