Atomistry » Cadmium » PDB 1gyn-1jre » 1jj2
Atomistry »
  Cadmium »
    PDB 1gyn-1jre »
      1jj2 »

Cadmium in PDB 1jj2: Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

Protein crystallography data

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2 was solved by D.J.Klein, 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) 15.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.660, 299.670, 573.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.2

Other elements in 1jj2:

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 117 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 86 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution (pdb code 1jj2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1jj2

Go back to Cadmium Binding Sites List in 1jj2
Cadmium binding site 1 out of 5 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cd8405

b:72.0
occ:1.00
 ND1 N:HIS40 2.6 25.6 1.0
O N:HOH5650 2.7 34.4 1.0
O 0:HOH5558 2.9 29.2 1.0
CE1 N:HIS40 3.5 29.7 1.0
CG N:HIS40 3.5 27.0 1.0
CB N:HIS40 3.8 28.4 1.0
CG N:ARG37 4.3 38.3 1.0
NE2 N:HIS40 4.6 32.1 1.0
CD2 N:HIS40 4.6 29.5 1.0
O 0:HOH3869 4.7 41.4 1.0
NH1 N:ARG37 4.8 39.8 1.0
CZ N:ARG37 4.8 40.1 1.0
NE N:ARG37 4.9 39.5 1.0
CB N:ARG37 4.9 35.5 1.0
CA N:ARG37 5.0 33.9 1.0
O N:ARG37 5.0 35.2 1.0

Cadmium binding site 2 out of 5 in 1jj2

Go back to Cadmium Binding Sites List in 1jj2
Cadmium binding site 2 out of 5 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd8401

b:49.6
occ:1.00
 SG T:CYS36 2.5 46.1 1.0
SG T:CYS32 2.5 29.1 1.0
SG T:CYS6 2.6 47.6 1.0
SG T:CYS9 2.7 43.3 1.0
CB T:CYS6 3.3 47.8 1.0
CB T:CYS9 3.4 44.4 1.0
CB T:CYS36 3.5 44.9 1.0
CB T:CYS32 3.7 33.8 1.0
N T:CYS9 3.8 46.7 1.0
N T:CYS32 4.1 35.2 1.0
CA T:CYS9 4.2 45.9 1.0
OG T:SER33 4.4 37.3 1.0
CA T:CYS32 4.4 36.4 1.0
OG1 T:THR11 4.5 51.6 1.0
CB T:TYR8 4.6 44.7 1.0
N T:SER33 4.7 39.3 1.0
CA T:CYS6 4.8 49.5 1.0
N T:GLY10 4.8 47.2 1.0
CA T:CYS36 4.9 44.2 1.0
C T:CYS9 4.9 46.7 1.0
C T:TYR8 4.9 47.1 1.0
C T:CYS32 5.0 38.3 1.0

Cadmium binding site 3 out of 5 in 1jj2

Go back to Cadmium Binding Sites List in 1jj2
Cadmium binding site 3 out of 5 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cd8403

b:50.0
occ:1.00
 SG Y:CYS60 2.4 48.4 1.0
SG Y:CYS57 2.5 44.3 1.0
SG Y:CYS39 2.5 53.2 1.0
SG Y:CYS42 2.8 60.7 1.0
CB Y:CYS57 3.2 46.4 1.0
CB Y:CYS39 3.3 55.0 1.0
CB Y:CYS42 3.6 57.9 1.0
CB Y:CYS60 3.6 48.6 1.0
N Y:CYS42 3.8 58.4 1.0
N Y:CYS60 4.0 51.1 1.0
CA Y:CYS42 4.3 58.0 1.0
CA Y:CYS60 4.4 49.8 1.0
CB Y:HIS59 4.6 53.8 1.0
CB Y:TYR62 4.7 45.8 1.0
CB Y:VAL41 4.7 58.7 1.0
CD2 Y:HIS59 4.7 55.8 1.0
CA Y:CYS57 4.7 46.3 1.0
CA Y:CYS39 4.8 55.9 1.0
C Y:CYS42 4.8 57.6 1.0
CG1 Y:VAL41 4.8 60.0 1.0
C Y:VAL41 5.0 58.6 1.0

Cadmium binding site 4 out of 5 in 1jj2

Go back to Cadmium Binding Sites List in 1jj2
Cadmium binding site 4 out of 5 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8402

b:37.9
occ:1.00
 SG Z:CYS37 2.4 24.7 1.0
SG Z:CYS22 2.5 23.3 1.0
SG Z:CYS34 2.5 23.0 1.0
SG Z:CYS19 2.5 21.7 1.0
CB Z:CYS19 3.1 20.5 1.0
CB Z:CYS34 3.2 20.0 1.0
CB Z:CYS37 3.2 23.4 1.0
CB Z:CYS22 3.3 22.9 1.0
N Z:CYS22 3.7 27.0 1.0
N Z:CYS37 3.8 24.4 1.0
CA Z:CYS37 4.0 22.5 1.0
CA Z:CYS22 4.1 23.6 1.0
CB Z:PHE39 4.3 24.1 1.0
CA Z:CYS19 4.6 22.7 1.0
CA Z:CYS34 4.6 20.7 1.0
CB Z:ARG21 4.7 28.6 1.0
C Z:ARG21 4.7 27.0 1.0
C Z:CYS37 4.7 23.7 1.0
CB Z:SER36 4.8 24.0 1.0
O Z:HOH8418 4.8 24.6 1.0
C Z:CYS22 4.9 23.9 1.0
N Z:PHE39 4.9 22.7 1.0
C Z:SER36 4.9 25.5 1.0
N Z:GLY38 4.9 23.1 1.0
N Z:GLY23 4.9 24.8 1.0

Cadmium binding site 5 out of 5 in 1jj2

Go back to Cadmium Binding Sites List in 1jj2
Cadmium binding site 5 out of 5 in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8404

b:47.8
occ:1.00
 SG 2:CYS71 2.4 49.7 1.0
SG 2:CYS11 2.5 42.0 1.0
SG 2:CYS74 2.6 53.7 1.0
SG 2:CYS14 2.9 56.3 1.0
CB 2:CYS14 3.0 53.6 1.0
CB 2:CYS71 3.2 50.4 1.0
O 2:HOH8560 3.2 96.3 1.0
CB 2:CYS74 3.3 51.8 1.0
CB 2:CYS11 3.6 43.0 1.0
N 2:CYS14 3.7 52.9 1.0
CA 2:CYS14 3.9 54.0 1.0
N 2:CYS74 4.1 52.9 1.0
CA 2:CYS74 4.3 51.6 1.0
CB 2:HIS13 4.6 49.8 1.0
CA 2:CYS71 4.6 49.9 1.0
OE1 2:GLN18 4.7 60.8 1.0
C 2:HIS13 4.8 51.1 1.0
CA 2:CYS11 5.0 43.7 1.0

Reference:

D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz. The Kink-Turn: A New Rna Secondary Structure Motif. Embo J. V. 20 4214 2001.
ISSN: ISSN 0261-4189
PubMed: 11483524
DOI: 10.1093/EMBOJ/20.15.4214
Page generated: Sat Dec 12 08:10:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy