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Cadmium in PDB 1kqs: The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis

Protein crystallography data

The structure of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis, PDB code: 1kqs was solved by T.M.Schmeing, A.C.Seila, J.L.Hansen, B.Freeborn, J.K.Soukup, S.A.Scaringe, S.A.Strobel, 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) 20.00 / 3.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.784, 300.349, 574.961, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22

Other elements in 1kqs:

The structure of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis 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 The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis (pdb code 1kqs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis, PDB code: 1kqs:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1kqs

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Cadmium binding site 1 out of 5 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cd8405

b:0.5
occ:1.00
 ND1 N:HIS40 2.4 28.6 1.0
O 0:HOH5515 2.9 32.2 1.0
O N:HOH5650 3.0 37.8 1.0
CG N:HIS40 3.4 28.9 1.0
CE1 N:HIS40 3.4 28.6 1.0
CB N:HIS40 3.6 30.5 1.0
CG N:ARG37 4.4 44.4 1.0
NE2 N:HIS40 4.5 28.8 1.0
CD2 N:HIS40 4.5 29.2 1.0
CB N:ARG37 4.7 42.0 1.0
O N:HOH3002 4.7 24.8 1.0
CA N:ARG37 4.7 40.7 1.0
O N:ARG37 4.8 40.3 1.0
CZ N:ARG37 4.8 45.9 1.0
NH1 N:ARG37 4.8 45.4 1.0
NE N:ARG37 5.0 44.3 1.0

Cadmium binding site 2 out of 5 in 1kqs

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Cadmium binding site 2 out of 5 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Cd8401

b:0.0
occ:1.00
 SG T:CYS6 2.5 0.7 1.0
SG T:CYS36 2.8 0.7 1.0
N T:CYS9 3.1 0.9 1.0
CB T:CYS9 3.2 0.5 1.0
CB T:CYS36 3.3 0.6 1.0
CB T:CYS6 3.4 0.7 1.0
SG T:CYS32 3.5 0.6 1.0
CB T:TYR8 3.7 0.6 1.0
CA T:CYS9 3.7 0.6 1.0
SG T:CYS9 3.7 0.3 1.0
C T:TYR8 4.2 0.9 1.0
N T:CYS32 4.2 0.0 1.0
CB T:CYS32 4.3 0.9 1.0
CD2 T:TYR8 4.3 0.5 1.0
CA T:TYR8 4.3 1.0 1.0
N T:GLY10 4.4 0.6 1.0
CG T:TYR8 4.5 0.1 1.0
N T:TYR8 4.5 0.1 1.0
C T:CYS9 4.6 0.6 1.0
CA T:CYS6 4.8 0.2 1.0
CA T:CYS32 4.8 0.1 1.0
CA T:CYS36 4.8 0.4 1.0
OG1 T:THR11 4.9 0.9 1.0
C T:CYS6 5.0 0.4 1.0

Cadmium binding site 3 out of 5 in 1kqs

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Cadmium binding site 3 out of 5 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Cd8403

b:0.0
occ:1.00
 CB Y:CYS42 3.1 0.7 1.0
SG Y:CYS57 3.2 0.9 1.0
CB Y:CYS60 3.2 0.6 1.0
SG Y:CYS60 3.2 0.9 1.0
SG Y:CYS39 3.3 0.9 1.0
SG Y:CYS42 3.5 0.1 1.0
N Y:CYS42 3.8 0.9 1.0
N Y:CYS60 3.8 0.3 1.0
CB Y:CYS57 3.8 0.9 1.0
CB Y:CYS39 3.9 0.5 1.0
CA Y:CYS42 4.0 0.6 1.0
CA Y:CYS60 4.1 0.5 1.0
CD2 Y:HIS59 4.2 0.7 1.0
CB Y:HIS59 4.4 0.6 1.0
CB Y:VAL41 4.6 0.1 1.0
CG1 Y:VAL41 4.6 0.8 1.0
CG Y:HIS59 4.7 0.5 1.0
C Y:CYS42 4.8 0.4 1.0
C Y:HIS59 4.8 0.1 1.0
CB Y:TYR62 4.8 0.6 1.0
C Y:CYS60 4.9 0.1 1.0
C Y:VAL41 4.9 0.8 1.0

Cadmium binding site 4 out of 5 in 1kqs

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Cadmium binding site 4 out of 5 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd8402

b:49.5
occ:1.00
 SG Z:CYS37 2.3 31.4 1.0
SG Z:CYS22 2.4 28.4 1.0
SG Z:CYS34 2.4 28.8 1.0
SG Z:CYS19 2.5 27.8 1.0
CB Z:CYS19 3.1 24.8 1.0
CB Z:CYS22 3.2 27.2 1.0
CB Z:CYS34 3.2 25.1 1.0
CB Z:CYS37 3.3 26.2 1.0
N Z:CYS22 3.5 27.5 1.0
N Z:CYS37 3.8 25.1 1.0
CA Z:CYS22 3.9 27.3 1.0
CA Z:CYS37 4.1 25.5 1.0
CB Z:PHE39 4.4 31.0 1.0
CB Z:ARG21 4.6 26.2 1.0
C Z:ARG21 4.6 27.1 1.0
CA Z:CYS19 4.6 26.3 1.0
O Z:HOH8421 4.6 28.7 1.0
CA Z:CYS34 4.7 25.2 1.0
C Z:CYS22 4.7 26.4 1.0
C Z:CYS37 4.7 24.5 1.0
CB Z:SER36 4.8 25.7 1.0
N Z:GLY23 4.8 25.9 1.0
CD Z:ARG21 4.9 27.8 1.0
N Z:PHE39 4.9 29.1 1.0
C Z:SER36 4.9 24.7 1.0
CA Z:ARG21 4.9 26.6 1.0
N Z:GLY38 4.9 24.5 1.0
N Z:ARG21 4.9 26.8 1.0

Cadmium binding site 5 out of 5 in 1kqs

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Cadmium binding site 5 out of 5 in the The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The Haloarcula Marismortui 50S Complexed with A Pretranslocational Intermediate in Protein Synthesis within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Cd8404

b:0.0
occ:1.00
 SG 2:CYS11 2.6 0.6 1.0
CB 2:CYS14 2.8 0.4 1.0
SG 2:CYS71 3.1 0.8 1.0
N 2:CYS14 3.1 0.1 1.0
CB 2:CYS11 3.3 0.2 1.0
SG 2:CYS74 3.4 0.2 1.0
CA 2:CYS14 3.5 0.6 1.0
CB 2:CYS71 3.6 0.3 1.0
CB 2:CYS74 3.8 0.9 1.0
O 2:HOH8567 3.8 89.4 1.0
SG 2:CYS14 3.9 0.6 1.0
CB 2:HIS13 4.1 0.3 1.0
C 2:HIS13 4.3 0.6 1.0
CA 2:HIS13 4.6 0.4 1.0
CA 2:CYS11 4.6 0.1 1.0
N 2:HIS13 4.7 0.4 1.0
O 2:CYS11 4.7 0.3 1.0
C 2:CYS14 4.7 0.0 1.0
C 2:CYS11 4.8 0.8 1.0
N 2:CYS74 4.8 0.4 1.0
OE1 2:GLN18 4.9 0.3 1.0
CA 2:CYS74 4.9 0.0 1.0
NE2 2:GLN18 5.0 0.1 1.0
N 2:ASN15 5.0 0.3 1.0

Reference:

T.M.Schmeing, A.C.Seila, J.L.Hansen, B.Freeborn, J.K.Soukup, S.A.Scaringe, S.A.Strobel, P.B.Moore, T.A.Steitz. A Pre-Translocational Intermediate in Protein Synthesis Observed in Crystals of Enzymatically Active 50S Subunits. Nat.Struct.Biol. V. 9 225 2002.
ISSN: ISSN 1072-8368
PubMed: 11828326
Page generated: Fri Jul 19 13:44:26 2024

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