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Cadmium in PDB 1vqp: The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqp was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.610, 298.189, 574.980, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.7

Other elements in 1vqp:

The structure of The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium (Sr) 114 atoms
Magnesium (Mg) 94 atoms
Potassium (K) 3 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqp). 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 Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqp:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 1vqp

Go back to Cadmium Binding Sites List in 1vqp
Cadmium binding site 1 out of 5 in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cd9205

b:0.3
occ:1.00
O O:HOH5650 2.4 78.2 1.0
ND1 O:HIS40 2.9 32.8 1.0
CE1 O:HIS40 3.6 35.4 1.0
CG O:HIS40 3.9 34.8 1.0
CB O:HIS40 4.3 37.5 1.0
CD2 O:LEU7 4.6 53.7 1.0
CG1 O:VAL79 4.6 45.8 1.0
O O:HOH3002 4.7 64.0 1.0
CD1 O:LEU7 4.8 55.0 1.0
NE2 O:HIS40 4.8 35.6 1.0
CG O:ARG37 4.9 50.2 1.0

Cadmium binding site 2 out of 5 in 1vqp

Go back to Cadmium Binding Sites List in 1vqp
Cadmium binding site 2 out of 5 in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cd9201

b:58.4
occ:1.00
SG U:CYS36 2.5 48.6 1.0
SG U:CYS6 2.5 44.7 1.0
SG U:CYS9 2.5 51.3 1.0
SG U:CYS32 2.5 39.3 1.0
CB U:CYS6 3.2 47.2 1.0
CB U:CYS9 3.3 46.5 1.0
CB U:CYS36 3.5 47.3 1.0
CB U:CYS32 3.7 40.6 1.0
N U:CYS9 3.8 46.5 1.0
N U:CYS32 4.1 40.4 1.0
CA U:CYS9 4.1 48.4 1.0
CA U:CYS32 4.4 41.9 1.0
OG1 U:THR11 4.5 58.8 1.0
OG U:SER33 4.5 45.1 1.0
CB U:TYR8 4.7 45.5 1.0
CA U:CYS6 4.7 47.3 1.0
N U:SER33 4.8 44.8 1.0
N U:GLY10 4.9 50.3 1.0
C U:CYS9 4.9 49.2 1.0
C U:TYR8 4.9 47.3 1.0
CA U:CYS36 4.9 47.2 1.0
C U:CYS32 4.9 43.8 1.0

Cadmium binding site 3 out of 5 in 1vqp

Go back to Cadmium Binding Sites List in 1vqp
Cadmium binding site 3 out of 5 in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Cd9203

b:57.3
occ:1.00
SG Z:CYS60 2.4 47.1 1.0
SG Z:CYS39 2.5 59.8 1.0
SG Z:CYS57 2.5 61.3 1.0
SG Z:CYS42 2.6 75.0 1.0
CB Z:CYS39 2.9 61.3 1.0
CB Z:CYS57 3.3 57.9 1.0
CB Z:CYS42 3.6 71.7 1.0
CB Z:CYS60 3.6 54.8 1.0
N Z:CYS42 3.8 70.8 1.0
N Z:CYS60 4.0 58.2 1.0
CA Z:CYS42 4.3 71.5 1.0
CA Z:CYS39 4.4 63.0 1.0
CA Z:CYS60 4.4 55.7 1.0
CB Z:ASN41 4.5 69.5 1.0
CB Z:TYR59 4.5 62.2 1.0
CD2 Z:TYR59 4.5 67.2 1.0
CB Z:TYR62 4.7 51.6 1.0
CA Z:CYS57 4.8 56.5 1.0
N Z:GLY43 4.8 70.4 1.0
C Z:ASN41 4.9 70.3 1.0
C Z:CYS39 5.0 64.3 1.0

Cadmium binding site 4 out of 5 in 1vqp

Go back to Cadmium Binding Sites List in 1vqp
Cadmium binding site 4 out of 5 in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Cd9202

b:50.4
occ:1.00
SG 1:CYS22 2.4 30.8 1.0
SG 1:CYS37 2.4 31.9 1.0
SG 1:CYS34 2.5 32.9 1.0
SG 1:CYS19 2.5 28.8 1.0
CB 1:CYS19 3.0 29.6 1.0
CB 1:CYS34 3.2 29.7 1.0
CB 1:CYS37 3.2 26.3 1.0
CB 1:CYS22 3.3 33.4 1.0
N 1:CYS37 3.7 27.7 1.0
N 1:CYS22 3.7 35.4 1.0
CA 1:CYS37 4.0 28.3 1.0
CA 1:CYS22 4.1 33.2 1.0
CB 1:PHE39 4.4 30.4 1.0
CA 1:CYS19 4.5 31.9 1.0
CA 1:CYS34 4.6 31.5 1.0
C 1:CYS37 4.7 28.9 1.0
CB 1:ARG21 4.7 33.9 1.0
C 1:ARG21 4.8 34.5 1.0
C 1:SER36 4.8 31.3 1.0
C 1:CYS22 4.8 32.5 1.0
N 1:PHE39 4.8 30.7 1.0
CB 1:SER36 4.8 27.1 1.0
N 1:GLY38 4.8 29.9 1.0
O 1:HOH9476 4.8 40.2 1.0
N 1:GLY23 4.8 32.5 1.0

Cadmium binding site 5 out of 5 in 1vqp

Go back to Cadmium Binding Sites List in 1vqp
Cadmium binding site 5 out of 5 in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Cd9204

b:57.7
occ:1.00
SG 3:CYS71 2.3 58.6 1.0
SG 3:CYS11 2.4 50.8 1.0
SG 3:CYS74 2.5 59.5 1.0
SG 3:CYS14 2.5 63.6 1.0
CB 3:CYS71 3.1 61.2 1.0
CB 3:CYS14 3.3 59.3 1.0
CB 3:CYS74 3.4 61.0 1.0
CB 3:CYS11 3.5 50.9 1.0
N 3:CYS14 3.6 60.2 1.0
CA 3:CYS14 4.0 59.7 1.0
N 3:CYS74 4.0 62.7 1.0
OE1 3:GLN18 4.3 66.6 1.0
CA 3:CYS74 4.3 61.1 1.0
CB 3:HIS13 4.4 59.1 1.0
CA 3:CYS71 4.5 60.7 1.0
C 3:HIS13 4.6 60.1 1.0
O 3:HOH9492 4.7 0.1 1.0
CA 3:CYS11 4.9 52.1 1.0
CD 3:GLN18 4.9 62.5 1.0
CA 3:HIS13 4.9 59.0 1.0

Reference:

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006
Page generated: Sat Dec 12 08:15:17 2020

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