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Tungsten in PDB 1dv4: Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus

Protein crystallography data

The structure of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus, PDB code: 1dv4 was solved by A.Tocilj, F.Schlunzen, D.Janell, M.Gluhmann, H.Hansen, J.Harms, A.Bashan, H.Bartels, I.Agmon, F.Franceschi, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 4.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 407.100, 407.100, 176.008, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Tungsten Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Tungsten atom in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus (pdb code 1dv4). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 18 binding sites of Tungsten where determined in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus, PDB code: 1dv4:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tungsten binding site 1 out of 18 in 1dv4

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Tungsten binding site 1 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W1 E:WO21 0.0 0.0 1.0
O21 E:WO21 1.7 0.0 1.0
O14 E:WO21 1.9 0.0 1.0
O7 E:WO21 1.9 0.0 1.0
O52 E:WO21 1.9 0.0 1.0
O5 E:WO21 2.0 0.0 1.0
OP3 E:WO21 2.3 0.0 1.0
W9 E:WO21 3.4 0.0 1.0
P1 E:WO21 3.5 0.0 1.0
O53 E:WO21 3.5 0.0 1.0
W5 E:WO21 3.7 0.0 1.0
O6 E:WO21 3.7 0.0 1.0
W17 E:WO21 3.7 0.0 1.0
O12 E:WO21 3.7 0.0 1.0
W2 E:WO21 3.8 0.0 1.0
OP4 E:WO21 3.8 0.0 1.0
OP1 E:WO21 3.8 0.0 1.0
O28 E:WO21 3.9 0.0 1.0
OP7 E:WO21 4.1 0.0 1.0
O18 E:WO21 4.4 0.0 1.0
O44 E:WO21 4.4 0.0 1.0
O4 E:WO21 4.4 0.0 1.0
O27 E:WO21 4.5 0.0 1.0
O37 E:WO21 4.5 0.0 1.0
O22 E:WO21 4.5 0.0 1.0
O20 E:WO21 4.7 0.0 1.0
O9 E:WO21 4.7 0.0 1.0
OP2 E:WO21 4.9 0.0 1.0
W18 E:WO21 4.9 0.0 1.0

Tungsten binding site 2 out of 18 in 1dv4

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Tungsten binding site 2 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W2 E:WO21 0.0 0.0 1.0
O44 E:WO21 1.6 0.0 1.0
O5 E:WO21 1.9 0.0 1.0
O28 E:WO21 1.9 0.0 1.0
O37 E:WO21 1.9 0.0 1.0
O31 E:WO21 2.0 0.0 1.0
OP7 E:WO21 2.4 0.0 1.0
W10 E:WO21 3.4 0.0 1.0
P2 E:WO21 3.5 0.0 1.0
O32 E:WO21 3.7 0.0 1.0
W6 E:WO21 3.7 0.0 1.0
W14 E:WO21 3.7 0.0 1.0
O6 E:WO21 3.7 0.0 1.0
W1 E:WO21 3.8 0.0 1.0
OP5 E:WO21 3.8 0.0 1.0
O7 E:WO21 3.8 0.0 1.0
O35 E:WO21 3.8 0.0 1.0
OP8 E:WO21 3.9 0.0 1.0
CA E:ARG49 3.9 67.5 1.0
OP3 E:WO21 4.1 0.0 1.0
O21 E:WO21 4.4 0.0 1.0
O4 E:WO21 4.4 0.0 1.0
O14 E:WO21 4.4 0.0 1.0
O41 E:WO21 4.4 0.0 1.0
O45 E:WO21 4.5 0.0 1.0
O50 E:WO21 4.6 0.0 1.0
O43 E:WO21 4.6 0.0 1.0
CA E:GLY48 4.7 63.1 1.0
O30 E:WO21 4.8 0.0 1.0
OP6 E:WO21 4.9 0.0 1.0

Tungsten binding site 3 out of 18 in 1dv4

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Tungsten binding site 3 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W3 E:WO21 0.0 0.0 1.0
O24 E:WO21 1.7 0.0 1.0
O15 E:WO21 1.9 0.0 1.0
O2 E:WO21 1.9 0.0 1.0
O8 E:WO21 2.0 0.0 1.0
O11 E:WO21 2.0 0.0 1.0
OP2 E:WO21 2.3 0.0 1.0
W7 E:WO21 3.3 0.0 1.0
O10 E:WO21 3.5 0.0 1.0
P1 E:WO21 3.5 0.0 1.0
W11 E:WO21 3.7 0.0 1.0
W16 E:WO21 3.7 0.0 1.0
O1 E:WO21 3.7 0.0 1.0
W4 E:WO21 3.8 0.0 1.0
O29 E:WO21 3.8 0.0 1.0
OP4 E:WO21 3.9 0.0 1.0
O13 E:WO21 3.9 0.0 1.0
OP1 E:WO21 3.9 0.0 1.0
OP6 E:WO21 4.0 0.0 1.0
O47 E:WO21 4.3 0.0 1.0
O3 E:WO21 4.4 0.0 1.0
O38 E:WO21 4.4 0.0 1.0
O19 E:WO21 4.5 0.0 1.0
O25 E:WO21 4.5 0.0 1.0
O23 E:WO21 4.6 0.0 1.0
O54 E:WO21 4.7 0.0 1.0
O9 E:WO21 4.8 0.0 1.0
OP3 E:WO21 4.9 0.0 1.0

Tungsten binding site 4 out of 18 in 1dv4

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Tungsten binding site 4 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W4 E:WO21 0.0 0.0 1.0
O47 E:WO21 1.7 0.0 1.0
O2 E:WO21 1.9 0.0 1.0
O38 E:WO21 1.9 0.0 1.0
O34 E:WO21 1.9 0.0 1.0
O29 E:WO21 2.0 0.0 1.0
OP6 E:WO21 2.3 0.0 1.0
W8 E:WO21 3.4 0.0 1.0
P2 E:WO21 3.5 0.0 1.0
O33 E:WO21 3.6 0.0 1.0
W12 E:WO21 3.7 0.0 1.0
W13 E:WO21 3.7 0.0 1.0
O1 E:WO21 3.7 0.0 1.0
O36 E:WO21 3.7 0.0 1.0
W3 E:WO21 3.8 0.0 1.0
O8 E:WO21 3.9 0.0 1.0
OP5 E:WO21 3.9 0.0 1.0
OP8 E:WO21 3.9 0.0 1.0
OP2 E:WO21 4.1 0.0 1.0
O42 E:WO21 4.3 0.0 1.0
O15 E:WO21 4.4 0.0 1.0
O3 E:WO21 4.4 0.0 1.0
O24 E:WO21 4.4 0.0 1.0
O51 E:WO21 4.6 0.0 1.0
O46 E:WO21 4.6 0.0 1.0
O30 E:WO21 4.7 0.0 1.0
O48 E:WO21 4.8 0.0 1.0
OP7 E:WO21 4.8 0.0 1.0
W15 E:WO21 4.9 0.0 1.0

Tungsten binding site 5 out of 18 in 1dv4

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Tungsten binding site 5 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W5 E:WO21 0.0 0.0 1.0
O22 E:WO21 1.7 0.0 1.0
O4 E:WO21 1.9 0.0 1.0
O53 E:WO21 1.9 0.0 1.0
O7 E:WO21 1.9 0.0 1.0
O16 E:WO21 2.0 0.0 1.0
OP1 E:WO21 2.3 0.0 1.0
W11 E:WO21 3.4 0.0 1.0
P1 E:WO21 3.5 0.0 1.0
O3 E:WO21 3.7 0.0 1.0
W1 E:WO21 3.7 0.0 1.0
O52 E:WO21 3.7 0.0 1.0
W17 E:WO21 3.7 0.0 1.0
W6 E:WO21 3.8 0.0 1.0
O28 E:WO21 3.8 0.0 1.0
O10 E:WO21 3.8 0.0 1.0
OP3 E:WO21 3.9 0.0 1.0
OP4 E:WO21 3.9 0.0 1.0
OP5 E:WO21 4.1 0.0 1.0
O45 E:WO21 4.4 0.0 1.0
O5 E:WO21 4.4 0.0 1.0
O39 E:WO21 4.5 0.0 1.0
O27 E:WO21 4.5 0.0 1.0
O17 E:WO21 4.6 0.0 1.0
O23 E:WO21 4.6 0.0 1.0
O21 E:WO21 4.6 0.0 1.0
O8 E:WO21 4.7 0.0 1.0
OP2 E:WO21 4.8 0.0 1.0
W12 E:WO21 5.0 0.0 1.0

Tungsten binding site 6 out of 18 in 1dv4

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Tungsten binding site 6 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W6 E:WO21 0.0 0.0 1.0
O45 E:WO21 1.7 0.0 1.0
O28 E:WO21 1.9 0.0 1.0
O39 E:WO21 1.9 0.0 1.0
O32 E:WO21 1.9 0.0 1.0
O4 E:WO21 2.0 0.0 1.0
OP5 E:WO21 2.3 0.0 1.0
W12 E:WO21 3.4 0.0 1.0
P2 E:WO21 3.5 0.0 1.0
O31 E:WO21 3.6 0.0 1.0
W2 E:WO21 3.7 0.0 1.0
O3 E:WO21 3.7 0.0 1.0
W14 E:WO21 3.7 0.0 1.0
W5 E:WO21 3.8 0.0 1.0
O33 E:WO21 3.8 0.0 1.0
OP7 E:WO21 3.8 0.0 1.0
OP8 E:WO21 3.9 0.0 1.0
O7 E:WO21 3.9 0.0 1.0
OP1 E:WO21 4.1 0.0 1.0
O40 E:WO21 4.3 0.0 1.0
O5 E:WO21 4.5 0.0 1.0
O22 E:WO21 4.5 0.0 1.0
O44 E:WO21 4.5 0.0 1.0
O16 E:WO21 4.6 0.0 1.0
O50 E:WO21 4.6 0.0 1.0
O46 E:WO21 4.6 0.0 1.0
OP6 E:WO21 4.8 0.0 1.0
O29 E:WO21 4.8 0.0 1.0
W13 E:WO21 4.9 0.0 1.0

Tungsten binding site 7 out of 18 in 1dv4

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Tungsten binding site 7 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W7 E:WO21 0.0 0.0 1.0
O25 E:WO21 1.8 0.0 1.0
O15 E:WO21 1.8 0.0 1.0
O1 E:WO21 1.9 0.0 1.0
O9 E:WO21 1.9 0.0 1.0
O13 E:WO21 2.0 0.0 1.0
OP2 E:WO21 2.4 0.0 1.0
W3 E:WO21 3.3 0.0 1.0
P1 E:WO21 3.5 0.0 1.0
W9 E:WO21 3.7 0.0 1.0
W18 E:WO21 3.7 0.0 1.0
O12 E:WO21 3.7 0.0 1.0
W8 E:WO21 3.8 0.0 1.0
O2 E:WO21 3.8 0.0 1.0
O11 E:WO21 3.8 0.0 1.0
OP4 E:WO21 3.9 0.0 1.0
OP3 E:WO21 3.9 0.0 1.0
O30 E:WO21 4.0 0.0 1.0
OP6 E:WO21 4.1 0.0 1.0
O38 E:WO21 4.4 0.0 1.0
O6 E:WO21 4.4 0.0 1.0
O19 E:WO21 4.5 0.0 1.0
O24 E:WO21 4.5 0.0 1.0
O20 E:WO21 4.6 0.0 1.0
O48 E:WO21 4.7 0.0 1.0
O26 E:WO21 4.8 0.0 1.0
O8 E:WO21 4.8 0.0 1.0
OP1 E:WO21 4.9 0.0 1.0
W16 E:WO21 5.0 0.0 1.0

Tungsten binding site 8 out of 18 in 1dv4

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Tungsten binding site 8 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 8 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W8 E:WO21 0.0 0.0 1.0
O30 E:WO21 1.8 0.0 1.0
O1 E:WO21 1.9 0.0 1.0
O38 E:WO21 1.9 0.0 1.0
O48 E:WO21 2.0 0.0 1.0
O36 E:WO21 2.0 0.0 1.0
OP6 E:WO21 2.5 0.0 1.0
W4 E:WO21 3.4 0.0 1.0
P2 E:WO21 3.6 0.0 1.0
W10 E:WO21 3.7 0.0 1.0
O35 E:WO21 3.7 0.0 1.0
W15 E:WO21 3.7 0.0 1.0
O2 E:WO21 3.7 0.0 1.0
W7 E:WO21 3.8 0.0 1.0
O9 E:WO21 3.9 0.0 1.0
O34 E:WO21 3.9 0.0 1.0
OP7 E:WO21 3.9 0.0 1.0
OP8 E:WO21 4.0 0.0 1.0
OP2 E:WO21 4.2 0.0 1.0
O6 E:WO21 4.4 0.0 1.0
O15 E:WO21 4.4 0.0 1.0
O42 E:WO21 4.4 0.0 1.0
O25 E:WO21 4.6 0.0 1.0
O49 E:WO21 4.6 0.0 1.0
O43 E:WO21 4.6 0.0 1.0
O47 E:WO21 4.6 0.0 1.0
O29 E:WO21 4.9 0.0 1.0
OP5 E:WO21 4.9 0.0 1.0

Tungsten binding site 9 out of 18 in 1dv4

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Tungsten binding site 9 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 9 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W9 E:WO21 0.0 0.0 1.0
O20 E:WO21 1.8 0.0 1.0
O9 E:WO21 1.8 0.0 1.0
O6 E:WO21 1.8 0.0 1.0
O14 E:WO21 2.0 0.0 1.0
O12 E:WO21 2.0 0.0 1.0
OP3 E:WO21 2.4 0.0 1.0
W1 E:WO21 3.4 0.0 1.0
P1 E:WO21 3.5 0.0 1.0
O13 E:WO21 3.6 0.0 1.0
W7 E:WO21 3.7 0.0 1.0
W18 E:WO21 3.7 0.0 1.0
O5 E:WO21 3.7 0.0 1.0
W10 E:WO21 3.7 0.0 1.0
O30 E:WO21 3.9 0.0 1.0
O52 E:WO21 3.9 0.0 1.0
OP4 E:WO21 3.9 0.0 1.0
OP2 E:WO21 3.9 0.0 1.0
OP7 E:WO21 4.1 0.0 1.0
O1 E:WO21 4.3 0.0 1.0
O18 E:WO21 4.4 0.0 1.0
O43 E:WO21 4.5 0.0 1.0
O37 E:WO21 4.5 0.0 1.0
O21 E:WO21 4.6 0.0 1.0
O26 E:WO21 4.7 0.0 1.0
CA E:GLU75 4.7 25.3 1.0
O25 E:WO21 4.8 0.0 1.0
O7 E:WO21 4.8 0.0 1.0
OP1 E:WO21 4.9 0.0 1.0

Tungsten binding site 10 out of 18 in 1dv4

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Tungsten binding site 10 out of 18 in the Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 10 of Partial Structure of 16S Rna of the Small Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W1

b:0.0
occ:1.00
W10 E:WO21 0.0 0.0 1.0
O43 E:WO21 1.7 0.0 1.0
O30 E:WO21 1.9 0.0 1.0
O35 E:WO21 1.9 0.0 1.0
O6 E:WO21 1.9 0.0 1.0
O37 E:WO21 2.0 0.0 1.0
OP7 E:WO21 2.4 0.0 1.0
W2 E:WO21 3.4 0.0 1.0
P2 E:WO21 3.5 0.0 1.0
O36 E:WO21 3.6 0.0 1.0
W8 E:WO21 3.7 0.0 1.0
W15 E:WO21 3.7 0.0 1.0
O5 E:WO21 3.7 0.0 1.0
W9 E:WO21 3.7 0.0 1.0
O31 E:WO21 3.8 0.0 1.0
OP8 E:WO21 3.9 0.0 1.0
OP6 E:WO21 3.9 0.0 1.0
O9 E:WO21 4.0 0.0 1.0
OP3 E:WO21 4.1 0.0 1.0
O41 E:WO21 4.4 0.0 1.0
O1 E:WO21 4.4 0.0 1.0
O20 E:WO21 4.4 0.0 1.0
O14 E:WO21 4.4 0.0 1.0
O44 E:WO21 4.6 0.0 1.0
O49 E:WO21 4.6 0.0 1.0
O48 E:WO21 4.7 0.0 1.0
O28 E:WO21 4.8 0.0 1.0
OP5 E:WO21 4.9 0.0 1.0
W14 E:WO21 5.0 0.0 1.0

Reference:

A.Tocilj, F.Schlunzen, D.Janell, M.Gluhmann, H.A.Hansen, J.Harms, A.Bashan, H.Bartels, I.Agmon, F.Franceschi, A.Yonath. The Small Ribosomal Subunit From Thermus Thermophilus at 4.5 A Resolution: Pattern Fittings and the Identification of A Functional Site. Proc.Natl.Acad.Sci.Usa V. 96 14252 1999.
ISSN: ISSN 0027-8424
PubMed: 10588692
DOI: 10.1073/PNAS.96.25.14252
Page generated: Wed Dec 16 02:33:00 2020

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