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Tantalum in PDB 1dd4: Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim

Protein crystallography data

The structure of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim, PDB code: 1dd4 was solved by M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 144.744, 144.744, 144.744, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 24.1

Other elements in 1dd4:

The structure of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim also contains other interesting chemical elements:

Bromine (Br) 24 atoms

Tantalum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Tantalum atom in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim (pdb code 1dd4). This binding sites where shown within 5.0 Angstroms radius around Tantalum atom.
In total 12 binding sites of Tantalum where determined in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim, PDB code: 1dd4:
Jump to Tantalum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tantalum binding site 1 out of 12 in 1dd4

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Tantalum binding site 1 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 1 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta401

b:81.6
occ:0.20
TA1 A:TBR401 0.0 81.6 0.2
BR3 A:TBR401 2.6 81.6 0.2
BR2 A:TBR401 2.6 81.3 0.2
BR4 A:TBR401 2.6 81.2 0.2
BR1 A:TBR401 2.6 81.8 0.2
TA5 A:TBR401 2.9 81.6 0.2
TA2 A:TBR401 2.9 81.8 0.2
TA6 A:TBR401 2.9 81.8 0.2
TA3 A:TBR401 2.9 81.6 0.2
OE2 A:GLU55 3.1 71.5 1.0
CD A:GLU55 3.9 70.3 1.0
OE1 A:GLU55 4.1 70.3 1.0
TA4 A:TBR401 4.1 81.6 0.2
BRB A:TBR401 4.2 80.6 0.2
BR6 A:TBR401 4.2 81.4 0.2
BR5 A:TBR401 4.2 80.6 0.2
BRC A:TBR401 4.2 81.3 0.2

Tantalum binding site 2 out of 12 in 1dd4

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Tantalum binding site 2 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 2 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta401

b:81.8
occ:0.20
TA2 A:TBR401 0.0 81.8 0.2
BRC A:TBR401 2.6 81.3 0.2
BR5 A:TBR401 2.6 80.6 0.2
BR9 A:TBR401 2.6 82.4 0.2
BR1 A:TBR401 2.6 81.8 0.2
TA4 A:TBR401 2.9 81.6 0.2
TA1 A:TBR401 2.9 81.6 0.2
TA6 A:TBR401 2.9 81.8 0.2
TA3 A:TBR401 3.0 81.6 0.2
TA5 A:TBR401 4.1 81.6 0.2
BRA A:TBR401 4.2 81.4 0.2
BR4 A:TBR401 4.2 81.2 0.2
BR2 A:TBR401 4.2 81.3 0.2
BR8 A:TBR401 4.2 80.4 0.2
O B:HOH187 4.4 67.5 1.0

Tantalum binding site 3 out of 12 in 1dd4

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Tantalum binding site 3 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 3 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta401

b:81.6
occ:0.20
TA3 A:TBR401 0.0 81.6 0.2
BRA A:TBR401 2.6 81.4 0.2
BR6 A:TBR401 2.6 81.4 0.2
BR5 A:TBR401 2.6 80.6 0.2
BR2 A:TBR401 2.6 81.3 0.2
TA5 A:TBR401 2.9 81.6 0.2
TA4 A:TBR401 2.9 81.6 0.2
TA1 A:TBR401 2.9 81.6 0.2
TA2 A:TBR401 3.0 81.8 0.2
BR3 A:TBR401 4.2 81.6 0.2
BR1 A:TBR401 4.2 81.8 0.2
BR9 A:TBR401 4.2 82.4 0.2
TA6 A:TBR401 4.2 81.8 0.2
BR7 A:TBR401 4.2 81.0 0.2
O A:HOH450 4.9 55.3 1.0

Tantalum binding site 4 out of 12 in 1dd4

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Tantalum binding site 4 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 4 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta401

b:81.6
occ:0.20
TA4 A:TBR401 0.0 81.6 0.2
BR9 A:TBR401 2.6 82.4 0.2
BR8 A:TBR401 2.6 80.4 0.2
BRA A:TBR401 2.6 81.4 0.2
BR7 A:TBR401 2.6 81.0 0.2
TA5 A:TBR401 2.9 81.6 0.2
TA2 A:TBR401 2.9 81.8 0.2
TA6 A:TBR401 2.9 81.8 0.2
TA3 A:TBR401 2.9 81.6 0.2
O A:LYS12 4.1 45.4 1.0
TA1 A:TBR401 4.1 81.6 0.2
BRC A:TBR401 4.2 81.3 0.2
BR5 A:TBR401 4.2 80.6 0.2
BRB A:TBR401 4.2 80.6 0.2
BR6 A:TBR401 4.2 81.4 0.2
NZ B:LYS103 4.6 53.2 1.0
CE B:LYS103 4.6 52.5 1.0

Tantalum binding site 5 out of 12 in 1dd4

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Tantalum binding site 5 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 5 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta401

b:81.6
occ:0.20
TA5 A:TBR401 0.0 81.6 0.2
BR6 A:TBR401 2.6 81.4 0.2
BRB A:TBR401 2.6 80.6 0.2
BR3 A:TBR401 2.6 81.6 0.2
BR7 A:TBR401 2.6 81.0 0.2
TA1 A:TBR401 2.9 81.6 0.2
TA4 A:TBR401 2.9 81.6 0.2
TA3 A:TBR401 2.9 81.6 0.2
TA6 A:TBR401 3.0 81.8 0.2
TA2 A:TBR401 4.1 81.8 0.2
BR4 A:TBR401 4.2 81.2 0.2
BRA A:TBR401 4.2 81.4 0.2
BR8 A:TBR401 4.2 80.4 0.2
BR2 A:TBR401 4.2 81.3 0.2
CB A:ALA51 4.9 54.5 1.0

Tantalum binding site 6 out of 12 in 1dd4

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Tantalum binding site 6 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 6 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta401

b:81.8
occ:0.20
TA6 A:TBR401 0.0 81.8 0.2
BR4 A:TBR401 2.6 81.2 0.2
BRC A:TBR401 2.6 81.3 0.2
BRB A:TBR401 2.6 80.6 0.2
BR8 A:TBR401 2.6 80.4 0.2
TA2 A:TBR401 2.9 81.8 0.2
TA4 A:TBR401 2.9 81.6 0.2
TA1 A:TBR401 2.9 81.6 0.2
TA5 A:TBR401 3.0 81.6 0.2
OE1 B:GLU110 4.1 94.6 1.0
BR9 A:TBR401 4.2 82.4 0.2
BR7 A:TBR401 4.2 81.0 0.2
BR3 A:TBR401 4.2 81.6 0.2
TA3 A:TBR401 4.2 81.6 0.2
BR1 A:TBR401 4.2 81.8 0.2
CG B:GLU110 4.6 91.8 1.0
CD B:GLU110 4.7 93.4 1.0

Tantalum binding site 7 out of 12 in 1dd4

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Tantalum binding site 7 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 7 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta402

b:68.0
occ:0.20
TA1 A:TBR402 0.0 68.0 0.2
BR3 A:TBR402 2.6 67.7 0.2
BR2 A:TBR402 2.6 67.8 0.2
BR1 A:TBR402 2.6 67.2 0.2
BR4 A:TBR402 2.6 68.0 0.2
TA5 A:TBR402 2.9 68.4 0.2
TA2 A:TBR402 2.9 67.5 0.2
TA6 A:TBR402 2.9 68.1 0.2
TA3 A:TBR402 2.9 68.7 0.2
OE2 A:GLU110 3.6 69.2 1.0
CD A:GLU110 3.7 67.2 1.0
OE1 A:GLU110 3.8 67.9 1.0
TA4 A:TBR402 4.1 68.2 0.2
BR6 A:TBR402 4.1 70.4 0.2
BRC A:TBR402 4.2 68.2 0.2
BRB A:TBR402 4.2 66.7 0.2
BR5 A:TBR402 4.2 68.5 0.2
CG A:GLU110 4.4 64.2 1.0

Tantalum binding site 8 out of 12 in 1dd4

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Tantalum binding site 8 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 8 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta402

b:67.5
occ:0.20
TA2 A:TBR402 0.0 67.5 0.2
BRC A:TBR402 2.6 68.2 0.2
BR5 A:TBR402 2.6 68.5 0.2
BR9 A:TBR402 2.6 65.1 0.2
BR1 A:TBR402 2.6 67.2 0.2
TA4 A:TBR402 2.9 68.2 0.2
TA1 A:TBR402 2.9 68.0 0.2
TA3 A:TBR402 2.9 68.7 0.2
TA6 A:TBR402 2.9 68.1 0.2
TA5 A:TBR402 4.1 68.4 0.2
BRA A:TBR402 4.2 68.8 0.2
O B:HOH152 4.2 44.9 1.0
BR2 A:TBR402 4.2 67.8 0.2
BR4 A:TBR402 4.2 68.0 0.2
BR8 A:TBR402 4.2 68.2 0.2

Tantalum binding site 9 out of 12 in 1dd4

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Tantalum binding site 9 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 9 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta402

b:68.7
occ:0.20
TA3 A:TBR402 0.0 68.7 0.2
BRA A:TBR402 2.6 68.8 0.2
BR6 A:TBR402 2.6 70.4 0.2
BR5 A:TBR402 2.6 68.5 0.2
BR2 A:TBR402 2.6 67.8 0.2
TA2 A:TBR402 2.9 67.5 0.2
TA4 A:TBR402 2.9 68.2 0.2
TA1 A:TBR402 2.9 68.0 0.2
TA5 A:TBR402 2.9 68.4 0.2
BR1 A:TBR402 4.2 67.2 0.2
BR3 A:TBR402 4.2 67.7 0.2
BR9 A:TBR402 4.2 65.1 0.2
O B:LYS12 4.2 36.9 1.0
TA6 A:TBR402 4.2 68.1 0.2
BR7 A:TBR402 4.2 67.3 0.2
CE A:LYS103 4.9 44.0 1.0
C B:LYS12 4.9 36.4 1.0
NZ A:LYS103 5.0 44.1 1.0

Tantalum binding site 10 out of 12 in 1dd4

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Tantalum binding site 10 out of 12 in the Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim


Mono view


Stereo pair view

A full contact list of Tantalum with other atoms in the Ta binding site number 10 of Crystal Structure of Ribosomal Protein L12 From Thermotoga Maritim within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta402

b:68.2
occ:0.20
TA4 A:TBR402 0.0 68.2 0.2
BR9 A:TBR402 2.6 65.1 0.2
BR8 A:TBR402 2.6 68.2 0.2
BR7 A:TBR402 2.6 67.3 0.2
BRA A:TBR402 2.6 68.8 0.2
TA2 A:TBR402 2.9 67.5 0.2
TA5 A:TBR402 2.9 68.4 0.2
TA3 A:TBR402 2.9 68.7 0.2
TA6 A:TBR402 2.9 68.1 0.2
TA1 A:TBR402 4.1 68.0 0.2
BRC A:TBR402 4.1 68.2 0.2
BR6 A:TBR402 4.2 70.4 0.2
BR5 A:TBR402 4.2 68.5 0.2
BRB A:TBR402 4.2 66.7 0.2

Reference:

M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, R.Huber. Flexibility, Conformational Diversity and Two Dimerization Modes in Complexes of Ribosomal Protein L12. Embo J. V. 19 174 2000.
ISSN: ISSN 0261-4189
PubMed: 10637222
DOI: 10.1093/EMBOJ/19.2.174
Page generated: Wed Dec 16 02:26:06 2020

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