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Tantalum in PDB 2bvl: Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion, PDB code: 2bvl was solved by D.J.Reinert, T.Jank, K.Aktories, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.2
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.010, 95.797, 112.915, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.4

Other elements in 2bvl:

The structure of Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion also contains other interesting chemical elements:

Manganese (Mn) 1 atom
Bromine (Br) 48 atoms

Tantalum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Tantalum atom in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion (pdb code 2bvl). This binding sites where shown within 5.0 Angstroms radius around Tantalum atom.
In total 24 binding sites of Tantalum where determined in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion, PDB code: 2bvl:
Jump to Tantalum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tantalum binding site 1 out of 24 in 2bvl

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Tantalum binding site 1 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1548

b:45.5
occ:0.25
TA1 A:TBR1548 0.0 45.5 0.2
BR1 A:TBR1548 2.6 45.4 0.2
BR2 A:TBR1548 2.6 47.9 0.2
BR3 A:TBR1548 2.7 47.0 0.2
BR4 A:TBR1548 2.7 46.4 0.2
TA3 A:TBR1548 2.8 49.0 0.2
TA2 A:TBR1548 2.8 44.5 0.2
TA5 A:TBR1548 2.9 47.7 0.2
TA6 A:TBR1548 2.9 46.9 0.2
TA4 A:TBR1548 4.1 50.0 0.2
BRC A:TBR1548 4.1 48.6 0.2
BR6 A:TBR1548 4.2 46.3 0.2
BRB A:TBR1548 4.2 47.5 0.2
BR5 A:TBR1548 4.3 46.4 0.2

Tantalum binding site 2 out of 24 in 2bvl

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Tantalum binding site 2 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1548

b:47.7
occ:0.25
TA5 A:TBR1548 0.0 47.7 0.2
BR3 A:TBR1548 2.6 47.0 0.2
BR7 A:TBR1548 2.6 48.6 0.2
BRB A:TBR1548 2.7 47.5 0.2
BR6 A:TBR1548 2.7 46.3 0.2
TA6 A:TBR1548 2.9 46.9 0.2
TA4 A:TBR1548 2.9 50.0 0.2
TA1 A:TBR1548 2.9 45.5 0.2
TA2 A:TBR1548 2.9 44.5 0.2
TA3 A:TBR1548 4.0 49.0 0.2
BR8 A:TBR1548 4.1 48.3 0.2
BR4 A:TBR1548 4.2 46.4 0.2
BRA A:TBR1548 4.2 45.6 0.2
BR1 A:TBR1548 4.3 45.4 0.2
ND2 A:ASN36 4.7 47.1 1.0

Tantalum binding site 3 out of 24 in 2bvl

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Tantalum binding site 3 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1548

b:46.9
occ:0.25
TA6 A:TBR1548 0.0 46.9 0.2
BRC A:TBR1548 2.6 48.6 0.2
BR4 A:TBR1548 2.7 46.4 0.2
BR8 A:TBR1548 2.7 48.3 0.2
BRB A:TBR1548 2.7 47.5 0.2
TA5 A:TBR1548 2.9 47.7 0.2
TA1 A:TBR1548 2.9 45.5 0.2
TA3 A:TBR1548 2.9 49.0 0.2
TA4 A:TBR1548 2.9 50.0 0.2
TA2 A:TBR1548 4.1 44.5 0.2
BR7 A:TBR1548 4.2 48.6 0.2
BR3 A:TBR1548 4.2 47.0 0.2
BR9 A:TBR1548 4.2 49.2 0.2
BR2 A:TBR1548 4.3 47.9 0.2

Tantalum binding site 4 out of 24 in 2bvl

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Tantalum binding site 4 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1548

b:44.5
occ:0.25
TA2 A:TBR1548 0.0 44.5 0.2
BRA A:TBR1548 2.7 45.6 0.2
BR1 A:TBR1548 2.7 45.4 0.2
BR5 A:TBR1548 2.7 46.4 0.2
BR6 A:TBR1548 2.7 46.3 0.2
TA3 A:TBR1548 2.8 49.0 0.2
TA1 A:TBR1548 2.8 45.5 0.2
TA4 A:TBR1548 2.9 50.0 0.2
TA5 A:TBR1548 2.9 47.7 0.2
TA6 A:TBR1548 4.1 46.9 0.2
BR2 A:TBR1548 4.1 47.9 0.2
BR3 A:TBR1548 4.2 47.0 0.2
BR9 A:TBR1548 4.2 49.2 0.2
BR7 A:TBR1548 4.3 48.6 0.2
OE2 A:GLU33 4.3 45.0 1.0
CG A:GLU33 4.7 40.3 1.0

Tantalum binding site 5 out of 24 in 2bvl

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Tantalum binding site 5 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1548

b:49.0
occ:0.25
TA3 A:TBR1548 0.0 49.0 0.2
BR2 A:TBR1548 2.6 47.9 0.2
BR9 A:TBR1548 2.7 49.2 0.2
BR5 A:TBR1548 2.7 46.4 0.2
BRC A:TBR1548 2.7 48.6 0.2
TA2 A:TBR1548 2.8 44.5 0.2
TA1 A:TBR1548 2.8 45.5 0.2
TA4 A:TBR1548 2.9 50.0 0.2
TA6 A:TBR1548 2.9 46.9 0.2
TA5 A:TBR1548 4.0 47.7 0.2
BR1 A:TBR1548 4.1 45.4 0.2
BRA A:TBR1548 4.2 45.6 0.2
BR4 A:TBR1548 4.2 46.4 0.2
BR8 A:TBR1548 4.2 48.3 0.2

Tantalum binding site 6 out of 24 in 2bvl

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Tantalum binding site 6 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1548

b:50.0
occ:0.25
TA4 A:TBR1548 0.0 50.0 0.2
BR7 A:TBR1548 2.6 48.6 0.2
BR9 A:TBR1548 2.7 49.2 0.2
BRA A:TBR1548 2.7 45.6 0.2
BR8 A:TBR1548 2.7 48.3 0.2
TA2 A:TBR1548 2.9 44.5 0.2
TA5 A:TBR1548 2.9 47.7 0.2
TA3 A:TBR1548 2.9 49.0 0.2
TA6 A:TBR1548 2.9 46.9 0.2
TA1 A:TBR1548 4.1 45.5 0.2
BR5 A:TBR1548 4.1 46.4 0.2
BR6 A:TBR1548 4.2 46.3 0.2
BRC A:TBR1548 4.2 48.6 0.2
BRB A:TBR1548 4.3 47.5 0.2
OD1 A:ASP29 4.7 32.6 1.0
NH1 A:ARG6 4.7 38.5 1.0

Tantalum binding site 7 out of 24 in 2bvl

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Tantalum binding site 7 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1549

b:56.3
occ:0.15
TA1 A:TBR1549 0.0 56.3 0.1
BR3 A:TBR1549 2.6 55.2 0.1
BR2 A:TBR1549 2.6 55.1 0.1
BR4 A:TBR1549 2.7 55.5 0.1
BR1 A:TBR1549 2.7 55.7 0.1
TA3 A:TBR1549 2.8 54.8 0.1
TA5 A:TBR1549 2.8 54.6 0.1
TA2 A:TBR1549 2.8 57.3 0.1
TA6 A:TBR1549 2.8 54.4 0.1
OG A:SER379 3.4 49.7 1.0
TA4 A:TBR1549 4.0 55.2 0.1
BRC A:TBR1549 4.0 54.3 0.1
BR6 A:TBR1549 4.1 55.3 0.1
BR5 A:TBR1549 4.2 55.1 0.1
BRB A:TBR1549 4.3 54.4 0.1
CB A:SER379 4.8 48.5 1.0

Tantalum binding site 8 out of 24 in 2bvl

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Tantalum binding site 8 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1549

b:54.6
occ:0.15
TA5 A:TBR1549 0.0 54.6 0.1
BRB A:TBR1549 2.7 54.4 0.1
BR7 A:TBR1549 2.7 54.3 0.1
BR3 A:TBR1549 2.7 55.2 0.1
BR6 A:TBR1549 2.7 55.3 0.1
TA6 A:TBR1549 2.7 54.4 0.1
TA1 A:TBR1549 2.8 56.3 0.1
TA4 A:TBR1549 2.8 55.2 0.1
TA2 A:TBR1549 2.9 57.3 0.1
TA3 A:TBR1549 4.0 54.8 0.1
BR4 A:TBR1549 4.1 55.5 0.1
BR8 A:TBR1549 4.2 54.8 0.1
BRA A:TBR1549 4.2 55.1 0.1
BR1 A:TBR1549 4.3 55.7 0.1
CG A:LYS380 4.5 52.8 1.0
ND2 A:ASN378 4.7 44.6 1.0

Tantalum binding site 9 out of 24 in 2bvl

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Tantalum binding site 9 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1549

b:54.4
occ:0.15
TA6 A:TBR1549 0.0 54.4 0.1
BRC A:TBR1549 2.6 54.3 0.1
BR8 A:TBR1549 2.7 54.8 0.1
BR4 A:TBR1549 2.7 55.5 0.1
BRB A:TBR1549 2.7 54.4 0.1
TA5 A:TBR1549 2.7 54.6 0.1
TA1 A:TBR1549 2.8 56.3 0.1
TA4 A:TBR1549 2.9 55.2 0.1
TA3 A:TBR1549 2.9 54.8 0.1
BR3 A:TBR1549 4.1 55.2 0.1
TA2 A:TBR1549 4.1 57.3 0.1
BR7 A:TBR1549 4.1 54.3 0.1
OE2 A:GLU515 4.2 38.8 1.0
O A:HOH2227 4.2 34.5 1.0
BR9 A:TBR1549 4.3 54.4 0.1
BR2 A:TBR1549 4.3 55.1 0.1
ND2 A:ASN378 4.3 44.6 1.0
O A:HOH2084 4.4 31.1 1.0
O A:HOH2327 4.6 32.7 1.0

Tantalum binding site 10 out of 24 in 2bvl

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Tantalum binding site 10 out of 24 in the Crystal Structure of the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion


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 the Catalytic Domain of Toxin B From Clostridium Difficile in Complex with Udp, Glc and Manganese Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ta1549

b:57.3
occ:0.15
TA2 A:TBR1549 0.0 57.3 0.1
BR5 A:TBR1549 2.7 55.1 0.1
BR1 A:TBR1549 2.7 55.7 0.1
BR6 A:TBR1549 2.7 55.3 0.1
BRA A:TBR1549 2.7 55.1 0.1
TA3 A:TBR1549 2.8 54.8 0.1
TA1 A:TBR1549 2.8 56.3 0.1
TA4 A:TBR1549 2.9 55.2 0.1
TA5 A:TBR1549 2.9 54.6 0.1
TA6 A:TBR1549 4.1 54.4 0.1
BR9 A:TBR1549 4.1 54.4 0.1
BR2 A:TBR1549 4.2 55.1 0.1
BR7 A:TBR1549 4.2 54.3 0.1
BR3 A:TBR1549 4.2 55.2 0.1

Reference:

D.J.Reinert, T.Jank, K.Aktories, G.E.Schulz. Structural Basis For the Function of Clostridium Difficile Toxin B. J.Mol.Biol. V. 351 973 2005.
ISSN: ISSN 0022-2836
PubMed: 16054646
DOI: 10.1016/J.JMB.2005.06.071
Page generated: Wed Dec 16 02:26:07 2020

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