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Thallium in PDB 3e76: Crystal Structure of Wild-Type Groel with Bound Thallium Ions

Enzymatic activity of Crystal Structure of Wild-Type Groel with Bound Thallium Ions

All present enzymatic activity of Crystal Structure of Wild-Type Groel with Bound Thallium Ions:
3.6.4.9;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Groel with Bound Thallium Ions, PDB code: 3e76 was solved by P.D.Kiser, G.H.Lorimer, K.Palczewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 3.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.676, 260.954, 287.872, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 29.3

Other elements in 3e76:

The structure of Crystal Structure of Wild-Type Groel with Bound Thallium Ions also contains other interesting chemical elements:

Magnesium (Mg) 14 atoms

Thallium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 46;

Binding sites:

The binding sites of Thallium atom in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions (pdb code 3e76). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 46 binding sites of Thallium where determined in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions, PDB code: 3e76:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 46 in 3e76

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Thallium binding site 1 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl550

b:0.2
occ:0.40
O A:SER217 2.7 0.2 1.0
OE1 A:GLN319 2.8 0.2 1.0
O A:PRO218 3.1 0.2 1.0
C A:SER217 3.5 0.2 1.0
CD A:GLN319 3.6 0.2 1.0
C A:PRO218 3.6 0.2 1.0
CG A:GLN319 3.8 0.2 1.0
CZ A:PHE219 3.9 0.2 1.0
CE1 A:PHE219 3.9 0.2 1.0
CE2 A:PHE219 4.0 0.2 1.0
CD A:LYS245 4.1 0.2 1.0
CD1 A:PHE219 4.1 0.2 1.0
N A:PRO218 4.1 0.2 1.0
CB A:SER217 4.1 0.2 1.0
CD2 A:PHE219 4.2 0.2 1.0
CA A:PRO218 4.2 0.2 1.0
CG A:PHE219 4.2 0.2 1.0
N A:PHE219 4.3 0.2 1.0
CA A:SER217 4.3 0.2 1.0
CB A:GLN319 4.5 0.2 1.0
O A:ALA320 4.6 0.2 1.0
NE2 A:GLN319 4.7 0.2 1.0
OG A:SER217 4.7 0.2 1.0
CA A:PHE219 4.7 0.2 1.0
CE A:LYS245 4.8 0.2 1.0
CG A:LYS245 4.9 0.2 1.0
NZ A:LYS245 4.9 0.2 1.0
CB A:LYS245 5.0 0.2 1.0

Thallium binding site 2 out of 46 in 3e76

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Thallium binding site 2 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl551

b:0.2
occ:0.50
OE2 A:GLU483 2.3 0.2 1.0
O A:CYS458 2.7 0.2 1.0
OD1 B:ASN112 3.1 0.2 1.0
OD2 B:ASP115 3.4 0.2 1.0
CD A:GLU483 3.5 0.2 1.0
C A:CYS458 3.9 0.2 1.0
SG A:CYS458 4.0 0.2 1.0
CG B:ASN112 4.2 0.2 1.0
CG A:GLU483 4.4 0.2 1.0
CG B:ASP115 4.4 0.2 1.0
OE1 A:GLU483 4.4 0.2 1.0
OE2 A:GLU460 4.6 0.2 1.0
CB B:ASN112 4.6 0.2 1.0
ND2 B:ASN433 4.7 0.2 1.0
OD1 B:ASP115 4.7 0.2 1.0
CG A:GLU460 4.8 0.2 1.0
CA A:GLY459 4.8 0.2 1.0
N A:GLY459 4.8 0.2 1.0
CA A:CYS458 4.8 0.2 1.0

Thallium binding site 3 out of 46 in 3e76

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Thallium binding site 3 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl552

b:0.2
occ:0.60
O A:THR30 2.2 0.2 1.0
O A:LYS51 3.0 0.2 1.0
O1A A:AGS549 3.0 0.2 1.0
OG1 A:THR30 3.1 0.2 1.0
C A:THR30 3.2 0.2 1.0
OG1 A:THR90 3.4 0.2 1.0
O3G A:AGS549 3.5 0.2 1.0
CB A:THR30 3.5 0.2 1.0
O3A A:AGS549 3.7 0.2 1.0
PA A:AGS549 4.0 0.2 1.0
CA A:THR30 4.0 0.2 1.0
N A:GLY53 4.1 0.2 1.0
N A:LEU31 4.1 0.2 1.0
C A:LYS51 4.1 0.2 1.0
CB A:THR90 4.2 0.2 1.0
CA A:LEU31 4.3 0.2 1.0
CG2 A:THR90 4.3 0.2 1.0
PG A:AGS549 4.6 0.2 1.0
CA A:GLY53 4.7 0.2 1.0
O3B A:AGS549 4.8 0.2 1.0
CG2 A:THR30 4.9 0.2 1.0
CA A:ASP52 4.9 0.2 1.0
C A:ASP52 5.0 0.2 1.0
PB A:AGS549 5.0 0.2 1.0
O5' A:AGS549 5.0 0.2 1.0
CB A:LYS51 5.0 0.2 1.0
N A:ASP52 5.0 0.2 1.0

Thallium binding site 4 out of 46 in 3e76

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Thallium binding site 4 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl550

b:0.2
occ:0.40
O B:CYS458 2.5 0.2 1.0
OE2 B:GLU483 2.6 0.2 1.0
OD1 C:ASN112 3.3 0.2 1.0
C B:CYS458 3.7 0.2 1.0
CD B:GLU483 3.8 0.2 1.0
OD2 C:ASP115 4.1 0.2 1.0
OE2 B:GLU460 4.1 0.2 1.0
SG B:CYS458 4.1 0.2 1.0
CG B:GLU460 4.3 0.2 1.0
CG C:ASN112 4.4 0.2 1.0
CA B:GLY459 4.4 0.2 1.0
N B:GLU460 4.5 0.2 1.0
N B:GLY459 4.5 0.2 1.0
CG B:GLU483 4.6 0.2 1.0
C B:GLY459 4.6 0.2 1.0
OE1 B:GLU483 4.7 0.2 1.0
CD B:GLU460 4.7 0.2 1.0
CA B:CYS458 4.8 0.2 1.0
CB C:ASN112 4.8 0.2 1.0

Thallium binding site 5 out of 46 in 3e76

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Thallium binding site 5 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl551

b:0.2
occ:0.70
O B:THR30 2.5 0.2 1.0
O3G B:AGS549 2.7 0.2 1.0
OG1 B:THR30 3.0 0.2 1.0
OG1 B:THR90 3.0 0.2 1.0
O B:LYS51 3.1 0.2 1.0
O1A B:AGS549 3.2 0.2 1.0
C B:THR30 3.4 0.2 1.0
O3A B:AGS549 3.5 0.2 1.0
CB B:THR30 3.5 0.2 1.0
N B:GLY53 3.9 0.2 1.0
CB B:THR90 3.9 0.2 1.0
PG B:AGS549 4.0 0.2 1.0
PA B:AGS549 4.0 0.2 1.0
CG2 B:THR90 4.0 0.2 1.0
CA B:THR30 4.1 0.2 1.0
O3B B:AGS549 4.2 0.2 1.0
C B:LYS51 4.2 0.2 1.0
N B:LEU31 4.2 0.2 1.0
CA B:GLY53 4.3 0.2 1.0
CA B:LEU31 4.4 0.2 1.0
PB B:AGS549 4.6 0.2 1.0
C B:ASP52 4.8 0.2 1.0
O2G B:AGS549 4.8 0.2 1.0
CA B:ASP52 4.9 0.2 1.0
CG2 B:THR30 4.9 0.2 1.0
O2A B:AGS549 4.9 0.2 1.0
N B:ASP52 5.0 0.2 1.0

Thallium binding site 6 out of 46 in 3e76

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Thallium binding site 6 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl552

b:0.2
occ:0.40
O B:SER217 2.9 0.2 1.0
O B:PRO218 3.4 0.2 1.0
CD B:LYS245 3.5 0.2 1.0
C B:PRO218 3.5 0.2 1.0
C B:SER217 3.5 0.2 1.0
CZ B:PHE219 3.7 0.2 1.0
CE2 B:PHE219 3.7 0.2 1.0
CE1 B:PHE219 3.8 0.2 1.0
CG B:LYS245 3.8 0.2 1.0
CD2 B:PHE219 3.8 0.2 1.0
CB B:LYS245 3.9 0.2 1.0
CD1 B:PHE219 3.9 0.2 1.0
CG B:PHE219 3.9 0.2 1.0
N B:PHE219 3.9 0.2 1.0
CA B:PRO218 4.0 0.2 1.0
N B:PRO218 4.0 0.2 1.0
OG B:SER217 4.0 0.2 1.0
OE1 B:GLN319 4.1 0.2 1.0
CE B:LYS245 4.2 0.2 1.0
CG B:GLN319 4.3 0.2 1.0
O B:ALA320 4.4 0.2 1.0
CA B:PHE219 4.5 0.2 1.0
CA B:SER217 4.6 0.2 1.0
CB B:GLN319 4.6 0.2 1.0
CB B:SER217 4.6 0.2 1.0
CD B:GLN319 4.7 0.2 1.0
NZ B:LYS245 4.7 0.2 1.0
CB B:PHE219 4.8 0.2 1.0
CA B:GLN319 4.9 0.2 1.0

Thallium binding site 7 out of 46 in 3e76

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Thallium binding site 7 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 7 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl550

b:0.2
occ:0.40
OE2 C:GLU483 2.3 0.2 1.0
O C:CYS458 2.5 0.2 1.0
OD1 D:ASN112 3.1 0.2 1.0
CD C:GLU483 3.4 0.2 1.0
SG C:CYS458 3.5 0.2 1.0
C C:CYS458 3.7 0.2 1.0
OD2 D:ASP115 4.0 0.2 1.0
CG C:GLU483 4.1 0.2 1.0
CG D:ASN112 4.3 0.2 1.0
CA C:CYS458 4.4 0.2 1.0
OE1 C:GLU483 4.4 0.2 1.0
CB C:CYS458 4.6 0.2 1.0
CG D:ASP115 4.7 0.2 1.0
OD1 D:ASP115 4.7 0.2 1.0
N C:GLY459 4.7 0.2 1.0
CE C:LYS34 4.8 0.2 1.0
CA C:GLY459 4.9 0.2 1.0

Thallium binding site 8 out of 46 in 3e76

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Thallium binding site 8 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 8 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl551

b:0.2
occ:0.50
O C:THR30 2.4 0.2 1.0
O C:LYS51 3.1 0.2 1.0
OG1 C:THR30 3.1 0.2 1.0
OG1 C:THR90 3.1 0.2 1.0
O1A C:AGS549 3.2 0.2 1.0
O3G C:AGS549 3.2 0.2 1.0
C C:THR30 3.4 0.2 1.0
CB C:THR30 3.6 0.2 1.0
O3A C:AGS549 3.7 0.2 1.0
N C:GLY53 4.0 0.2 1.0
CB C:THR90 4.0 0.2 1.0
PA C:AGS549 4.1 0.2 1.0
CA C:THR30 4.2 0.2 1.0
CG2 C:THR90 4.2 0.2 1.0
C C:LYS51 4.2 0.2 1.0
N C:LEU31 4.3 0.2 1.0
CA C:LEU31 4.4 0.2 1.0
PG C:AGS549 4.5 0.2 1.0
CA C:GLY53 4.5 0.2 1.0
O3B C:AGS549 4.7 0.2 1.0
C C:ASP52 4.8 0.2 1.0
CA C:ASP52 4.9 0.2 1.0
PB C:AGS549 4.9 0.2 1.0
N C:ASP52 5.0 0.2 1.0

Thallium binding site 9 out of 46 in 3e76

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Thallium binding site 9 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 9 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl552

b:0.2
occ:0.40
O C:SER217 3.1 0.2 1.0
C C:PRO218 3.6 0.2 1.0
CE2 C:PHE219 3.6 0.2 1.0
CZ C:PHE219 3.6 0.2 1.0
O C:PRO218 3.7 0.2 1.0
C C:SER217 3.7 0.2 1.0
CD2 C:PHE219 3.8 0.2 1.0
CE1 C:PHE219 3.8 0.2 1.0
OE1 C:GLN319 3.8 0.2 1.0
N C:PHE219 3.9 0.2 1.0
CG C:PHE219 3.9 0.2 1.0
CD1 C:PHE219 3.9 0.2 1.0
CG C:GLN319 4.0 0.2 1.0
CD C:LYS245 4.0 0.2 1.0
CA C:PRO218 4.0 0.2 1.0
N C:PRO218 4.1 0.2 1.0
CB C:LYS245 4.2 0.2 1.0
CB C:GLN319 4.2 0.2 1.0
CD C:GLN319 4.4 0.2 1.0
O C:ALA320 4.4 0.2 1.0
OG C:SER217 4.4 0.2 1.0
CA C:PHE219 4.5 0.2 1.0
CA C:GLN319 4.6 0.2 1.0
CA C:SER217 4.7 0.2 1.0
CG C:LYS245 4.7 0.2 1.0
N C:ALA320 4.8 0.2 1.0
CB C:PHE219 4.8 0.2 1.0
CB C:SER217 4.9 0.2 1.0

Thallium binding site 10 out of 46 in 3e76

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Thallium binding site 10 out of 46 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tl550

b:0.2
occ:0.40
O D:SER217 2.7 0.2 1.0
O D:PRO218 3.1 0.2 1.0
OE1 D:GLN319 3.2 0.2 1.0
C D:PRO218 3.3 0.2 1.0
CZ D:PHE219 3.4 0.2 1.0
CE2 D:PHE219 3.5 0.2 1.0
CE1 D:PHE219 3.5 0.2 1.0
C D:SER217 3.5 0.2 1.0
CG D:GLN319 3.5 0.2 1.0
CD1 D:PHE219 3.6 0.2 1.0
CD2 D:PHE219 3.6 0.2 1.0
CG D:PHE219 3.6 0.2 1.0
N D:PHE219 3.7 0.2 1.0
CD D:GLN319 3.8 0.2 1.0
N D:PRO218 3.9 0.2 1.0
CA D:PRO218 4.0 0.2 1.0
CB D:GLN319 4.1 0.2 1.0
CD D:LYS245 4.2 0.2 1.0
CA D:PHE219 4.2 0.2 1.0
CB D:PHE219 4.5 0.2 1.0
CA D:SER217 4.6 0.2 1.0
CB D:LYS245 4.6 0.2 1.0
CB D:SER217 4.6 0.2 1.0
CA D:GLN319 4.6 0.2 1.0
CG D:LYS245 4.7 0.2 1.0

Reference:

P.D.Kiser, G.H.Lorimer, K.Palczewski. Use of Thallium to Identify Monovalent Cation Binding Sites in Groel. Acta Crystallogr.,Sect.F V. 65 967 2009.
ISSN: ESSN 1744-3091
PubMed: 19851000
DOI: 10.1107/S1744309109032928
Page generated: Wed Dec 16 02:28:50 2020

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