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Thallium in PDB 7q82: Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)

Protein crystallography data

The structure of Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine), PDB code: 7q82 was solved by M.Mieczkowski, C.Hoebartner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.59 / 2.95
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.983, 71.983, 84.45, 90, 90, 90
R / Rfree (%) 20.9 / 22.5

Other elements in 7q82:

The structure of Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Thallium Binding Sites:

The binding sites of Thallium atom in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) (pdb code 7q82). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 10 binding sites of Thallium where determined in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine), PDB code: 7q82:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 10 in 7q82

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Thallium binding site 1 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl101

b:126.4
occ:0.77
 N3 B:C16 2.5 114.5 1.0
O2 B:C16 3.2 113.6 1.0
C2 B:C16 3.2 114.0 1.0
C4 B:C16 3.4 101.0 1.0
N4 B:C16 3.6 120.9 1.0
N1 B:A15 3.6 99.6 1.0
N6 B:A15 3.9 103.2 1.0
C6 B:A15 4.1 96.5 1.0
C2 B:A15 4.4 108.0 1.0
N1 B:C16 4.5 93.0 1.0
C5 B:C16 4.7 97.3 1.0

Thallium binding site 2 out of 10 in 7q82

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Thallium binding site 2 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl102

b:192.8
occ:0.53
 O6 B:G2 2.8 147.3 1.0
N7 B:G2 2.8 141.9 1.0
C6 B:G2 3.4 153.5 1.0
C5 B:G2 3.4 147.7 1.0
O6 B:G1 4.0 159.4 1.0
C8 B:G2 4.0 138.1 1.0
C6 B:G1 4.0 155.6 1.0
C5 B:G1 4.1 153.7 1.0
N7 B:G1 4.2 155.6 1.0
N6 B:A3 4.3 149.1 1.0
N1 B:G1 4.7 150.9 1.0
TL B:TL105 4.7 317.5 1.0
C4 B:G2 4.8 140.1 1.0
N1 B:G2 4.8 151.1 1.0
C4 B:G1 4.9 146.0 1.0
C8 B:G1 4.9 133.3 1.0

Thallium binding site 3 out of 10 in 7q82

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Thallium binding site 3 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl103

b:137.7
occ:0.30
 O6 B:G14 3.1 92.9 1.0
N7 B:G14 3.6 105.7 1.0
C6 B:G14 3.9 87.2 1.0
N4 B:C13 4.0 97.0 1.0
C5 B:G14 4.1 88.2 1.0
C5 B:C13 4.3 84.3 1.0
C4 B:C13 4.3 98.8 1.0
C2 C:A33 4.6 88.0 1.0
N1 C:A33 4.7 94.0 1.0
C8 B:G14 4.7 99.0 1.0

Thallium binding site 4 out of 10 in 7q82

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Thallium binding site 4 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl104

b:128.5
occ:0.30
 N7 B:G22 2.4 94.7 1.0
O6 B:G22 2.8 103.5 1.0
C5 B:G22 3.1 93.8 1.0
C6 B:G22 3.3 99.3 1.0
N7 B:A21 3.4 89.0 1.0
C8 B:G22 3.6 104.0 1.0
C5 B:A21 3.7 90.3 1.0
N6 B:A21 4.0 93.9 1.0
C6 B:A21 4.0 96.7 1.0
C8 B:A21 4.1 94.5 1.0
N4 B:C23 4.1 111.6 1.0
C4 B:G22 4.5 95.2 1.0
C4 B:A21 4.5 80.9 1.0
N9 B:G22 4.7 96.0 1.0
N1 B:G22 4.7 100.1 1.0
C4 B:C23 4.7 110.2 1.0
N9 B:A21 4.7 75.8 1.0
C5 B:C23 4.9 124.8 1.0
N1 B:A21 5.0 94.2 1.0

Thallium binding site 5 out of 10 in 7q82

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Thallium binding site 5 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tl105

b:317.5
occ:1.00
 N7 B:G1 2.7 155.6 1.0
O6 B:G1 3.6 159.4 1.0
C5 B:G1 3.7 153.7 1.0
C8 B:G1 3.7 133.3 1.0
C6 B:G1 4.0 155.6 1.0
TL B:TL102 4.7 192.8 0.5
C4 B:G1 4.9 146.0 1.0
N9 B:G1 4.9 126.7 1.0

Thallium binding site 6 out of 10 in 7q82

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Thallium binding site 6 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl102

b:142.7
occ:0.72
 O6 C:G30 2.2 106.4 1.0
N7 C:G30 2.8 100.0 1.0
C6 C:G30 3.0 90.2 1.0
O6 C:G29 3.2 95.7 1.0
C5 C:G30 3.2 90.4 1.0
C6 C:G29 3.4 95.7 1.0
N6 C:A31 3.7 74.9 1.0
C5 C:G29 3.7 92.5 1.0
N7 C:G29 3.8 106.2 1.0
C8 C:G30 4.1 95.5 1.0
N1 C:G29 4.2 85.2 1.0
C6 C:A31 4.3 85.5 1.0
N1 C:G30 4.3 80.2 1.0
TL C:TL105 4.4 149.5 0.6
C4 C:G30 4.6 88.7 1.0
C4 C:G29 4.6 78.1 1.0
C8 C:G29 4.8 85.1 1.0
C5 C:A31 4.8 83.7 1.0
N7 C:A31 4.9 92.4 1.0
N1 C:A31 5.0 92.1 1.0

Thallium binding site 7 out of 10 in 7q82

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Thallium binding site 7 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl103

b:118.9
occ:0.22
 OP2 C:G38 2.4 114.8 1.0
O4 C:U42 3.1 118.5 1.0
P C:G38 3.4 120.7 1.0
OP1 C:G38 3.4 120.7 1.0
C5 C:U42 3.5 121.4 1.0
C2 C:A41 3.6 119.7 1.0
C4 C:U42 3.6 119.6 1.0
OP2 C:A41 3.8 113.0 1.0
N1 C:A41 4.3 128.1 1.0
N3 C:A41 4.3 110.2 1.0
O5' C:G38 4.4 99.9 1.0
O3' C:A37 4.5 100.4 1.0
C5' C:A41 4.7 100.6 1.0
C6 C:U42 4.7 120.8 1.0
C5' C:G38 4.9 88.3 1.0
N3 C:U42 4.9 107.6 1.0
OP2 C:C40 5.0 89.5 1.0

Thallium binding site 8 out of 10 in 7q82

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Thallium binding site 8 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl104

b:194.9
occ:0.50
 N7 C:G46 2.4 125.5 1.0
O6 C:G46 2.8 108.7 1.0
C5 C:G46 3.1 113.9 1.0
O4 C:U47 3.1 114.0 1.0
C6 C:G46 3.3 108.9 1.0
C8 C:G46 3.6 122.5 1.0
N7 C:A45 3.6 118.8 1.0
C5 C:A45 3.7 110.8 1.0
N6 C:A45 3.8 112.3 1.0
C6 C:A45 3.8 119.6 1.0
C4 C:U47 3.8 128.0 1.0
C8 C:A45 4.3 123.8 1.0
C5 C:U47 4.4 135.8 1.0
C4 C:G46 4.4 111.9 1.0
C4 C:A45 4.5 110.0 1.0
N1 C:A45 4.6 121.8 1.0
N9 C:G46 4.6 118.5 1.0
N1 C:G46 4.6 105.5 1.0
N3 C:U47 4.7 122.8 1.0
N9 C:A45 4.8 123.4 1.0

Thallium binding site 9 out of 10 in 7q82

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Thallium binding site 9 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl105

b:149.5
occ:0.57
 O6 C:G29 2.8 95.7 1.0
O6 C:G28 3.0 126.7 1.0
N7 C:G28 3.3 118.3 1.0
C6 C:G28 3.5 106.4 1.0
C5 C:G28 3.6 101.0 1.0
N7 C:G29 3.7 106.2 1.0
C6 C:G29 3.7 95.7 1.0
O4 C:U27 4.0 104.0 1.0
C5 C:G29 4.0 92.5 1.0
C4 C:U27 4.3 94.2 1.0
C8 C:G28 4.4 96.4 1.0
TL C:TL102 4.4 142.7 0.7
C5 C:U27 4.5 106.0 1.0
N1 C:G28 4.8 86.0 1.0
C4 C:G28 4.9 81.5 1.0
C8 C:G29 4.9 85.1 1.0
N1 C:G29 5.0 85.2 1.0
N3 C:U27 5.0 100.5 1.0

Thallium binding site 10 out of 10 in 7q82

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Thallium binding site 10 out of 10 in the Crystal Structure of the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine)


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 the Methyltransferase-Ribozyme 1, Thallium Derivative (with 1-Methyl-Adenosine) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tl106

b:177.5
occ:0.37
 O2' A:1MA7 2.3 150.0 1.0
OP2 C:C35 2.9 127.4 1.0
O3' C:A34 3.1 120.4 1.0
C2' A:1MA7 3.6 136.2 1.0
P C:C35 3.6 117.4 1.0
OP2 A:G8 3.7 141.8 1.0
O2' C:A34 3.8 128.5 1.0
O3' A:1MA7 3.8 126.3 1.0
C3' A:1MA7 4.0 144.7 1.0
O5' C:C35 4.2 112.3 1.0
C3' C:A34 4.3 113.2 1.0
P A:G8 4.4 124.4 1.0
C2' C:A34 4.4 113.0 1.0
C1' C:A34 4.6 105.8 1.0
C1' A:1MA7 4.7 116.9 1.0
OP1 C:C35 4.9 123.2 1.0

Reference:

C.P.M.Scheitl, M.Mieczkowski, H.Schindelin, C.Hobartner. Structure and Mechanism of the Methyltransferase Ribozyme MTR1. Nat.Chem.Biol. V. 18 547 2022.
ISSN: ESSN 1552-4469
PubMed: 35301481
DOI: 10.1038/S41589-022-00976-X
Page generated: Fri Oct 11 10:24:38 2024

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