Atomistry » Magnesium » PDB 6ufg-6uok » 6ufg
Atomistry »
  Magnesium »
    PDB 6ufg-6uok »
      6ufg »

Magnesium in PDB 6ufg: Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh

Protein crystallography data

The structure of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh, PDB code: 6ufg was solved by R.A.Battaglia, J.C.Grigg, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.21 / 2.93
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 77.209, 77.209, 172.754, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.5

Other elements in 6ufg:

The structure of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh (pdb code 6ufg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh, PDB code: 6ufg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 1 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:0.9
occ:1.00
OP2 B:U12 3.2 0.9 1.0
OP2 B:U8 3.4 91.0 1.0
OP2 B:A9 4.1 0.7 1.0
OP1 B:A9 4.3 0.2 1.0
P B:U8 4.4 0.6 1.0
C5 B:U12 4.5 0.6 1.0
OP1 B:U8 4.5 0.8 1.0
P B:U12 4.7 0.1 1.0
P B:A9 4.7 0.3 1.0
OP2 B:C11 4.8 0.5 1.0
C5 B:C13 4.8 0.9 1.0

Magnesium binding site 2 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 2 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:0.8
occ:1.00
N7 B:G69 3.6 83.1 1.0
O6 B:G70 3.8 82.8 1.0
O6 B:G69 3.8 90.8 1.0
C5 B:G69 4.1 81.4 1.0
C6 B:G69 4.2 78.7 1.0
C8 B:G69 4.6 85.5 1.0
N7 B:G70 4.6 85.5 1.0
C6 B:G70 4.7 81.9 1.0

Magnesium binding site 3 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 3 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:78.1
occ:1.00
OP1 B:A77 2.4 95.4 1.0
O4 A:U160 2.8 79.2 1.0
O6 A:G132 3.0 77.4 1.0
N4 A:C131 3.2 0.5 1.0
P B:A77 3.7 78.6 1.0
O6 A:G96 3.7 83.6 1.0
C5' B:A77 3.7 72.4 1.0
C4 A:U160 3.9 71.9 1.0
O6 A:G159 4.0 77.2 1.0
O3' B:C76 4.1 91.5 1.0
O5' B:A77 4.2 71.1 1.0
C6 A:G132 4.2 84.2 1.0
N3 A:U160 4.2 64.6 1.0
C4 A:C131 4.3 87.1 1.0
C6 A:G96 4.8 74.0 1.0
N7 A:G132 4.8 83.0 1.0
N4 A:C133 4.9 70.2 1.0
C5 A:G132 4.9 85.7 1.0
OP2 B:A77 4.9 68.0 1.0
C6 A:G159 5.0 69.1 1.0
C5 A:C131 5.0 80.3 1.0

Magnesium binding site 4 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 4 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:96.3
occ:1.00
N7 A:G70 3.6 0.3 1.0
OP2 A:C82 3.6 0.1 1.0
O6 A:G70 3.9 0.5 1.0
O6 A:G84 3.9 0.5 1.0
C5 A:G70 4.2 0.8 1.0
C6 A:G70 4.4 0.6 1.0
C8 A:G70 4.5 0.3 1.0
P A:C82 4.7 0.0 1.0
N7 A:G84 4.7 0.5 1.0
N2 A:G69 4.7 98.2 1.0
N7 A:A83 4.8 0.1 1.0
OP2 A:A83 4.8 0.6 1.0
C2 A:G69 4.9 97.1 1.0
C6 A:G84 4.9 0.3 1.0
N3 A:G69 4.9 97.7 1.0
N6 A:A83 5.0 0.9 1.0

Magnesium binding site 5 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 5 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:61.4
occ:1.00
O6 A:G135 2.5 85.3 1.0
O4 A:U157 2.8 68.6 1.0
O6 A:G134 3.0 77.8 1.0
O6 A:G156 3.2 80.9 1.0
C6 A:G135 3.6 71.3 1.0
N4 A:C136 3.7 91.2 1.0
C6 A:G134 3.7 71.7 1.0
C4 A:U157 3.8 66.1 1.0
N3 A:U157 4.0 73.8 1.0
N4 A:C158 4.1 71.6 1.0
C6 A:G156 4.2 67.3 1.0
N7 A:G135 4.3 83.4 1.0
C5 A:G135 4.3 69.6 1.0
C5 A:G134 4.5 59.5 1.0
N1 A:G134 4.5 64.4 1.0
C4 A:C136 4.6 67.7 1.0
N7 A:G134 4.7 77.6 1.0
N1 A:G135 4.7 75.2 1.0
C4 A:C158 5.0 60.8 1.0
N1 A:G156 5.0 64.4 1.0

Magnesium binding site 6 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 6 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:95.0
occ:1.00
OP2 A:G94 2.4 80.9 1.0
P A:G94 3.9 97.0 1.0
O5' A:G96 4.1 99.0 1.0
OP1 A:G96 4.3 0.7 1.0
OP1 A:G94 4.5 0.2 1.0
O3' A:C93 4.6 0.6 1.0
C4' A:G96 4.7 0.2 1.0
O4' A:G96 4.8 0.2 1.0
O5' A:G94 4.9 88.1 1.0
C5' A:G94 4.9 58.6 1.0
P A:G96 4.9 0.2 1.0

Magnesium binding site 7 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 7 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:88.3
occ:1.00
OP1 A:G94 2.0 0.2 1.0
P A:G94 3.5 97.0 1.0
OP1 A:C93 3.6 0.5 1.0
C3' A:C93 4.1 0.3 1.0
O5' A:G94 4.1 88.1 1.0
O3' A:C93 4.2 0.6 1.0
OP2 A:G94 4.5 80.9 1.0
OP2 A:C161 4.6 64.8 1.0
P A:C93 4.8 0.5 1.0
O2' A:C161 4.8 95.5 1.0
O3' A:C161 4.9 75.2 1.0
C4' A:C93 4.9 0.9 1.0
C5' A:C93 5.0 0.8 1.0

Magnesium binding site 8 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 8 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:83.6
occ:1.00
O6 A:G121 3.3 64.0 1.0
N7 A:G121 3.4 61.9 1.0
O6 A:G122 3.7 76.4 1.0
C6 A:G121 3.8 65.4 1.0
C5 A:G121 3.9 53.8 1.0
N7 A:G122 4.1 56.8 1.0
C6 A:G122 4.5 62.2 1.0
C8 A:G121 4.5 55.6 1.0
N4 A:C120 4.6 77.4 1.0
C5 A:G122 4.6 52.5 1.0
OP1 A:G159 4.6 78.8 1.0

Magnesium binding site 9 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 9 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:93.7
occ:1.00
O6 A:G127 3.7 84.7 1.0
O6 A:G126 4.1 88.5 1.0
N7 A:G126 4.1 81.7 1.0
N7 A:G127 4.4 79.0 1.0
C6 A:G126 4.7 72.2 1.0
C6 A:G127 4.7 76.7 1.0
C5 A:G126 4.7 79.4 1.0
O4 A:U125 4.7 62.4 1.0
C5 A:G127 5.0 68.8 1.0

Magnesium binding site 10 out of 11 in 6ufg

Go back to Magnesium Binding Sites List in 6ufg
Magnesium binding site 10 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:0.8
occ:1.00
OP1 A:A90 2.9 0.7 1.0
OP1 A:C88 3.1 0.6 1.0
N7 A:G91 3.8 96.5 1.0
P A:A90 4.2 0.9 1.0
OP2 A:G91 4.2 0.5 1.0
O5' A:A90 4.3 0.1 1.0
P A:C88 4.4 0.4 1.0
C8 A:G91 4.5 80.9 1.0
OP2 A:C88 4.8 0.7 1.0
C5 A:G91 4.9 86.7 1.0
O6 A:G91 4.9 82.3 1.0

Reference:

R.A.Battaglia, J.C.Grigg, A.Ke. Structural Basis For Trna Decoding and Aminoacylation Sensing By T-Box Riboregulators. Nat.Struct.Mol.Biol. 2019.
ISSN: ESSN 1545-9985
PubMed: 31740853
DOI: 10.1038/S41594-019-0327-6
Page generated: Tue Oct 1 21:01:27 2024

Last articles

Zn in 1E3L
Zn in 1E3I
Zn in 1E48
Zn in 1E49
Zn in 1E47
Zn in 1E46
Zn in 1E3E
Zn in 1E3J
Zn in 1E1H
Zn in 1E0E
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy