Magnesium in PDB 6ufh: Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate

Protein crystallography data

The structure of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate, PDB code: 6ufh was solved by R.A.Battaglia, J.A.Grigg, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.68 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.276, 61.430, 122.520, 90.00, 93.97, 90.00
R / Rfree (%) 22 / 26.9

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 6 in 6ufh

Go back to Magnesium Binding Sites List in 6ufh
Magnesium binding site 1 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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'-2'3'Cyclic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:0.0
occ:1.00
OP2 B:U8 3.2 0.3 1.0
OP2 B:U12 3.6 0.2 1.0
OP1 B:U8 3.9 0.2 1.0
OP2 B:A9 3.9 0.9 1.0
P B:U8 3.9 0.3 1.0
OP1 B:A9 4.0 1.0 1.0
OP2 B:C11 4.1 0.8 1.0
P B:A9 4.5 0.2 1.0
O5' B:U8 4.8 0.0 1.0
OP1 B:C11 4.8 0.7 1.0
P B:C11 4.8 0.8 1.0

Magnesium binding site 2 out of 6 in 6ufh

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


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'-2'3'Cyclic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:0.3
occ:1.00
OP2 B:A14 2.6 0.2 1.0
OP1 B:A7 2.9 0.4 1.0
O3' B:U6 2.9 0.1 1.0
P B:A7 3.3 0.6 1.0
O5' B:A7 3.3 0.6 1.0
P B:A14 3.8 0.8 1.0
O2' B:U6 3.9 0.9 1.0
OP1 B:A14 4.1 0.7 1.0
C3' B:U6 4.1 0.8 1.0
C5' B:A7 4.2 0.6 1.0
O3' B:C13 4.4 0.5 1.0
O4 B:U8 4.5 0.8 1.0
C2' B:U6 4.6 0.2 1.0
C4' B:U6 4.6 0.4 1.0
C3' B:C13 4.7 0.9 1.0
OP2 B:A7 4.7 0.2 1.0
C5 B:U8 4.7 0.6 1.0
C5' B:C13 5.0 0.7 1.0

Magnesium binding site 3 out of 6 in 6ufh

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


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'-2'3'Cyclic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:95.4
occ:1.00
OP1 A:A119 2.1 85.5 1.0
P A:A119 3.5 96.5 1.0
O5' A:A119 4.0 0.7 1.0
OP2 A:A119 4.3 71.7 1.0
OP1 A:G120 4.4 99.0 1.0
C5' A:A119 4.5 0.4 1.0
O5' A:G120 4.5 56.1 1.0
O3' A:A118 4.6 69.2 1.0

Magnesium binding site 4 out of 6 in 6ufh

Go back to Magnesium Binding Sites List in 6ufh
Magnesium binding site 4 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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'-2'3'Cyclic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:88.1
occ:1.00
OP1 A:A118 2.7 0.4 1.0
P A:A118 4.1 0.1 1.0
O3' A:C117 4.6 81.9 1.0
O5' A:A118 5.0 0.1 1.0

Magnesium binding site 5 out of 6 in 6ufh

Go back to Magnesium Binding Sites List in 6ufh
Magnesium binding site 5 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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'-2'3'Cyclic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:75.4
occ:1.00
OP1 B:A2377 2.4 0.1 1.0
O6 A:G160 3.2 84.2 1.0
O4 A:U161 3.3 72.9 1.0
O6 A:G133 3.3 69.0 1.0
N4 A:C132 3.4 70.4 1.0
P B:A2377 3.9 81.6 1.0
N4 A:C134 4.0 75.1 1.0
N3 A:U161 4.1 51.5 1.0
C4 A:U161 4.1 64.0 1.0
C5' B:A2377 4.1 85.8 1.0
C6 A:G160 4.3 64.3 1.0
C6 A:G133 4.3 88.2 1.0
C4 A:C132 4.3 82.9 1.0
N7 A:G133 4.5 63.3 1.0
O5' B:A2377 4.5 68.3 1.0
O3' B:C76 4.5 0.5 1.0
O6 A:G97 4.8 77.1 1.0
C5 A:G133 4.8 76.7 1.0
C5 A:C132 4.9 92.0 1.0
OP2 B:A2377 4.9 80.0 1.0

Magnesium binding site 6 out of 6 in 6ufh

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


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'-2'3'Cyclic Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:0.3
occ:1.00
N7 A:G41 4.0 0.0 1.0
N7 A:G42 4.3 0.2 1.0
C5 A:G41 4.5 0.8 1.0
OP2 A:G41 4.6 0.9 1.0
C8 A:G41 4.6 0.6 1.0
O6 A:G41 4.6 0.3 1.0
O6 A:G42 4.6 0.8 1.0
OP2 A:C40 4.8 0.7 1.0
C6 A:G41 4.8 0.5 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 Dec 15 01:01:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy