Atomistry » Magnesium » PDB 6woc-6wvj » 6wtl
Atomistry »
  Magnesium »
    PDB 6woc-6wvj »
      6wtl »

Magnesium in PDB 6wtl: Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold

Protein crystallography data

The structure of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6wtl was solved by G.M.Shoffner, Z.Peng, F.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.49 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.34, 115.34, 115.28, 90, 90, 120
R / Rfree (%) 18.7 / 21.3

Other elements in 6wtl:

The structure of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold (pdb code 6wtl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold, PDB code: 6wtl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6wtl

Go back to Magnesium Binding Sites List in 6wtl
Magnesium binding site 1 out of 4 in the Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:60.1
occ:1.00
OP2 A:G29 2.0 96.0 1.0
OP2 A:C97 2.1 100.7 1.0
O4 A:U98 2.2 85.0 1.0
OP1 A:G96 2.5 89.0 1.0
C4 A:U98 3.3 84.7 1.0
P A:C97 3.4 85.5 1.0
P A:G29 3.5 75.1 1.0
O3' A:A95 3.6 94.3 1.0
P A:G96 3.6 89.4 1.0
OP1 A:C97 3.8 83.6 1.0
C5 A:U98 3.9 86.8 1.0
OP1 A:G28 3.9 77.2 1.0
O5' A:G28 4.0 81.7 1.0
O5' A:G29 4.1 76.3 1.0
N7 A:G29 4.2 82.3 1.0
P A:G28 4.3 77.6 1.0
O3' A:G28 4.3 81.5 1.0
C5' A:G96 4.3 82.7 1.0
O3' A:G96 4.4 82.8 1.0
O5' A:C97 4.4 82.9 1.0
O5' A:G96 4.4 86.3 1.0
C3' A:G28 4.4 78.6 1.0
C8 A:G29 4.4 78.6 1.0
N3 A:U98 4.5 81.4 1.0
OP2 A:G28 4.5 82.2 1.0
OP1 A:G29 4.5 83.2 1.0
C3' A:G96 4.6 83.2 1.0
C5' A:G28 4.7 73.9 1.0
C5 A:C97 4.8 88.1 1.0
O2' A:A95 4.8 96.3 1.0
OP2 A:G96 4.9 92.5 1.0
C3' A:A95 5.0 92.0 1.0

Magnesium binding site 2 out of 4 in 6wtl

Go back to Magnesium Binding Sites List in 6wtl
Magnesium binding site 2 out of 4 in the Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:104.7
occ:1.00
OP2 A:U46 3.0 72.9 1.0
OP1 A:A27 3.1 74.3 1.0
OP1 A:U45 3.2 75.5 1.0
O3' A:G26 3.7 71.5 1.0
P A:A27 3.9 73.7 1.0
P A:U46 4.0 76.2 1.0
OP1 A:U46 4.1 79.8 1.0
C5' A:G26 4.3 67.1 1.0
OP2 A:A27 4.4 73.8 1.0
P A:U45 4.4 76.0 1.0
C5' A:U45 4.5 74.8 1.0
O5' A:U45 4.5 76.8 1.0
OP1 A:G26 4.6 69.5 1.0
O3' A:U45 4.7 72.4 1.0
C3' A:G26 4.7 66.9 1.0
C4' A:G26 4.8 70.7 1.0

Magnesium binding site 3 out of 4 in 6wtl

Go back to Magnesium Binding Sites List in 6wtl
Magnesium binding site 3 out of 4 in the Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:79.4
occ:1.00
OP2 A:G96 2.5 92.5 1.0
P A:G96 3.5 89.4 1.0
OP1 A:G96 3.6 89.0 1.0
OP1 A:A30 4.0 81.1 1.0
OP2 A:A30 4.2 84.2 1.0
N4 A:C97 4.2 85.5 1.0
OP1 A:G29 4.3 83.2 1.0
N7 A:G96 4.3 93.8 1.0
P A:A30 4.6 78.8 1.0
O5' A:G96 4.6 86.3 1.0
O3' A:A95 4.6 94.3 1.0
C8 A:G96 4.7 89.2 1.0
C4' A:A95 4.9 90.5 1.0

Magnesium binding site 4 out of 4 in 6wtl

Go back to Magnesium Binding Sites List in 6wtl
Magnesium binding site 4 out of 4 in the Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human Pir-Mirna-19B-2 Apical Loop and One-Base-Pair Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:97.0
occ:1.00
OP1 A:C7 3.0 65.6 1.0
OP1 A:A72 3.3 68.5 1.0
P A:C7 4.5 67.9 1.0
P A:A72 4.5 72.0 1.0
OP1 A:U77 5.0 79.8 1.0
OP2 A:A72 5.0 68.5 1.0

Reference:

G.M.Shoffner, Z.Peng, F.Guo. Three-Dimensional Structures of Pri-Mirna Apical Junctions and Loops Revealed By Scaffold-Directed Crystallography To Be Published.
Page generated: Sun Jul 11 14:59:13 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy