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Magnesium in PDB 6wtr: Structure of Human Pir-Mirna-300 Apical Loop Fused to the Ydao Riboswitch Scaffold

Protein crystallography data

The structure of Structure of Human Pir-Mirna-300 Apical Loop Fused to the Ydao Riboswitch Scaffold, PDB code: 6wtr 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) 74.30 / 3.08
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.07, 113.07, 114.05, 90, 90, 120
R / Rfree (%) 16.5 / 19.2

Other elements in 6wtr:

The structure of Structure of Human Pir-Mirna-300 Apical Loop 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-300 Apical Loop Fused to the Ydao Riboswitch Scaffold (pdb code 6wtr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Human Pir-Mirna-300 Apical Loop Fused to the Ydao Riboswitch Scaffold, PDB code: 6wtr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wtr

Go back to Magnesium Binding Sites List in 6wtr
Magnesium binding site 1 out of 3 in the Structure of Human Pir-Mirna-300 Apical Loop 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-300 Apical Loop Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:70.8
occ:1.00
OP2 A:C98 2.0 106.5 1.0
OP2 A:G30 2.1 91.6 1.0
O4 A:U99 2.4 92.1 1.0
OP1 A:G97 2.5 113.4 1.0
P A:C98 3.3 97.9 1.0
O3' A:A96 3.4 96.7 1.0
C4 A:U99 3.4 90.9 1.0
P A:G97 3.5 103.0 1.0
P A:G30 3.5 84.5 1.0
OP1 A:C98 3.8 88.2 1.0
OP1 A:G29 3.8 90.6 1.0
O5' A:G29 3.8 88.7 1.0
C5 A:U99 3.9 101.5 1.0
C5' A:G97 4.0 82.1 1.0
O3' A:G97 4.2 80.2 1.0
O5' A:G97 4.2 88.1 1.0
N7 A:G30 4.2 104.3 1.0
P A:G29 4.2 88.3 1.0
O2' A:A96 4.2 91.8 1.0
O5' A:G30 4.3 88.5 1.0
O3' A:G29 4.4 83.1 1.0
O5' A:C98 4.4 89.8 1.0
C3' A:G97 4.4 80.0 1.0
C3' A:G29 4.4 84.6 1.0
C5' A:G29 4.5 93.8 1.0
OP1 A:G30 4.5 94.7 1.0
C8 A:G30 4.5 89.8 1.0
OP2 A:G29 4.5 107.0 1.0
N3 A:U99 4.6 96.4 1.0
C3' A:A96 4.7 87.8 1.0
C5 A:C98 4.7 104.3 1.0
OP2 A:G97 4.8 116.0 1.0
C4' A:G97 4.8 86.6 1.0
C2' A:A96 4.9 90.8 1.0

Magnesium binding site 2 out of 3 in 6wtr

Go back to Magnesium Binding Sites List in 6wtr
Magnesium binding site 2 out of 3 in the Structure of Human Pir-Mirna-300 Apical Loop 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-300 Apical Loop Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:120.8
occ:1.00
OP1 A:U46 2.3 102.0 1.0
OP1 A:A28 2.5 90.8 1.0
P A:U46 3.8 91.4 1.0
P A:A28 3.9 84.7 1.0
O3' A:G27 4.5 88.6 1.0
OP2 A:U46 4.6 82.5 1.0
O5' A:U46 4.6 84.8 1.0
O3' A:G45 4.6 80.1 1.0
OP2 A:A28 4.6 70.6 1.0
OP2 A:U47 4.8 84.0 1.0
O5' A:A28 4.9 73.6 1.0
C5' A:U46 4.9 77.4 1.0

Magnesium binding site 3 out of 3 in 6wtr

Go back to Magnesium Binding Sites List in 6wtr
Magnesium binding site 3 out of 3 in the Structure of Human Pir-Mirna-300 Apical Loop 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-300 Apical Loop Fused to the Ydao Riboswitch Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:85.0
occ:1.00
OP2 A:G97 2.2 116.0 1.0
P A:G97 3.3 103.0 1.0
OP1 A:G97 3.5 113.4 1.0
OP1 A:A31 3.9 76.1 1.0
OP1 A:G30 4.0 94.7 1.0
OP2 A:A31 4.1 78.2 1.0
N4 A:C98 4.2 83.9 1.0
O3' A:A96 4.3 96.7 1.0
P A:A31 4.5 85.7 1.0
O5' A:G97 4.5 88.1 1.0
C4' A:A96 4.7 94.8 1.0
N7 A:G97 4.7 104.8 1.0
P A:G30 4.8 84.5 1.0
O5' A:G30 4.9 88.5 1.0
OP2 A:G30 4.9 91.6 1.0
C3' A:A96 5.0 87.8 1.0
C8 A:G97 5.0 95.1 1.0

Reference:

G.M.Shoffner, Z.Peng, F.Guo. Structures of Microrna-Precursor Apical Junctions and Loops Revealed By Scaffold-Directed Crystallography: Importance of Non-Canonical Base Pairs in Processing To Be Published.
Page generated: Sun Jul 11 14:59:13 2021

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