Atomistry » Magnesium » PDB 4zi2-4zol » 4znp
Atomistry »
  Magnesium »
    PDB 4zi2-4zol »
      4znp »

Magnesium in PDB 4znp: The Structure of A Pfi Riboswitch Bound to Zmp

Protein crystallography data

The structure of The Structure of A Pfi Riboswitch Bound to Zmp, PDB code: 4znp was solved by A.Ren, D.J.Patel, R.K.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.20 / 2.94
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 152.195, 152.195, 86.891, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 24.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of A Pfi Riboswitch Bound to Zmp (pdb code 4znp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Structure of A Pfi Riboswitch Bound to Zmp, PDB code: 4znp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4znp

Go back to Magnesium Binding Sites List in 4znp
Magnesium binding site 1 out of 3 in the The Structure of A Pfi Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of A Pfi Riboswitch Bound to Zmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:70.7
occ:1.00
O A:HOH202 1.9 73.9 1.0
OP1 A:U13 2.1 77.5 1.0
O A:HOH203 2.2 80.5 1.0
O A:HOH201 2.3 69.2 1.0
O5 A:AMZ101 2.3 70.2 1.0
OP2 A:C31 2.4 75.8 1.0
C6 A:AMZ101 3.2 69.5 1.0
P A:C31 3.2 77.4 1.0
O5' A:C31 3.3 75.8 1.0
N2 A:AMZ101 3.4 73.3 1.0
P A:U13 3.5 73.9 1.0
C5' A:C31 3.6 78.0 1.0
OP1 A:C31 3.8 83.6 1.0
OP2 A:U13 4.1 90.0 1.0
N3 A:G67 4.1 79.8 1.0
O2' A:G67 4.2 87.7 1.0
N2 A:G67 4.4 77.2 1.0
O3' A:C12 4.4 78.8 1.0
C3A A:AMZ101 4.5 70.6 1.0
O4' A:G14 4.5 65.4 1.0
O5' A:U13 4.6 66.9 1.0
C1' A:G67 4.6 81.8 1.0
O3' A:A30 4.7 77.1 1.0
C2 A:G67 4.7 78.0 1.0
C1' A:G14 4.7 70.7 1.0
N3 A:AMZ101 4.8 66.8 1.0
C5' A:U13 4.9 72.2 1.0
C2' A:G67 4.9 85.3 1.0

Magnesium binding site 2 out of 3 in 4znp

Go back to Magnesium Binding Sites List in 4znp
Magnesium binding site 2 out of 3 in the The Structure of A Pfi Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of A Pfi Riboswitch Bound to Zmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:87.9
occ:1.00
O A:HOH205 2.0 79.8 1.0
O A:HOH204 2.6 84.9 1.0
OP1 A:G23 3.4 93.5 1.0
O2' A:A22 3.5 80.2 1.0
C2' A:A22 4.4 77.5 1.0
O6 A:G18 4.5 77.7 1.0
P A:G23 4.6 99.0 1.0
C3' A:A22 4.8 80.2 1.0
N7 A:G18 4.9 80.9 1.0

Magnesium binding site 3 out of 3 in 4znp

Go back to Magnesium Binding Sites List in 4znp
Magnesium binding site 3 out of 3 in the The Structure of A Pfi Riboswitch Bound to Zmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of A Pfi Riboswitch Bound to Zmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg102

b:0.5
occ:1.00
OP2 B:C31 2.0 1.0 1.0
OP1 B:U13 2.1 0.4 1.0
O5 B:AMZ101 2.5 0.6 1.0
P B:C31 3.2 1.0 1.0
C6 B:AMZ101 3.2 0.3 1.0
N2 B:AMZ101 3.3 0.8 1.0
P B:U13 3.5 0.3 1.0
C5' B:C31 3.5 0.1 1.0
O5' B:C31 3.6 0.1 1.0
OP1 B:C31 3.9 0.3 1.0
O2' B:G67 4.2 0.3 1.0
OP2 B:U13 4.3 0.9 1.0
O3' B:C12 4.4 0.2 1.0
O5' B:U13 4.4 0.0 1.0
O3' B:A30 4.5 0.6 1.0
N3 B:G67 4.6 0.5 1.0
O4' B:G14 4.6 0.5 1.0
C3A B:AMZ101 4.7 0.6 1.0
N2 B:G67 4.8 0.6 1.0

Reference:

A.Ren, K.R.Rajashankar, D.J.Patel. Global Rna Fold and Molecular Recognition For A Pfl Riboswitch Bound to Zmp, A Master Regulator of One-Carbon Metabolism. Structure V. 23 1375 2015.
ISSN: ISSN 0969-2126
PubMed: 26118534
DOI: 10.1016/J.STR.2015.05.016
Page generated: Mon Dec 14 19:57:40 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