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Magnesium in PDB 4y1m: An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State

Protein crystallography data

The structure of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State, PDB code: 4y1m was solved by I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 123.60 / 3.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 159.384, 159.384, 277.108, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.2

Other elements in 4y1m:

The structure of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State also contains other interesting chemical elements:

Strontium (Sr) 65 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State (pdb code 4y1m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State, PDB code: 4y1m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4y1m

Go back to Magnesium Binding Sites List in 4y1m
Magnesium binding site 1 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg211

b:0.5
occ:1.00
 O B:HOH325 2.1 0.1 1.0
OP2 B:C77 3.1 0.0 1.0
OP1 B:A76 3.7 0.0 1.0
OP1 B:C77 3.9 0.0 1.0
P B:C77 3.9 0.2 1.0
O5' B:A76 4.4 0.2 1.0
P B:A76 4.5 0.5 1.0
C5' B:A76 4.6 0.8 1.0
O3' B:A76 4.6 0.7 1.0

Magnesium binding site 2 out of 9 in 4y1m

Go back to Magnesium Binding Sites List in 4y1m
Magnesium binding site 2 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg246

b:0.5
occ:1.00
 O2' B:A27 4.1 0.9 1.0

Magnesium binding site 3 out of 9 in 4y1m

Go back to Magnesium Binding Sites List in 4y1m
Magnesium binding site 3 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg247

b:0.9
occ:1.00
 OP1 B:A100 4.9 0.0 1.0

Magnesium binding site 4 out of 9 in 4y1m

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Magnesium binding site 4 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg248

b:0.3
occ:1.00
 OP1 B:U5 4.7 1.0 1.0

Magnesium binding site 5 out of 9 in 4y1m

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Magnesium binding site 5 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg249

b:0.3
occ:1.00
 O B:HOH358 3.7 0.1 1.0
OP1 B:U54 3.7 0.5 1.0
OP2 B:U55 4.3 93.9 1.0
P B:U54 4.9 0.2 1.0
OP1 B:U55 5.0 0.2 1.0

Magnesium binding site 6 out of 9 in 4y1m

Go back to Magnesium Binding Sites List in 4y1m
Magnesium binding site 6 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:0.7
occ:1.00
 OP1 A:G63 4.0 0.6 1.0
OP1 A:G39 4.0 0.0 1.0

Magnesium binding site 7 out of 9 in 4y1m

Go back to Magnesium Binding Sites List in 4y1m
Magnesium binding site 7 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg225

b:0.9
occ:1.00
 OP2 A:U64 2.2 0.4 1.0
P A:U64 3.3 0.1 1.0
OP1 A:U64 3.7 0.3 1.0
O3' A:G63 4.2 0.1 1.0
O5' A:U64 4.5 0.2 1.0
O5' A:G63 4.5 0.6 1.0
C3' A:G63 4.6 0.4 1.0
OP1 A:G63 4.7 0.6 1.0
OP2 A:G39 4.8 0.7 1.0

Magnesium binding site 8 out of 9 in 4y1m

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Magnesium binding site 8 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:

Magnesium binding site 9 out of 9 in 4y1m

Go back to Magnesium Binding Sites List in 4y1m
Magnesium binding site 9 out of 9 in the An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of An Escherichia Coli Yybp-Ykoy Mn Riboswitch in the MN2+-Free State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg227

b:0.9
occ:1.00
 N2 A:G35 3.9 0.6 1.0
C2 A:G35 4.9 1.0 1.0

Reference:

I.R.Price, A.Gaballa, F.Ding, J.D.Helmann, A.Ke. Mn(2+)-Sensing Mechanisms of Yybp-Ykoy Orphan Riboswitches. Mol.Cell V. 57 1110 2015.
ISSN: ISSN 1097-2765
PubMed: 25794619
DOI: 10.1016/J.MOLCEL.2015.02.016
Page generated: Tue Aug 20 16:06:19 2024

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