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Magnesium in PDB 3f2w: Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.

Protein crystallography data

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak., PDB code: 3f2w was solved by A.A.Serganov, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.003, 71.003, 139.745, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 21.7

Other elements in 3f2w:

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. also contains other interesting chemical elements:

Barium (Ba) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. (pdb code 3f2w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak., PDB code: 3f2w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 1 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg302

b:0.3
occ:1.00
N7 X:G19 4.0 0.9 1.0
OP1 X:A21 4.7 0.8 1.0
BA X:BA406 4.7 0.9 0.6
C8 X:G19 4.7 0.1 1.0
OP2 X:A21 4.8 0.7 1.0
C5 X:G19 5.0 0.0 1.0
O6 X:G19 5.0 0.2 1.0

Magnesium binding site 2 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 2 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg309

b:89.8
occ:1.00
O6 X:G68 3.6 0.0 1.0
O6 X:G67 4.5 0.9 1.0
N7 X:G67 4.5 0.1 1.0
C6 X:G68 4.7 0.4 1.0
C4' X:U74 4.8 0.3 1.0
OP2 X:U75 4.8 0.2 1.0
N7 X:G68 5.0 0.3 1.0

Magnesium binding site 3 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 3 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg311

b:84.5
occ:1.00
O6 X:G41 3.6 0.6 1.0
O6 X:G32 3.8 0.5 1.0
N7 X:G32 4.1 0.8 1.0
C6 X:G41 4.6 0.3 1.0
C6 X:G32 4.6 0.4 1.0
C5 X:C31 4.7 0.2 1.0
C5 X:G32 4.8 0.5 1.0
N4 X:C82 4.8 0.8 1.0
N4 X:C31 4.8 0.8 1.0
N7 X:G41 4.9 0.6 1.0
C4 X:C31 5.0 0.1 1.0

Magnesium binding site 4 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 4 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg313

b:0.0
occ:1.00
N3 X:A14 4.1 0.9 1.0
O2' X:A29 4.3 0.2 1.0
O3' X:A29 4.4 0.1 1.0
C2 X:A14 4.4 0.8 1.0
C4 X:A14 4.9 1.0 1.0
OP1 X:C30 4.9 0.7 1.0

Magnesium binding site 5 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 5 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg314

b:0.6
occ:1.00
OP1 X:U6 4.6 0.8 1.0

Magnesium binding site 6 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 6 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg315

b:0.1
occ:1.00
OP1 X:U65 4.5 0.6 1.0
OP1 X:C43 4.7 0.1 1.0
OP2 X:U65 4.8 0.7 1.0
C5' X:C43 4.9 0.7 1.0

Magnesium binding site 7 out of 7 in 3f2w

Go back to Magnesium Binding Sites List in 3f2w
Magnesium binding site 7 out of 7 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, BA2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg316

b:0.4
occ:1.00
OP1 X:G91 3.0 0.3 1.0
OP2 X:A90 4.0 0.6 1.0
P X:G91 4.5 0.0 1.0

Reference:

A.Serganov, L.Huang, D.J.Patel. Coenzyme Recognition and Gene Regulation By A Flavin Mononucleotide Riboswitch. Nature V. 458 233 2009.
ISSN: ISSN 0028-0836
PubMed: 19169240
DOI: 10.1038/NATURE07642
Page generated: Mon Dec 14 08:07:40 2020

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