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Manganese in PDB 3f2y: Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.

Protein crystallography data

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak., PDB code: 3f2y 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 / 3.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.988, 70.988, 140.004, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 23.7

Other elements in 3f2y:

The structure of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. also contains other interesting chemical elements:

Magnesium (Mg) 11 atoms
Potassium (K) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. (pdb code 3f2y). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak., PDB code: 3f2y:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3f2y

Go back to Manganese Binding Sites List in 3f2y
Manganese binding site 1 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn401

b:0.3
occ:0.50
N7 X:G19 3.6 0.5 1.0
C8 X:G19 4.2 0.6 1.0
OP2 X:G19 4.3 0.6 1.0
C5 X:G19 4.7 0.5 1.0
OP2 X:U18 4.8 0.3 1.0
O6 X:G19 5.0 0.8 1.0

Manganese binding site 2 out of 4 in 3f2y

Go back to Manganese Binding Sites List in 3f2y
Manganese binding site 2 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn402

b:0.2
occ:1.00
N7 X:G93 2.6 95.6 1.0
C8 X:G93 3.4 95.4 1.0
C5 X:G93 3.8 95.5 1.0
O6 X:G93 4.1 95.2 1.0
OP1 X:G93 4.1 94.7 1.0
O4 X:U94 4.3 90.5 1.0
C6 X:G93 4.3 95.6 1.0
N7 X:G84 4.5 93.2 1.0
N9 X:G93 4.7 94.9 1.0
C4 X:G93 4.9 95.3 1.0
MG X:MG310 5.0 0.4 1.0

Manganese binding site 3 out of 4 in 3f2y

Go back to Manganese Binding Sites List in 3f2y
Manganese binding site 3 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn403

b:0.9
occ:1.00
OP2 X:A92 2.1 88.7 1.0
O4 X:U89 2.1 0.6 1.0
C4 X:U89 3.3 0.6 1.0
P X:A92 3.5 89.2 1.0
C5 X:U89 4.0 0.1 1.0
N7 X:G88 4.0 1.0 1.0
O6 X:G88 4.2 0.4 1.0
OP1 X:A92 4.2 89.1 1.0
O5' X:A92 4.3 90.1 1.0
N3 X:U89 4.4 0.7 1.0
O3' X:G91 4.5 88.0 1.0
C5' X:G91 4.6 88.9 1.0
C8 X:A92 4.7 92.6 1.0
C3' X:G91 4.7 87.0 1.0
C4' X:G91 4.7 87.2 1.0
C5 X:G88 4.8 0.8 1.0
C6 X:G88 4.8 0.0 1.0

Manganese binding site 4 out of 4 in 3f2y

Go back to Manganese Binding Sites List in 3f2y
Manganese binding site 4 out of 4 in the Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Fmn Riboswitch Bound to Fmn, MN2+ Soak. within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn404

b:85.2
occ:1.00
N7 X:G33 2.3 0.4 1.0
O1P X:FMN200 2.4 78.1 1.0
C8 X:G33 3.2 0.5 1.0
O3P X:FMN200 3.3 78.3 1.0
C5 X:G33 3.4 0.3 1.0
P X:FMN200 3.4 78.1 1.0
O6 X:G33 3.6 0.7 1.0
O2' X:G41 3.9 99.2 1.0
C6 X:G33 3.9 0.4 1.0
O4' X:G41 4.2 99.4 1.0
OP2 X:G33 4.3 0.0 1.0
O6 X:G62 4.3 0.5 1.0
N1 X:G10 4.3 0.5 1.0
N2 X:G10 4.3 0.5 1.0
C4' X:G41 4.3 99.3 1.0
O5' X:FMN200 4.4 79.5 1.0
N9 X:G33 4.5 0.5 1.0
O2P X:FMN200 4.6 79.0 1.0
C4 X:G33 4.6 0.2 1.0
N1 X:G62 4.7 0.1 1.0
C1' X:G41 4.7 99.2 1.0
C2 X:G10 4.8 0.4 1.0
C2' X:G41 4.8 99.2 1.0
C6 X:G62 5.0 0.2 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: Sat Oct 5 16:15:20 2024

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