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Manganese in PDB 3vrs: Crystal Structure of Fluoride Riboswitch, Soaked in MN2+

Protein crystallography data

The structure of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+, PDB code: 3vrs was solved by A.M.Ren, K.R.Rajashankar, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.78 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.846, 77.203, 42.094, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.2

Other elements in 3vrs:

The structure of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ also contains other interesting chemical elements:

Fluorine (F) 1 atom
Potassium (K) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ (pdb code 3vrs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+, PDB code: 3vrs:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 3vrs

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Manganese binding site 1 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


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 Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn101

b:49.0
occ:1.00
 OP2 A:U7 1.9 51.2 1.0
OP2 A:A6 2.1 48.0 1.0
OP1 A:U41 2.1 50.6 1.0
F A:F111 2.2 46.2 1.0
OP2 A:G42 2.2 54.7 1.0
O A:HOH204 2.2 49.2 1.0
P A:U7 3.2 44.2 1.0
P A:G42 3.2 56.6 1.0
P A:A6 3.3 47.3 1.0
O A:HOH201 3.4 48.4 1.0
OP1 A:G42 3.5 53.7 1.0
P A:U41 3.5 49.5 1.0
OP1 A:U7 3.7 42.5 1.0
MN A:MN102 3.7 49.9 1.0
OP1 A:A6 3.7 49.4 1.0
MN A:MN103 3.7 43.8 1.0
O3' A:A6 3.9 50.3 1.0
O5' A:U41 4.0 49.6 1.0
C5' A:U41 4.1 55.4 1.0
O3' A:U41 4.1 53.2 1.0
C3' A:A6 4.1 52.7 1.0
O3' A:G5 4.3 57.9 1.0
O5' A:U7 4.4 51.8 1.0
O5' A:A6 4.4 57.7 1.0
OP2 A:U41 4.4 58.2 1.0
N2 A:G39 4.5 50.5 1.0
O3' A:A40 4.5 51.0 1.0
O5' A:G42 4.5 67.7 1.0
C3' A:U41 4.6 55.6 1.0
C5' A:A6 4.7 54.4 1.0
O A:HOH211 4.8 42.4 1.0
C5' A:G42 4.8 60.1 1.0
C4' A:U41 4.9 58.3 1.0
O A:HOH203 4.9 39.4 1.0

Manganese binding site 2 out of 9 in 3vrs

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Manganese binding site 2 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


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 Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn102

b:49.9
occ:1.00
 OP1 A:A6 2.1 49.4 1.0
F A:F111 2.1 46.2 1.0
O A:HOH213 2.2 51.7 1.0
O A:HOH202 2.2 46.8 1.0
OP1 A:G42 2.2 53.7 1.0
O A:HOH211 2.3 42.4 1.0
P A:A6 3.2 47.3 1.0
MN A:MN103 3.3 43.8 1.0
P A:G42 3.4 56.6 1.0
OP2 A:A6 3.6 48.0 1.0
MN A:MN101 3.7 49.0 1.0
O A:HOH203 3.8 39.4 1.0
O3' A:U41 3.8 53.2 1.0
O A:HOH217 3.8 58.7 1.0
O3' A:G5 3.9 57.9 1.0
OP1 A:U7 3.9 42.5 1.0
OP2 A:G42 4.0 54.7 1.0
K A:K110 4.0 67.6 1.0
C3' A:G5 4.0 59.6 1.0
O5' A:G5 4.1 54.1 1.0
OP2 A:G5 4.4 54.5 1.0
O5' A:A6 4.5 57.7 1.0
P A:G5 4.6 53.2 1.0
OP2 A:U7 4.6 51.2 1.0
OP1 A:G5 4.6 64.8 1.0
P A:U7 4.7 44.2 1.0
O5' A:G42 4.7 67.7 1.0
C5' A:G5 4.8 54.5 1.0
O A:HOH201 4.9 48.4 1.0
C4' A:G5 5.0 60.0 1.0

Manganese binding site 3 out of 9 in 3vrs

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Manganese binding site 3 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


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 Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn103

b:43.8
occ:1.00
 OP2 A:G8 1.9 52.2 1.0
OP1 A:U7 2.0 42.5 1.0
O A:HOH201 2.2 48.4 1.0
O A:HOH203 2.2 39.4 1.0
F A:F111 2.3 46.2 1.0
O A:HOH211 2.3 42.4 1.0
P A:U7 3.1 44.2 1.0
P A:G8 3.2 50.9 1.0
MN A:MN102 3.3 49.9 1.0
OP2 A:U7 3.4 51.2 1.0
O A:HOH213 3.6 51.7 1.0
MN A:MN101 3.7 49.0 1.0
OP1 A:G8 3.8 50.0 1.0
O3' A:U7 3.8 48.7 1.0
O A:HOH217 3.8 58.7 1.0
K A:K110 3.9 67.6 1.0
C3' A:U7 3.9 45.1 1.0
O5' A:U7 4.0 51.8 1.0
OP1 A:U41 4.2 50.6 1.0
OP1 A:A6 4.2 49.4 1.0
O3' A:A6 4.4 50.3 1.0
O5' A:G8 4.4 55.8 1.0
C5' A:U7 4.6 47.5 1.0
C5' A:U41 4.7 55.4 1.0
OP2 A:A6 4.7 48.0 1.0
O2' A:A40 4.7 49.7 1.0
C4' A:U7 4.9 50.3 1.0
OP1 A:G42 4.9 53.7 1.0
O3' A:A40 5.0 51.0 1.0
P A:A6 5.0 47.3 1.0

Manganese binding site 4 out of 9 in 3vrs

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Manganese binding site 4 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


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 Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn104

b:99.0
occ:1.00
 O A:HOH215 2.3 65.6 1.0
O A:HOH218 2.3 71.6 1.0
N7 A:G2 2.4 67.0 1.0
C8 A:G2 3.2 67.7 1.0
O A:HOH216 3.2 61.8 1.0
O A:HOH214 3.5 59.2 1.0
C5 A:G2 3.5 64.3 1.0
OP2 A:G2 3.8 75.2 1.0
O6 A:G2 3.9 66.4 1.0
O A:HOH207 4.0 62.3 1.0
C6 A:G2 4.1 63.4 1.0
N9 A:G2 4.5 65.1 1.0
O3' A:G1 4.6 77.4 1.0
C4 A:G2 4.6 61.9 1.0
C5' A:G1 4.7 77.5 1.0
P A:G2 4.8 80.5 1.0

Manganese binding site 5 out of 9 in 3vrs

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Manganese binding site 5 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn105

b:63.3
occ:1.00
 OP2 A:A40 2.1 51.6 1.0
O A:HOH210 2.2 56.9 1.0
O A:HOH209 2.2 63.6 1.0
O A:HOH205 2.3 45.5 1.0
O A:HOH206 2.3 52.1 1.0
P A:A40 3.2 53.1 1.0
O5' A:A40 3.3 55.3 1.0
O2 A:C50 3.8 63.5 1.0
O4 A:U7 4.1 52.3 1.0
OP1 A:A40 4.2 58.0 1.0
O3' A:G39 4.3 55.4 1.0
N3 A:C50 4.4 65.5 1.0
N1 A:A49 4.4 55.8 1.0
C3' A:G39 4.4 58.1 1.0
C2 A:C50 4.6 64.2 1.0
C5' A:A40 4.7 49.4 1.0
O4' A:A40 4.8 50.9 1.0
N6 A:A49 4.8 55.2 1.0
O5' A:G39 4.9 62.8 1.0

Manganese binding site 6 out of 9 in 3vrs

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Manganese binding site 6 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn106

b:84.2
occ:1.00
 N7 A:G24 2.7 55.8 1.0
O6 A:G24 3.3 55.4 1.0
C5 A:G24 3.5 52.2 1.0
C8 A:G24 3.7 56.2 1.0
C6 A:G24 3.8 55.1 1.0
N3 A:A6 4.5 52.0 1.0
C4 A:G24 4.8 54.0 1.0
N9 A:G24 4.8 56.5 1.0
C2 A:A6 4.9 51.2 1.0
N4 A:C25 4.9 55.2 1.0

Manganese binding site 7 out of 9 in 3vrs

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Manganese binding site 7 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn107

b:91.1
occ:1.00
 N7 A:G35 2.6 58.4 1.0
C8 A:G35 3.3 58.4 1.0
C5 A:G35 3.7 58.3 1.0
N7 A:G34 3.8 59.0 1.0
C5 A:G34 4.1 59.2 1.0
O6 A:G35 4.2 57.6 1.0
OP2 A:G35 4.2 64.7 1.0
C8 A:G34 4.3 62.4 1.0
C6 A:G35 4.3 57.8 1.0
C6 A:G34 4.4 60.0 1.0
O6 A:G34 4.5 62.7 1.0
N9 A:G35 4.6 60.1 1.0
C4 A:G34 4.8 60.7 1.0
C4 A:G35 4.8 59.9 1.0
N9 A:G34 4.9 65.6 1.0

Manganese binding site 8 out of 9 in 3vrs

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Manganese binding site 8 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn108

b:0.1
occ:1.00
 O6 A:G29 2.9 70.7 1.0
N7 A:G29 3.1 60.6 1.0
C6 A:G29 3.5 63.1 1.0
C5 A:G29 3.6 61.7 1.0
MN A:MN109 4.0 0.9 1.0
C8 A:G29 4.3 60.9 1.0
N1 A:G29 4.7 61.3 1.0
O4 A:U28 4.7 58.4 1.0
OP1 A:A31 4.7 74.0 1.0
C4 A:G29 4.8 62.4 1.0
C5 A:U28 4.9 56.2 1.0
OP2 A:A31 5.0 62.4 1.0
C4 A:U28 5.0 58.4 1.0

Manganese binding site 9 out of 9 in 3vrs

Go back to Manganese Binding Sites List in 3vrs
Manganese binding site 9 out of 9 in the Crystal Structure of Fluoride Riboswitch, Soaked in MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Fluoride Riboswitch, Soaked in MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn109

b:0.9
occ:1.00
 OP2 A:G29 2.7 68.4 1.0
O5' A:G29 3.6 59.5 1.0
C8 A:G29 3.7 60.9 1.0
OP2 A:A30 3.7 58.3 1.0
P A:G29 3.7 68.1 1.0
N7 A:G29 3.8 60.6 1.0
MN A:MN108 4.0 0.1 1.0
C3' A:G29 4.7 58.4 1.0
OP1 A:G29 4.8 66.2 1.0
C3' A:U28 4.8 60.9 1.0
N9 A:G29 4.8 61.2 1.0
O3' A:U28 4.8 59.7 1.0
OP2 A:U28 4.9 62.4 1.0
C5' A:G29 4.9 56.9 1.0
O5' A:U28 4.9 60.6 1.0
C5 A:G29 5.0 61.7 1.0
P A:A30 5.0 64.4 1.0

Reference:

A.Ren, K.R.Rajashankar, D.J.Patel. Fluoride Ion Encapsulation By MG2+ Ions and Phosphates in A Fluoride Riboswitch. Nature V. 486 85 2012.
ISSN: ISSN 0028-0836
PubMed: 22678284
DOI: 10.1038/NATURE11152
Page generated: Sat Oct 5 18:25:05 2024

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