Atomistry » Manganese » PDB 3vrs-3x2x » 3vrs
Atomistry »
  Manganese »
    PDB 3vrs-3x2x »
      3vrs »

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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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

Go back to Manganese Binding Sites List in 3vrs
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: Tue Dec 15 04:16:52 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