Atomistry » Manganese » PDB 2feu-2hr6 » 2hoj
Atomistry »
  Manganese »
    PDB 2feu-2hr6 »
      2hoj »

Manganese in PDB 2hoj: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions

Protein crystallography data

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions, PDB code: 2hoj was solved by T.E.Edwards, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 64.700, 64.700, 101.900, 90.00, 90.00, 120.00
R / Rfree (%) 22.9 / 25.7

Other elements in 2hoj:

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions (pdb code 2hoj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions, PDB code: 2hoj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 1 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn115

b:36.0
occ:1.00
O1B A:TPP114 1.9 65.8 1.0
O A:HOH113 1.9 79.0 1.0
O2A A:TPP114 2.1 67.4 1.0
O A:HOH112 2.2 21.3 1.0
O A:HOH109 2.4 26.2 1.0
O A:HOH104 2.5 28.0 1.0
PB A:TPP114 2.9 58.8 1.0
O3B A:TPP114 3.0 59.0 1.0
PA A:TPP114 3.4 63.0 1.0
O1A A:TPP114 3.7 67.8 1.0
O3A A:TPP114 3.8 65.3 1.0
N4 A:C77 4.2 51.2 1.0
O2B A:TPP114 4.2 59.0 1.0
N7 A:A75 4.3 46.9 1.0
O7 A:TPP114 4.7 65.9 1.0
N7 A:G76 4.8 47.2 1.0
N6 A:A75 4.8 48.9 1.0
OP2 A:A75 4.9 43.9 1.0
O A:HOH101 4.9 11.5 1.0
O6 A:G76 4.9 44.5 1.0
C5 A:A75 5.0 47.3 1.0

Manganese binding site 2 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 2 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn116

b:31.5
occ:1.00
O A:HOH103 2.0 29.5 1.0
O A:HOH105 2.1 14.7 1.0
O6 A:G60 2.2 34.7 1.0
O A:HOH101 2.2 11.5 1.0
O2B A:TPP114 2.3 59.0 1.0
O6 A:G78 2.5 31.9 1.0
C6 A:G60 3.3 34.2 1.0
C6 A:G78 3.4 35.8 1.0
PB A:TPP114 3.4 58.8 1.0
O4 A:U59 3.6 33.9 1.0
N1 A:G78 3.7 32.1 1.0
N1 A:G60 3.7 33.5 1.0
O1B A:TPP114 3.8 65.8 1.0
O3A A:TPP114 3.8 65.3 1.0
N1 A:A61 4.0 37.7 1.0
N3 A:C77 4.3 45.9 1.0
C2 A:A61 4.3 34.8 1.0
C4 A:U59 4.4 39.8 1.0
O A:HOH109 4.5 26.2 1.0
C5 A:G60 4.5 36.0 1.0
O1A A:TPP114 4.7 67.8 1.0
O3B A:TPP114 4.7 59.0 1.0
C5 A:G78 4.8 39.3 1.0
N4 A:C77 4.8 51.2 1.0
PA A:TPP114 4.9 63.0 1.0
O2 A:C77 5.0 47.5 1.0
C5 A:U59 5.0 37.9 1.0
C2 A:G78 5.0 33.4 1.0

Manganese binding site 3 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 3 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn117

b:35.6
occ:1.00
OP1 A:C63 1.9 33.7 1.0
O A:HOH107 2.1 50.9 1.0
OP2 A:U64 2.2 34.9 1.0
P A:C63 3.4 32.4 1.0
P A:U64 3.5 29.6 1.0
O3' A:C63 4.1 31.6 1.0
O3' A:U62 4.1 33.6 1.0
O5' A:C63 4.2 35.5 1.0
OP1 A:U64 4.2 29.2 1.0
OP2 A:C63 4.3 33.2 1.0
C3' A:C63 4.5 32.9 1.0
O5' A:U64 4.6 31.4 1.0

Manganese binding site 4 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 4 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn118

b:43.0
occ:1.00
N7 A:A41 2.3 27.7 1.0
O A:HOH96 2.5 19.9 1.0
C8 A:A41 3.2 26.4 1.0
C5 A:A41 3.4 24.5 1.0
N6 A:A41 3.7 22.5 1.0
C6 A:A41 4.0 23.4 1.0
O2' A:G40 4.2 27.6 1.0
O6 A:G42 4.3 29.3 1.0
N9 A:A41 4.5 28.8 1.0
C4 A:A41 4.6 27.8 1.0
C6 A:G42 5.0 28.8 1.0

Manganese binding site 5 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 5 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn119

b:49.8
occ:1.00
O A:HOH111 1.8 39.1 1.0
N7 A:G40 2.4 32.1 1.0
O A:HOH93 2.8 26.8 1.0
C8 A:G40 3.2 32.9 1.0
O A:HOH94 3.3 28.2 1.0
C5 A:G40 3.6 29.9 1.0
O6 A:G40 4.0 27.3 1.0
OP2 A:G40 4.2 35.2 1.0
C6 A:G40 4.2 29.1 1.0
N9 A:G40 4.5 30.8 1.0
OP2 A:U39 4.6 25.7 1.0
OP2 A:G42 4.7 30.4 1.0
C4 A:G40 4.7 28.5 1.0
C5 A:U39 4.7 29.9 1.0

Manganese binding site 6 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 6 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn120

b:83.7
occ:1.00
OP2 A:A80 3.0 71.6 1.0
N7 A:G81 3.5 50.7 1.0
OP2 A:G81 4.1 63.9 1.0
P A:A80 4.2 72.3 1.0
N7 A:G82 4.2 44.3 1.0
O6 A:G81 4.3 48.1 1.0
C8 A:G81 4.3 52.9 1.0
OP1 A:A80 4.4 71.5 1.0
O6 A:G83 4.4 52.8 1.0
C5 A:G81 4.4 51.4 1.0
C6 A:G81 4.7 50.6 1.0
O6 A:G82 4.7 53.5 1.0
N7 A:A80 4.9 60.0 1.0
O3' A:U79 5.0 70.8 1.0

Manganese binding site 7 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 7 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn121

b:92.3
occ:1.00
N7 A:G36 2.3 40.0 1.0
C8 A:G36 3.1 40.5 1.0
O A:HOH97 3.4 35.4 1.0
C5 A:G36 3.5 38.0 1.0
O6 A:G36 3.9 41.7 1.0
C6 A:G36 4.1 38.9 1.0
OP2 A:G36 4.1 50.7 1.0
OP2 A:A35 4.2 79.2 1.0
N9 A:G36 4.4 38.2 1.0
C4 A:G36 4.5 36.8 1.0
N7 A:A35 4.6 54.6 1.0
C8 A:A35 4.7 57.1 1.0
O5' A:A35 4.9 74.7 1.0
OP2 A:A34 4.9 85.3 1.0
O5' A:G36 4.9 48.9 1.0

Manganese binding site 8 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 8 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn122

b:1.0
occ:1.00
OP1 A:A69 2.2 45.0 1.0
P A:A69 3.5 39.9 1.0
O5' A:A69 4.0 41.2 1.0
C5' A:A69 4.1 39.7 1.0
OP2 A:A69 4.2 44.0 1.0
O3' A:U68 4.6 42.5 1.0
O4' A:A69 4.7 38.9 1.0
C8 A:A69 4.9 38.1 1.0

Manganese binding site 9 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 9 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn123

b:87.4
occ:1.00
N7 A:G66 3.7 42.0 1.0
O6 A:G66 3.9 49.2 1.0
N6 A:A67 4.2 43.6 1.0
C5 A:G66 4.5 46.9 1.0
N7 A:A67 4.5 49.4 1.0
C6 A:G66 4.6 46.5 1.0
C8 A:G66 4.8 45.7 1.0
N7 A:G65 5.0 49.9 1.0

Manganese binding site 10 out of 12 in 2hoj

Go back to Manganese Binding Sites List in 2hoj
Manganese binding site 10 out of 12 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn124

b:75.2
occ:1.00
OP2 A:A2391 2.3 41.7 1.0
P A:A2391 3.7 38.3 1.0
O3' A:C90 4.3 37.0 1.0
OP1 A:A2391 4.6 40.1 1.0
O5' A:A2391 4.7 41.1 1.0
C3' A:A2391 4.7 52.8 1.0
C2' A:A2391 4.8 54.1 1.0

Reference:

T.E.Edwards, A.R.Ferre-D'amare. Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive Rna-Small Molecule Recognition Structure V. 14 1459 2006.
ISSN: ISSN 0969-2126
PubMed: 16962976
DOI: 10.1016/J.STR.2006.07.008
Page generated: Tue Dec 15 04:02:29 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