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Manganese in PDB 7elq: Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok

Protein crystallography data

The structure of Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok, PDB code: 7elq was solved by X.C.Xu, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.472, 92.944, 40.298, 90, 90, 90
R / Rfree (%) 21.1 / 26.1

Other elements in 7elq:

The structure of Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 8 in 7elq

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Manganese binding site 1 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn103

b:50.0
occ:1.00
 O A:HOH229 2.0 42.1 1.0
O A:HOH220 2.0 54.6 1.0
O A:HOH203 2.1 49.3 1.0
OP2 A:A38 2.2 50.1 1.0
O A:HOH214 2.4 45.1 1.0
O A:HOH235 2.6 52.9 1.0
P A:A38 3.2 52.2 1.0
O5' A:A38 3.4 49.7 1.0
OP1 A:A38 4.0 55.1 1.0
N7 A:A39 4.2 54.9 1.0
C8 A:A38 4.4 55.2 1.0
C5' A:A38 4.4 51.4 1.0
N7 A:A38 4.5 55.2 1.0
OP2 A:A39 4.5 61.3 1.0
O2' A:G35 4.6 51.7 1.0
O3' A:A37 4.6 52.3 1.0
O4 A:U40 4.8 51.5 1.0
C3' A:A37 4.8 50.1 1.0
N9 A:XAN102 4.9 43.2 1.0

Manganese binding site 2 out of 8 in 7elq

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Manganese binding site 2 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn104

b:49.7
occ:1.00
 O A:HOH232 2.0 64.3 1.0
O A:HOH212 2.2 48.6 1.0
OP2 A:G7 2.3 45.7 1.0
O6 A:XAN102 2.4 46.0 1.0
O A:HOH204 2.5 50.6 1.0
O A:HOH210 2.6 52.1 1.0
O2' A:A6 2.6 55.4 1.0
C6 A:XAN102 3.6 43.2 1.0
P A:G7 3.8 50.2 1.0
N7 A:A8 3.8 50.2 1.0
O A:HOH217 4.0 47.5 1.0
C2' A:A6 4.1 51.9 1.0
O6 A:G10 4.1 53.2 1.0
O3' A:A6 4.2 51.5 1.0
N1 A:XAN102 4.4 42.8 1.0
N7 A:G7 4.4 43.9 1.0
OP2 A:A8 4.5 50.2 1.0
O5' A:G7 4.5 46.8 1.0
C8 A:A8 4.6 50.2 1.0
C5 A:XAN102 4.6 42.7 1.0
C8 A:G7 4.7 48.4 1.0
N3 A:A6 4.7 40.4 1.0
C3' A:A6 4.8 48.7 1.0
N6 A:A8 4.8 49.2 1.0
N7 A:A9 4.8 49.3 1.0
C1' A:A6 4.8 45.0 1.0
C5 A:A8 4.9 48.2 1.0
OP1 A:G7 4.9 44.3 1.0
N7 A:XAN102 4.9 41.8 1.0
O6 A:G35 4.9 47.1 1.0

Manganese binding site 3 out of 8 in 7elq

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Manganese binding site 3 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn105

b:60.4
occ:1.00
 OP1 A:G7 2.1 44.3 1.0
O A:HOH217 2.2 47.5 1.0
O A:HOH213 2.4 46.9 1.0
P A:G7 3.3 50.2 1.0
C3' A:A6 3.7 48.7 1.0
OP2 A:G7 3.9 45.7 1.0
O3' A:A6 3.9 51.5 1.0
C2' A:A6 4.0 51.9 1.0
O2' A:A6 4.3 55.4 1.0
N7 A:XAN102 4.5 41.8 1.0
OP2 A:G36 4.5 46.4 1.0
O5' A:G7 4.6 46.8 1.0
C8 A:G35 4.7 46.5 1.0
N7 A:G35 4.9 46.3 1.0

Manganese binding site 4 out of 8 in 7elq

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Manganese binding site 4 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn106

b:94.5
occ:1.00
 N7 A:G27 2.3 57.9 1.0
C8 A:G27 3.0 55.1 1.0
C5 A:G27 3.5 54.0 1.0
O A:HOH238 3.9 52.7 1.0
O6 A:G27 4.0 55.5 1.0
C6 A:G27 4.1 52.1 1.0
OP2 A:A26 4.1 54.2 1.0
N9 A:G27 4.3 53.6 1.0
C4 A:G27 4.5 52.1 1.0
OP2 A:G27 5.0 62.9 1.0

Manganese binding site 5 out of 8 in 7elq

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Manganese binding site 5 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn107

b:45.8
occ:1.00
 O A:HOH208 2.0 47.9 1.0
OP1 A:G36 2.0 51.4 1.0
O A:HOH222 2.2 45.7 1.0
OP1 A:C34 2.2 48.2 1.0
OP1 A:G35 2.5 48.3 1.0
P A:G36 3.5 47.8 1.0
O3' A:C34 3.6 49.4 1.0
P A:G35 3.6 47.4 1.0
P A:C34 3.7 38.9 1.0
O5' A:G36 4.2 47.6 1.0
O3' A:C33 4.3 44.0 1.0
O A:HOH205 4.3 39.4 1.0
C5' A:G35 4.3 50.0 1.0
O3' A:G35 4.3 47.8 1.0
C5' A:C34 4.4 40.4 1.0
OP2 A:G36 4.4 46.4 1.0
O5' A:G35 4.5 51.2 1.0
OP2 A:C34 4.5 43.3 1.0
C3' A:G35 4.5 48.6 1.0
C4' A:C34 4.6 42.9 1.0
O5' A:C34 4.6 43.0 1.0
C3' A:C34 4.6 50.8 1.0
N7 A:G36 4.6 45.8 1.0
O2' A:C33 4.8 44.9 1.0
OP2 A:G35 4.8 47.7 1.0
C8 A:G36 4.8 48.7 1.0

Manganese binding site 6 out of 8 in 7elq

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Manganese binding site 6 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn103

b:75.0
occ:1.00
 O B:HOH236 2.0 68.1 1.0
O B:HOH213 2.1 72.0 1.0
O B:HOH205 2.3 66.1 1.0
OP2 B:A38 2.4 72.5 1.0
O B:HOH206 2.6 62.3 1.0
O B:HOH203 2.6 62.5 1.0
P B:A38 3.7 74.2 1.0
O5' B:A38 3.8 73.9 1.0
N7 B:A39 4.1 65.1 1.0
O2' B:G35 4.3 65.2 1.0
N7 B:A38 4.4 69.2 1.0
C8 B:A38 4.5 69.7 1.0
OP1 B:A38 4.5 73.6 1.0
N9 B:XAN102 4.7 57.0 1.0
O4 B:U40 4.7 58.1 1.0
OP2 B:A39 4.8 65.0 1.0
O3' B:A37 4.8 71.0 1.0
N6 B:A39 4.8 59.3 1.0
C5' B:A38 4.9 71.4 1.0
C3' B:A37 4.9 69.4 1.0
OP2 B:A37 4.9 69.1 1.0
C8 B:A39 4.9 66.1 1.0

Manganese binding site 7 out of 8 in 7elq

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Manganese binding site 7 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn104

b:52.8
occ:1.00
 O B:HOH211 2.1 53.8 1.0
O B:HOH218 2.2 51.0 1.0
N7 B:G23 2.2 46.6 1.0
O B:HOH234 2.2 57.4 1.0
O B:HOH201 2.5 48.0 1.0
C8 B:G23 3.1 45.1 1.0
C5 B:G23 3.2 46.3 1.0
O6 B:G23 3.6 55.0 1.0
C6 B:G23 3.8 47.0 1.0
C5 B:C22 4.1 45.5 1.0
N9 B:G23 4.3 43.5 1.0
C4 B:G23 4.4 44.8 1.0
O B:HOH227 4.5 50.5 1.0
C4 B:C22 4.6 44.6 1.0
C6 B:C22 4.6 45.7 1.0
OP2 B:G23 4.7 43.7 1.0
N4 B:C22 4.7 44.9 1.0
OP2 B:C22 4.7 49.7 1.0

Manganese binding site 8 out of 8 in 7elq

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Manganese binding site 8 out of 8 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Manganese Saok


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 Xanthine Riboswitch with Xanthine, Manganese Saok within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn105

b:52.5
occ:1.00
 OP2 B:A24 2.3 46.5 1.0
O B:HOH231 2.6 49.9 1.0
O B:HOH227 2.7 50.5 1.0
P B:A24 3.2 52.8 1.0
OP1 B:A24 3.3 49.6 1.0
O5' B:A24 4.3 41.6 1.0
C5' B:A24 4.3 49.0 1.0
O3' B:G23 4.4 50.4 1.0
OP1 B:G23 4.7 53.1 1.0
O5' B:G23 4.8 44.5 1.0
C3' B:G23 4.9 45.1 1.0

Reference:

X.Xu, M.Egger, H.Chen, K.Bartosik, R.Micura, A.Ren. Insights Into Xanthine Riboswitch Structure and Metal Ion-Mediated Ligand Recognition. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34125892
DOI: 10.1093/NAR/GKAB486
Page generated: Sun Oct 6 08:30:58 2024

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