Magnesium in PDB 7elp: Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak

Protein crystallography data

The structure of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak, PDB code: 7elp 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) 39.73 / 2.79
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.465, 100.192, 40.267, 90, 90, 90
R / Rfree (%) 21.5 / 27.4

Other elements in 7elp:

The structure of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak also contains other interesting chemical elements:

Iridium (Ir) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak (pdb code 7elp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak, PDB code: 7elp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 7elp

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Magnesium binding site 1 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:61.7
occ:1.00
O A:HOH204 1.8 74.9 1.0
O A:HOH210 1.9 66.3 1.0
OP2 A:G7 1.9 70.7 1.0
O A:HOH216 2.1 80.8 1.0
O6 A:XAN104 2.1 74.3 1.0
O A:HOH214 2.5 75.5 1.0
C6 A:XAN104 3.4 68.3 1.0
P A:G7 3.4 73.1 1.0
N7 A:A8 3.6 78.6 1.0
O A:HOH211 3.8 67.2 1.0
O2' A:A6 4.0 69.0 1.0
O5' A:G7 4.0 70.5 1.0
O3' A:A6 4.1 72.1 1.0
N1 A:XAN104 4.3 67.4 1.0
O6 A:G35 4.3 74.9 1.0
O6 A:G10 4.3 77.2 1.0
N3 A:A6 4.3 70.1 1.0
C5 A:XAN104 4.4 65.1 1.0
OP2 A:A8 4.4 79.9 1.0
N6 A:A8 4.4 77.4 1.0
OP1 A:G7 4.4 69.0 1.0
C8 A:A8 4.5 79.9 1.0
N7 A:XAN104 4.6 68.1 1.0
N7 A:G35 4.7 67.8 1.0
C5 A:A8 4.7 77.9 1.0
N7 A:G7 4.7 73.3 1.0
C8 A:G7 4.7 75.3 1.0
O A:HOH226 4.7 74.9 1.0
C1' A:A6 4.8 67.8 1.0
C2' A:A6 4.8 67.1 1.0
C6 A:G35 4.9 70.4 1.0

Magnesium binding site 2 out of 16 in 7elp

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Magnesium binding site 2 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:70.5
occ:1.00
O A:HOH213 1.9 76.3 1.0
O A:HOH220 1.9 64.9 1.0
OP2 A:A38 2.0 72.4 1.0
O A:HOH227 2.2 66.6 1.0
O A:HOH223 2.3 70.5 1.0
O A:HOH206 2.3 71.7 1.0
P A:A38 3.3 82.5 1.0
O5' A:A38 3.6 77.3 1.0
C8 A:A38 3.9 76.9 1.0
N7 A:A38 3.9 74.1 1.0
O2' A:G35 4.1 63.0 1.0
N7 A:A39 4.2 78.1 1.0
OP1 A:A38 4.3 81.3 1.0
O3' A:A37 4.3 71.0 1.0
C3' A:A37 4.3 71.5 1.0
OP2 A:A39 4.8 89.7 1.0
O5' A:A37 4.9 65.9 1.0
C8 A:A39 4.9 81.8 1.0
C5' A:A38 5.0 72.6 1.0
N9 A:XAN104 5.0 70.4 1.0

Magnesium binding site 3 out of 16 in 7elp

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Magnesium binding site 3 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg107

b:54.9
occ:1.00
O A:HOH203 1.7 60.6 1.0
OP1 A:C34 2.1 67.5 1.0
OP1 A:G36 2.2 65.6 1.0
O A:HOH221 2.3 57.4 1.0
P A:C34 3.4 70.2 1.0
P A:G36 3.5 65.7 1.0
O5' A:G35 3.8 65.5 1.0
O A:HOH215 3.9 60.1 1.0
OP2 A:C34 4.0 70.2 1.0
OP1 A:G35 4.0 62.5 1.0
O5' A:G36 4.1 64.4 1.0
OP2 A:G36 4.3 62.0 1.0
O2' A:C33 4.4 64.7 1.0
O5' A:C34 4.5 66.5 1.0
C5' A:C34 4.5 67.1 1.0
O3' A:C33 4.5 68.6 1.0
P A:G35 4.5 71.1 1.0
O3' A:G35 4.7 63.9 1.0
O3' A:C34 4.8 68.1 1.0
C2' A:C33 4.8 66.4 1.0
C5' A:G35 4.8 63.5 1.0
C8 A:G36 4.9 64.6 1.0
N7 A:G36 4.9 61.2 1.0
C3' A:G35 5.0 67.2 1.0
C5' A:G36 5.0 69.6 1.0

Magnesium binding site 4 out of 16 in 7elp

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Magnesium binding site 4 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg108

b:65.4
occ:1.00
OP1 A:G7 2.0 69.0 1.0
O A:HOH211 2.1 67.2 1.0
O2' A:A6 2.5 69.0 1.0
P A:G7 3.2 73.1 1.0
C2' A:A6 3.2 67.1 1.0
C3' A:A6 3.4 66.5 1.0
O3' A:A6 3.8 72.1 1.0
OP2 A:G7 3.8 70.7 1.0
N7 A:XAN104 4.1 68.1 1.0
C8 A:G35 4.3 66.9 1.0
N7 A:G35 4.4 67.8 1.0
O5' A:G7 4.4 70.5 1.0
C1' A:A6 4.6 67.8 1.0
C8 A:XAN104 4.7 68.3 1.0
OP2 A:G36 4.8 62.0 1.0
C4' A:A6 4.9 68.1 1.0

Magnesium binding site 5 out of 16 in 7elp

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Magnesium binding site 5 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg109

b:96.4
occ:1.00
O A:HOH205 2.0 102.5 1.0
O A:HOH230 2.3 100.5 1.0
O A:HOH240 2.4 101.9 1.0
O A:HOH235 2.7 95.5 1.0
O A:HOH234 2.8 108.4 1.0
OP1 A:C15 3.9 103.4 1.0
OP1 A:C29 4.0 88.8 1.0
OP2 A:C29 4.2 78.0 1.0
P A:C29 4.6 88.4 1.0
OP1 A:G28 4.8 93.5 1.0

Magnesium binding site 6 out of 16 in 7elp

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Magnesium binding site 6 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg110

b:96.5
occ:1.00
O A:HOH243 2.1 96.4 1.0
O A:HOH231 2.3 85.7 1.0
O A:HOH208 2.4 81.4 1.0
O A:HOH242 2.5 91.6 1.0
O A:HOH244 2.5 88.9 1.0
O A:HOH229 2.9 91.9 1.0
OP1 A:U13 4.6 91.9 1.0
OP2 A:C32 4.8 70.9 1.0

Magnesium binding site 7 out of 16 in 7elp

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Magnesium binding site 7 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg111

b:95.7
occ:1.00
O A:HOH222 2.3 76.3 1.0
O A:HOH232 2.6 80.6 1.0
O A:HOH248 2.7 85.1 1.0
O A:HOH246 2.9 82.2 1.0
IR A:IR103 3.0 114.8 1.0
O A:HOH201 3.1 86.3 1.0
N7 A:G27 3.2 85.3 1.0
O6 A:G27 3.5 83.7 1.0
C5 A:G27 3.8 79.3 1.0
C6 A:G27 3.9 79.6 1.0
C8 A:G27 4.1 84.7 1.0
C4 A:G27 5.0 77.8 1.0

Magnesium binding site 8 out of 16 in 7elp

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Magnesium binding site 8 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg112

b:80.8
occ:1.00
MG A:MG113 1.9 72.6 1.0
O A:HOH247 1.9 72.4 1.0
O A:HOH209 2.0 76.4 1.0
O A:HOH241 2.2 69.8 1.0
O A:HOH237 3.5 78.1 1.0
O A:HOH212 3.7 81.5 1.0
O6 A:G23 4.1 85.0 1.0
OP1 A:A25 4.2 92.3 1.0
O A:HOH236 4.3 80.4 1.0
O A:HOH245 4.3 74.7 1.0
N7 A:G23 4.5 76.9 1.0
MG A:MG114 4.6 74.6 1.0
C6 A:G23 4.7 83.1 1.0
C5 A:G23 4.9 80.6 1.0

Magnesium binding site 9 out of 16 in 7elp

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Magnesium binding site 9 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg113

b:72.6
occ:1.00
MG A:MG112 1.9 80.8 1.0
O A:HOH237 2.2 78.1 1.0
O A:HOH241 2.3 69.8 1.0
O A:HOH245 2.5 74.7 1.0
O A:HOH212 2.6 81.5 1.0
O A:HOH209 2.9 76.4 1.0
O A:HOH247 3.2 72.4 1.0
MG A:MG114 3.2 74.6 1.0
O A:HOH236 3.7 80.4 1.0
OP1 A:A25 4.1 92.3 1.0
O A:HOH217 4.2 83.1 1.0
O A:HOH239 4.6 86.9 1.0

Magnesium binding site 10 out of 16 in 7elp

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Magnesium binding site 10 out of 16 in the Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Xanthine Riboswitch with Xanthine, Iridium Hexammine Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg114

b:74.6
occ:1.00
O A:HOH239 2.0 86.9 1.0
O A:HOH236 2.0 80.4 1.0
O A:HOH217 2.3 83.1 1.0
O A:HOH237 2.8 78.1 1.0
MG A:MG115 2.9 86.6 1.0
O A:HOH241 3.0 69.8 1.0
O A:HOH245 3.2 74.7 1.0
MG A:MG113 3.2 72.6 1.0
O A:HOH224 4.3 87.2 1.0
MG A:MG112 4.6 80.8 1.0
OP2 A:G23 4.6 92.5 1.0
O A:HOH209 4.8 76.4 1.0
O A:HOH212 4.8 81.5 1.0
O A:HOH247 4.9 72.4 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 Jul 11 17:36:24 2021

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