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Magnesium in PDB 3p49: Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum

Protein crystallography data

The structure of Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum, PDB code: 3p49 was solved by E.B.Butler, J.Wang, Y.Xiong, S.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 3.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.580, 104.617, 156.509, 90.00, 90.00, 90.00
R / Rfree (%) 28.2 / 31

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum (pdb code 3p49). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum, PDB code: 3p49:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 3p49

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Magnesium binding site 1 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg735

b:77.5
occ:1.00
OP2 A:A52 2.3 0.2 1.0
OP2 A:C51 2.4 0.6 1.0
O6 A:G53 2.4 0.4 1.0
C6 A:G53 3.3 0.6 1.0
N7 A:G53 3.5 0.8 1.0
P A:C51 3.6 0.7 1.0
P A:A52 3.8 0.4 1.0
C5 A:G53 3.8 1.0 1.0
O5' A:C51 3.8 0.1 1.0
O2' A:U50 4.1 0.5 1.0
O6 A:G54 4.3 0.9 1.0
O5' A:A52 4.4 0.3 1.0
N7 A:A52 4.4 0.6 1.0
OP1 A:C51 4.4 0.2 1.0
N1 A:G53 4.6 0.3 1.0
O3' A:C51 4.6 0.7 1.0
C3' A:C51 4.7 0.7 1.0
OP1 A:A52 4.7 0.9 1.0
O3' A:U50 4.8 0.6 1.0
C8 A:G53 4.8 0.7 1.0
C5 A:A52 4.9 0.4 1.0
C8 A:A52 4.9 0.0 1.0
C5' A:C51 5.0 1.0 1.0

Magnesium binding site 2 out of 13 in 3p49

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Magnesium binding site 2 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg736

b:91.6
occ:1.00
O A:HOH754 2.2 90.7 1.0
O A:HOH750 2.2 90.0 1.0
O A:HOH752 2.2 90.2 1.0
O A:HOH751 2.2 90.0 1.0
O A:HOH753 2.2 90.9 1.0
O6 A:G9 3.4 0.6 1.0
C6 A:G9 4.4 0.0 1.0
O6 A:G62 4.5 0.3 1.0
N7 A:G9 4.6 0.2 1.0
O6 A:G8 4.6 0.2 1.0
N6 A:A7 4.8 0.9 1.0
N7 A:A7 4.8 1.0 1.0
N7 A:G8 4.8 0.5 1.0
C5 A:G9 4.8 0.1 1.0

Magnesium binding site 3 out of 13 in 3p49

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Magnesium binding site 3 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg737

b:69.6
occ:1.00
OP2 A:A143 2.0 0.5 1.0
OP2 A:C142 2.4 0.4 1.0
O6 A:G144 2.6 0.8 1.0
P A:C142 3.2 0.2 1.0
O3' A:U141 3.3 0.8 1.0
P A:A143 3.4 0.3 1.0
O5' A:C142 3.4 0.5 1.0
C6 A:G144 3.6 0.4 1.0
N7 A:G144 3.7 0.8 1.0
O5' A:A143 3.9 0.6 1.0
C5 A:G144 4.0 0.9 1.0
O2' A:U141 4.1 0.7 1.0
N7 A:A143 4.3 0.3 1.0
O3' A:C142 4.3 0.0 1.0
C3' A:U141 4.3 0.3 1.0
C3' A:C142 4.4 0.8 1.0
OP1 A:A143 4.4 0.1 1.0
C5' A:C142 4.6 0.0 1.0
OP1 A:C142 4.6 0.9 1.0
C8 A:A143 4.7 0.6 1.0
N1 A:G144 4.8 0.0 1.0
C2' A:U141 4.8 0.2 1.0
C8 A:G144 4.9 0.0 1.0

Magnesium binding site 4 out of 13 in 3p49

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Magnesium binding site 4 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg738

b:97.6
occ:1.00
O A:HOH755 2.2 97.9 1.0
O A:HOH756 2.2 98.4 1.0
O A:HOH758 2.2 98.0 1.0
O A:HOH757 2.2 98.1 1.0
O4 A:U83 3.6 0.8 1.0
OP2 A:G152 3.6 0.2 1.0
O6 A:G85 3.7 0.2 1.0
N7 A:G152 4.3 0.1 1.0
C4 A:U83 4.3 0.3 1.0
OP1 A:G151 4.5 0.0 1.0
C5 A:U83 4.6 0.9 1.0
OP2 A:G151 4.8 0.1 1.0
C6 A:G85 4.9 0.2 1.0
C8 A:G152 5.0 0.0 1.0

Magnesium binding site 5 out of 13 in 3p49

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Magnesium binding site 5 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg739

b:34.8
occ:1.00
O2' A:G110 2.3 0.8 1.0
OP2 A:C138 2.5 0.5 1.0
O A:GLY746 2.7 71.8 1.0
OXT A:GLY746 2.8 71.9 1.0
OP2 A:A111 2.9 0.1 1.0
C A:GLY746 3.3 72.0 1.0
C2' A:G110 3.6 1.0 1.0
P A:C138 3.7 0.7 1.0
O3' A:A137 3.7 1.0 1.0
O5' A:A111 3.8 0.8 1.0
P A:A111 3.9 0.9 1.0
O4 A:U141 3.9 0.6 1.0
N4 A:C140 4.0 0.0 1.0
C4' A:A137 4.2 0.7 1.0
C3' A:A137 4.4 0.4 1.0
O3' A:G110 4.5 0.0 1.0
O4 A:U139 4.5 0.2 1.0
C3' A:G110 4.5 0.9 1.0
O5' A:C138 4.6 0.1 1.0
C5 A:C140 4.6 0.3 1.0
C1' A:G110 4.7 0.8 1.0
C5 A:U139 4.7 0.8 1.0
CA A:GLY746 4.8 72.1 1.0
C4 A:C140 4.8 0.1 1.0
C5' A:A111 4.8 0.2 1.0
OP1 A:C138 4.8 0.1 1.0
C4 A:U141 4.9 0.7 1.0
N3 A:U141 4.9 0.1 1.0
C5' A:A137 4.9 0.5 1.0
C4 A:U139 4.9 0.7 1.0

Magnesium binding site 6 out of 13 in 3p49

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Magnesium binding site 6 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg740

b:45.5
occ:1.00
O2' A:G35 2.3 0.0 1.0
OXT A:GLY745 2.7 0.5 1.0
OP2 A:C47 2.8 0.4 1.0
OP2 A:A36 2.9 0.1 1.0
O A:GLY745 3.1 0.5 1.0
C A:GLY745 3.3 0.5 1.0
C5' A:A36 3.6 0.8 1.0
C2' A:G35 3.6 0.3 1.0
O4 A:U48 3.7 0.2 1.0
C4' A:U46 3.9 0.2 1.0
P A:A36 4.0 0.8 1.0
C5' A:U46 4.0 0.4 1.0
O3' A:G35 4.0 0.2 1.0
P A:C47 4.2 0.3 1.0
C1' A:G35 4.2 0.6 1.0
O5' A:A36 4.3 0.8 1.0
C4 A:U48 4.3 0.8 1.0
C3' A:G35 4.4 0.4 1.0
C5 A:U48 4.4 0.7 1.0
O4 A:U49 4.5 0.3 1.0
O4 A:U50 4.5 0.1 1.0
O3' A:U46 4.5 0.9 1.0
C3' A:U46 4.6 0.9 1.0
CA A:GLY745 4.7 0.5 1.0
C4' A:A36 4.8 1.0 1.0
N9 A:G35 4.9 0.6 1.0
O4' A:U46 4.9 0.8 1.0

Magnesium binding site 7 out of 13 in 3p49

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Magnesium binding site 7 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg741

b:89.5
occ:1.00
O4 A:U42 2.1 0.5 1.0
OP2 A:A45 2.5 0.3 1.0
C4 A:U42 3.3 0.2 1.0
P A:A45 3.8 0.8 1.0
N7 A:A40 4.0 0.2 1.0
C5 A:U42 4.1 0.6 1.0
O6 A:G41 4.1 0.8 1.0
N7 A:G41 4.2 0.7 1.0
OP1 A:A45 4.3 1.0 1.0
N3 A:U42 4.4 0.2 1.0
O5' A:A45 4.5 0.1 1.0
N6 A:A40 4.5 0.5 1.0
C5 A:A40 4.6 0.6 1.0
C8 A:A40 4.8 0.6 1.0
C6 A:G41 4.9 0.9 1.0
C6 A:A40 4.9 0.9 1.0
C5 A:G41 4.9 0.3 1.0
O3' A:A44 4.9 0.9 1.0

Magnesium binding site 8 out of 13 in 3p49

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Magnesium binding site 8 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg742

b:86.6
occ:1.00
OP2 A:A148 2.0 0.8 1.0
OP1 A:A147 2.4 0.0 1.0
OP2 A:U146 3.2 0.5 1.0
P A:A148 3.5 0.7 1.0
P A:A147 3.6 0.8 1.0
N6 A:A149 3.7 0.7 1.0
P A:U146 3.8 0.3 1.0
OP1 A:U146 3.9 0.2 1.0
O5' A:U146 3.9 0.7 1.0
N7 A:A148 3.9 0.6 1.0
OP2 A:A147 3.9 0.4 1.0
O5' A:A148 4.0 0.1 1.0
C8 A:A148 4.2 0.1 1.0
C3' A:A147 4.4 0.8 1.0
O3' A:A147 4.4 0.3 1.0
N7 A:A149 4.4 0.3 1.0
O5' A:A147 4.5 0.7 1.0
OP1 A:A148 4.5 0.8 1.0
N6 A:A150 4.7 0.7 1.0
C6 A:A149 4.7 0.1 1.0
O3' A:U146 4.8 0.5 1.0
C5' A:A147 4.8 0.5 1.0
C5 A:A149 4.9 0.9 1.0
C4' A:U146 5.0 0.2 1.0

Magnesium binding site 9 out of 13 in 3p49

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Magnesium binding site 9 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg743

b:88.7
occ:1.00
OP2 A:G113 2.4 0.7 1.0
OP2 A:A137 2.6 0.6 1.0
OP1 A:A112 2.7 0.0 1.0
P A:A137 3.7 0.1 1.0
P A:G113 3.8 0.3 1.0
P A:A112 3.9 0.7 1.0
O5' A:A137 4.0 0.8 1.0
O5' A:A112 4.2 0.7 1.0
OP1 A:A137 4.3 0.1 1.0
OP1 A:G113 4.4 0.4 1.0
O A:GLY746 4.5 71.8 1.0
OP2 A:A112 4.6 0.7 1.0
O2' A:A153 4.6 0.3 1.0
O5' A:G113 4.7 0.1 1.0
CA A:GLY746 4.7 72.1 1.0
C5' A:A137 4.9 0.5 1.0
O3' A:A112 4.9 0.8 1.0
O A:HOH768 4.9 0.3 1.0

Magnesium binding site 10 out of 13 in 3p49

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Magnesium binding site 10 out of 13 in the Crystal Structure of A Glycine Riboswitch From Fusobacterium Nucleatum


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 A Glycine Riboswitch From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg744

b:95.2
occ:1.00
OP2 A:G38 2.3 0.3 1.0
OP1 A:A37 2.4 0.4 1.0
OP1 A:U46 3.0 0.9 1.0
P A:G38 3.7 0.3 1.0
P A:A37 3.7 0.1 1.0
O5' A:A37 3.9 0.8 1.0
N6 A:A39 4.2 0.7 1.0
P A:U46 4.3 0.9 1.0
OP1 A:G38 4.4 0.9 1.0
OXT A:GLY745 4.4 0.5 1.0
O5' A:G38 4.5 0.7 1.0
C4' A:A36 4.6 1.0 1.0
O2' A:A63 4.6 0.2 1.0
O3' A:A36 4.7 0.7 1.0
O3' A:A37 4.7 0.1 1.0
N7 A:A39 4.7 0.1 1.0
OP2 A:U46 4.8 0.8 1.0
OP2 A:A37 4.8 0.3 1.0
C5' A:U46 4.8 0.4 1.0
C5' A:A37 4.9 0.4 1.0

Reference:

E.B.Butler, Y.Xiong, J.Wang, S.A.Strobel. Structural Basis of Cooperative Ligand Binding By the Glycine Riboswitch. Chem.Biol. V. 18 293 2011.
ISSN: ISSN 1074-5521
PubMed: 21439473
DOI: 10.1016/J.CHEMBIOL.2011.01.013
Page generated: Mon Dec 14 08:38:40 2020

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