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Magnesium in PDB 3ucz: The C-Di-Gmp-I Riboswitch Bound to Gpg

Protein crystallography data

The structure of The C-Di-Gmp-I Riboswitch Bound to Gpg, PDB code: 3ucz was solved by K.D.Smith, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.808, 45.358, 77.334, 90.00, 95.81, 90.00
R / Rfree (%) 20.2 / 26.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The C-Di-Gmp-I Riboswitch Bound to Gpg (pdb code 3ucz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The C-Di-Gmp-I Riboswitch Bound to Gpg, PDB code: 3ucz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3ucz

Go back to Magnesium Binding Sites List in 3ucz
Magnesium binding site 1 out of 3 in the The C-Di-Gmp-I Riboswitch Bound to Gpg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The C-Di-Gmp-I Riboswitch Bound to Gpg within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg99

b:48.6
occ:1.00
O P:HOH102 2.2 49.0 1.0
O P:HOH101 2.2 49.1 1.0
O P:HOH100 2.2 48.1 1.0
NE2 P:HIS31 2.6 72.5 1.0
CE1 P:HIS31 3.1 77.0 1.0
CD2 P:HIS31 3.6 65.7 1.0
N P:ILE40 4.1 65.4 1.0
CB P:ILE40 4.2 57.3 1.0
ND1 P:HIS31 4.3 73.5 1.0
CD1 P:ILE40 4.3 54.5 1.0
O P:ILE40 4.3 69.7 1.0
CG P:HIS31 4.5 66.0 1.0
CG1 P:ILE40 4.5 54.7 1.0
CA P:ILE40 4.6 60.8 1.0
CB P:SER35 4.8 72.1 1.0
C P:ILE40 4.9 64.8 1.0

Magnesium binding site 2 out of 3 in 3ucz

Go back to Magnesium Binding Sites List in 3ucz
Magnesium binding site 2 out of 3 in the The C-Di-Gmp-I Riboswitch Bound to Gpg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The C-Di-Gmp-I Riboswitch Bound to Gpg within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg1

b:53.9
occ:1.00
O R:HOH674 2.2 54.6 1.0
O R:HOH675 2.2 54.0 1.0
O R:HOH672 2.2 54.3 1.0
O R:HOH671 2.2 53.6 1.0
O R:HOH676 2.2 53.9 1.0
O R:HOH673 2.2 54.0 1.0
O6 R:G42 3.4 41.1 1.0
OP2 R:G41 3.9 47.1 1.0
OP2 R:A23 4.2 41.8 1.0
C6 R:G42 4.3 41.5 1.0
OP2 R:G40 4.5 46.2 1.0
N7 R:G42 4.6 42.7 1.0
O R:HOH686 4.6 50.5 1.0
N6 R:A43 4.7 43.3 1.0
C5 R:G42 4.8 42.0 1.0
N7 R:G41 4.9 43.5 1.0

Magnesium binding site 3 out of 3 in 3ucz

Go back to Magnesium Binding Sites List in 3ucz
Magnesium binding site 3 out of 3 in the The C-Di-Gmp-I Riboswitch Bound to Gpg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The C-Di-Gmp-I Riboswitch Bound to Gpg within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg670

b:57.9
occ:1.00
O R:HOH691 2.2 58.0 1.0
O R:HOH690 2.2 57.6 1.0
O R:HOH687 2.2 57.5 1.0
O R:HOH688 2.2 57.8 1.0
O R:HOH692 2.2 57.5 1.0
O R:HOH689 2.2 57.4 1.0
OP1 R:C52 4.1 41.7 1.0
OP2 R:U53 4.1 43.3 1.0
OP2 R:U81 4.2 46.5 1.0
N7 R:A82 4.3 48.1 1.0
OP1 R:U81 4.5 44.5 1.0
OP2 R:C52 4.5 40.8 1.0
P R:C52 4.7 42.1 1.0
C8 R:A82 4.8 47.3 1.0
P R:U81 4.9 45.3 1.0

Reference:

K.D.Smith, S.V.Lipchock, S.A.Strobel. Structural and Biochemical Characterization of Linear Dinucleotide Analogues Bound to the C-Di-Gmp-I Aptamer. Biochemistry V. 51 425 2012.
ISSN: ISSN 0006-2960
PubMed: 22148472
DOI: 10.1021/BI2016662
Page generated: Mon Dec 14 08:56:27 2020

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