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Magnesium in PDB 3skt: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak

Protein crystallography data

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak, PDB code: 3skt was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.031, 34.632, 111.598, 90.00, 92.81, 90.00
R / Rfree (%) 19.6 / 25.2

Other elements in 3skt:

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak also contains other interesting chemical elements:

Manganese (Mn) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak (pdb code 3skt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak, PDB code: 3skt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3skt

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Magnesium binding site 1 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:58.2
occ:1.00
 OP1 A:A71 2.2 57.5 1.0
P A:A71 3.3 58.1 1.0
OP2 A:A71 3.6 59.3 1.0
O5' A:A71 4.3 57.3 1.0
O3' A:U70 4.5 59.7 1.0
C2' A:U70 4.6 63.7 1.0
C3' A:U70 4.6 62.2 1.0
C5' A:A71 4.9 59.4 1.0

Magnesium binding site 2 out of 9 in 3skt

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Magnesium binding site 2 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:58.2
occ:1.00
 O2A A:GTP23 2.2 68.6 1.0
O1B A:GTP23 2.7 74.5 1.0
PA A:GTP23 3.4 69.4 1.0
OP2 A:U83 3.4 61.5 1.0
PB A:GTP23 3.5 76.2 1.0
O2B A:GTP23 3.5 75.7 1.0
OP1 A:U83 3.8 65.2 1.0
O1A A:GTP23 3.9 69.4 1.0
O3A A:GTP23 3.9 73.4 1.0
P A:U83 4.1 62.9 1.0
O5' A:GTP23 4.7 68.5 1.0

Magnesium binding site 3 out of 9 in 3skt

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Magnesium binding site 3 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:41.0
occ:1.00
 N7 B:A37 4.1 49.5 1.0
O6 B:G38 4.1 58.6 1.0
N6 B:A37 4.4 48.0 1.0
N7 B:G38 4.8 60.3 1.0
C5 B:A37 4.8 49.4 1.0
C8 B:A37 5.0 50.4 1.0

Magnesium binding site 4 out of 9 in 3skt

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Magnesium binding site 4 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:54.5
occ:1.00
 O6 B:G53 3.3 39.1 1.0
OP1 B:C57 3.8 61.9 1.0
O6 B:G59 4.2 45.0 1.0
C6 B:G53 4.4 39.3 1.0
OP2 B:C57 4.7 62.2 1.0
P B:C57 4.7 61.6 1.0
N7 B:G53 4.7 40.1 1.0
N4 B:C60 4.8 46.0 1.0
OP2 B:C58 4.9 59.9 1.0
C5 B:G53 5.0 39.8 1.0

Magnesium binding site 5 out of 9 in 3skt

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Magnesium binding site 5 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:50.0
occ:1.00
 O2B B:GTP23 2.7 92.3 1.0
PB B:GTP23 3.9 90.5 1.0
O1B B:GTP23 4.0 90.0 1.0
O1G B:GTP23 4.2 87.3 1.0
O3B B:GTP23 4.5 88.1 1.0

Magnesium binding site 6 out of 9 in 3skt

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Magnesium binding site 6 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:25.0
occ:1.00
 OP2 B:G34 2.0 52.0 1.0
OP2 B:U73 2.8 72.6 1.0
O2' B:G33 3.5 54.6 1.0
P B:G34 3.5 51.8 1.0
MN B:MN206 3.9 70.1 1.0
P B:U73 4.1 74.7 1.0
OP1 B:G34 4.3 51.9 1.0
O3' B:G33 4.3 51.5 1.0
O5' B:G34 4.4 50.4 1.0
O2' B:U72 4.4 68.5 1.0
OP1 B:U73 4.6 74.6 1.0
C2' B:G33 4.7 53.6 1.0
OP2 B:G47 4.8 55.5 1.0
C3' B:G33 4.8 53.2 1.0

Magnesium binding site 7 out of 9 in 3skt

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Magnesium binding site 7 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:38.9
occ:1.00
 N7 B:G45 2.2 75.1 1.0
C8 B:G45 3.2 75.6 1.0
C5 B:G45 3.2 72.8 1.0
O6 B:G45 3.4 71.6 1.0
C6 B:G45 3.6 71.4 1.0
OP2 B:G45 4.2 84.5 1.0
N9 B:G45 4.4 73.7 1.0
C4 B:G45 4.4 71.8 1.0
C5' B:U44 4.8 92.9 1.0
N7 B:G46 5.0 66.3 1.0

Magnesium binding site 8 out of 9 in 3skt

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Magnesium binding site 8 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:49.0
occ:1.00
 O6 B:G75 2.2 77.5 1.0
OP1 B:G33 3.3 59.2 1.0
C6 B:G75 3.3 79.0 1.0
O4 B:U63 4.1 75.2 1.0
C5 B:G75 4.2 78.7 1.0
O3' B:A32 4.2 57.4 1.0
N1 B:G75 4.3 80.9 1.0
N7 B:G75 4.4 77.1 1.0
P B:G33 4.4 57.2 1.0
O4 B:U74 4.4 76.1 1.0
N4 B:C64 4.6 65.7 1.0
O6 B:G76 5.0 80.6 1.0

Magnesium binding site 9 out of 9 in 3skt

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Magnesium binding site 9 out of 9 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese 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 the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg309

b:55.6
occ:1.00
 OP2 B:C48 2.2 59.7 1.0
OP2 B:C61 2.2 58.0 1.0
P B:C48 3.1 61.0 1.0
N7 B:G33 3.2 55.9 1.0
MN B:MN205 3.3 65.2 1.0
O5' B:C48 3.4 61.7 1.0
C8 B:G33 3.5 55.3 1.0
OP1 B:C48 3.7 61.4 1.0
P B:C61 3.7 61.3 1.0
C5 B:G33 4.3 54.3 1.0
O3' B:C60 4.3 56.5 1.0
O5' B:C61 4.5 65.2 1.0
O3' B:G47 4.6 62.5 1.0
OP1 B:C61 4.6 61.3 1.0
N9 B:G33 4.7 53.8 1.0
C5' B:C48 4.8 64.5 1.0
C6 B:C48 4.8 60.2 1.0
OP2 B:U49 4.8 56.6 1.0

Reference:

O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov. Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631
Page generated: Thu Aug 15 11:02:22 2024

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