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Manganese 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:

Magnesium (Mg) 9 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 10 binding sites of Manganese where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Manganese Soak, PDB code: 3skt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 3skt

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Manganese binding site 1 out of 10 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 Manganese with other atoms in the Mn 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:Mn201

b:48.4
occ:1.00
 N7 A:G75 2.5 43.8 1.0
C8 A:G75 3.1 45.2 1.0
MN A:MN208 3.3 80.8 1.0
C5 A:G75 3.4 44.3 1.0
OP2 A:G75 3.8 52.2 1.0
O6 A:G75 3.9 42.2 1.0
C6 A:G75 4.0 43.7 1.0
N9 A:G75 4.2 46.5 1.0
C4 A:G75 4.3 45.5 1.0
N7 A:G76 4.6 45.9 1.0
O5' A:G75 4.7 52.4 1.0
C4 A:U74 4.9 42.1 1.0
C5 A:U74 4.9 42.2 1.0
P A:G75 4.9 54.9 1.0
C8 A:G76 5.0 47.5 1.0

Manganese binding site 2 out of 10 in 3skt

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Manganese binding site 2 out of 10 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 Manganese with other atoms in the Mn 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:Mn202

b:69.5
occ:1.00
 N7 A:G45 2.5 56.5 1.0
O6 A:G45 3.4 55.6 1.0
C5 A:G45 3.4 54.9 1.0
C8 A:G45 3.5 56.8 1.0
C6 A:G45 3.7 54.5 1.0
N7 A:G46 4.2 47.2 1.0
OP2 A:G45 4.5 69.8 1.0
C4 A:G45 4.6 54.5 1.0
N9 A:G45 4.6 55.6 1.0
O6 A:G46 5.0 48.7 1.0

Manganese binding site 3 out of 10 in 3skt

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Manganese binding site 3 out of 10 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 Manganese with other atoms in the Mn 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
A:Mn207

b:55.8
occ:1.00
 OP2 A:G34 2.2 45.3 1.0
OP2 A:U73 2.4 48.7 1.0
P A:G34 3.4 46.8 1.0
O3' A:G33 3.7 46.3 1.0
P A:U73 3.8 50.7 1.0
OP2 A:G35 3.8 42.9 1.0
O5' A:G34 3.9 46.0 1.0
O2' A:G33 3.9 45.9 1.0
C3' A:G33 4.4 45.1 1.0
O5' A:U73 4.4 50.1 1.0
OP1 A:U73 4.4 51.9 1.0
OP1 A:G34 4.7 47.3 1.0
O2' A:U72 4.7 53.1 1.0
C2' A:G33 4.7 45.1 1.0
O3' A:U72 4.9 51.9 1.0
C3' A:U72 4.9 54.0 1.0

Manganese binding site 4 out of 10 in 3skt

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Manganese binding site 4 out of 10 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 Manganese with other atoms in the Mn 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
A:Mn208

b:80.8
occ:1.00
 O6 A:G75 2.3 42.2 1.0
C6 A:G75 3.0 43.7 1.0
MN A:MN201 3.3 48.4 1.0
N7 A:G76 3.4 45.9 1.0
O6 A:G76 3.4 44.9 1.0
C5 A:G75 3.8 44.3 1.0
O4 A:U63 3.9 42.8 1.0
N1 A:G75 3.9 44.7 1.0
N7 A:G75 4.0 43.8 1.0
C5 A:G76 4.1 46.8 1.0
C6 A:G76 4.1 46.2 1.0
N6 A:A77 4.2 44.8 1.0
N4 A:C64 4.3 43.6 1.0
C8 A:G76 4.5 47.5 1.0
O4 A:U74 4.8 41.0 1.0
C4 A:U63 4.9 44.8 1.0
C4 A:G75 4.9 45.5 1.0
C6 A:A77 4.9 45.8 1.0

Manganese binding site 5 out of 10 in 3skt

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Manganese binding site 5 out of 10 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 Manganese with other atoms in the Mn 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
A:Mn209

b:52.2
occ:1.00
 OP1 A:C61 2.2 41.4 1.0
N7 A:G33 2.4 45.3 1.0
O6 A:G33 3.2 46.7 1.0
C5 A:G33 3.3 45.9 1.0
C8 A:G33 3.5 44.6 1.0
C6 A:G33 3.6 45.9 1.0
P A:C61 3.6 41.2 1.0
OP2 A:C60 3.9 46.7 1.0
OP2 A:U49 4.1 44.1 1.0
OP2 A:C61 4.2 41.9 1.0
C3' A:C60 4.3 41.7 1.0
O5' A:C60 4.4 45.1 1.0
O3' A:C60 4.5 40.2 1.0
O5' A:C61 4.6 41.4 1.0
C4 A:G33 4.6 46.1 1.0
P A:C60 4.6 47.0 1.0
N9 A:G33 4.7 45.2 1.0
C5' A:C60 4.9 44.0 1.0
OP1 A:C60 5.0 46.7 1.0
N1 A:G33 5.0 46.8 1.0

Manganese binding site 6 out of 10 in 3skt

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Manganese binding site 6 out of 10 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 Manganese with other atoms in the Mn 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
A:Mn210

b:64.7
occ:0.50
 O2' A:U70 2.3 63.9 1.0
OP2 A:A71 2.5 59.3 1.0
O3' A:U70 2.8 59.7 1.0
O2 A:U41 2.9 58.2 1.0
P A:A71 3.2 58.1 1.0
C2' A:U70 3.3 63.7 1.0
C3' A:U70 3.6 62.2 1.0
C2 A:U41 3.7 57.9 1.0
N3 A:U41 3.8 56.6 1.0
C4' A:U70 4.1 65.0 1.0
O5' A:A71 4.1 57.3 1.0
OP1 A:A71 4.5 57.5 1.0
C1' A:U70 4.6 65.8 1.0
O4' A:U70 4.9 66.5 1.0
N6 A:A42 4.9 58.2 1.0
N1 A:U41 4.9 58.3 1.0

Manganese binding site 7 out of 10 in 3skt

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Manganese binding site 7 out of 10 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 Manganese with other atoms in the Mn 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:Mn203

b:95.9
occ:1.00
 O1B B:GTP23 1.9 90.0 1.0
O2A B:GTP23 2.3 84.9 1.0
PB B:GTP23 3.1 90.5 1.0
O3A B:GTP23 3.2 89.8 1.0
PA B:GTP23 3.3 86.8 1.0
C8 B:GTP23 3.7 87.3 1.0
O3G B:GTP23 3.8 84.3 1.0
N7 B:GTP23 3.8 88.1 1.0
C5' B:GTP23 3.9 86.7 1.0
O3B B:GTP23 4.0 88.1 1.0
O5' B:GTP23 4.1 87.6 1.0
O1G B:GTP23 4.1 87.3 1.0
O2B B:GTP23 4.2 92.3 1.0
PG B:GTP23 4.2 86.3 1.0
O1A B:GTP23 4.5 83.9 1.0
N9 B:GTP23 4.9 90.4 1.0

Manganese binding site 8 out of 10 in 3skt

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Manganese binding site 8 out of 10 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 Manganese with other atoms in the Mn 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:Mn204

b:0.4
occ:1.00
 OP2 B:A32 2.4 56.2 1.0
P B:A32 3.7 55.3 1.0
O5' B:A32 3.9 55.0 1.0
N7 B:G78 4.0 70.3 1.0
O6 B:G78 4.0 66.5 1.0
N6 B:A77 4.4 69.9 1.0
N7 B:A77 4.5 72.5 1.0
OP1 B:A32 4.5 56.7 1.0
C5' B:A32 4.6 56.0 1.0
C5 B:G78 4.7 70.5 1.0
C6 B:G78 4.7 68.5 1.0
O3' B:C31 4.8 52.3 1.0
C5 B:A77 4.9 73.5 1.0
N4 B:C61 5.0 67.1 1.0
C6 B:A77 5.0 72.4 1.0

Manganese binding site 9 out of 10 in 3skt

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Manganese binding site 9 out of 10 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 Manganese with other atoms in the Mn 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:Mn205

b:65.2
occ:1.00
 OP1 B:C61 2.2 61.3 1.0
OP2 B:C61 2.2 58.0 1.0
P B:C61 2.4 61.3 1.0
O6 B:G33 2.7 55.1 1.0
N7 B:G33 2.8 55.9 1.0
MG B:MG309 3.3 55.6 1.0
OP2 B:U49 3.3 56.6 1.0
O3' B:C60 3.3 56.5 1.0
C6 B:G33 3.4 54.0 1.0
C5 B:G33 3.4 54.3 1.0
C3' B:C60 3.7 53.8 1.0
O5' B:C61 3.9 65.2 1.0
C8 B:G33 4.0 55.3 1.0
OP2 B:C60 4.1 55.3 1.0
O5' B:C60 4.5 54.6 1.0
O5' B:C48 4.6 61.7 1.0
P B:U49 4.6 58.4 1.0
P B:C60 4.7 56.1 1.0
N1 B:G33 4.8 52.4 1.0
C4 B:G33 4.8 53.5 1.0
C2' B:C60 4.8 51.8 1.0
C4' B:C60 4.9 54.4 1.0
C5' B:C60 4.9 55.5 1.0
OP1 B:C60 5.0 59.6 1.0

Manganese binding site 10 out of 10 in 3skt

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Manganese binding site 10 out of 10 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 Manganese with other atoms in the Mn binding site number 10 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:Mn206

b:70.1
occ:1.00
 OP2 B:G35 2.2 54.6 1.0
P B:G35 2.9 52.1 1.0
O5' B:G34 3.0 50.4 1.0
OP1 B:G35 3.1 52.2 1.0
OP1 B:U73 3.1 74.6 1.0
O5' B:U73 3.2 75.0 1.0
OP2 B:U73 3.2 72.6 1.0
P B:U73 3.2 74.7 1.0
C5' B:G34 3.3 49.2 1.0
OP2 B:G34 3.3 52.0 1.0
O3' B:G34 3.4 51.1 1.0
C3' B:G34 3.5 49.1 1.0
P B:G34 3.7 51.8 1.0
MG B:MG305 3.9 25.0 1.0
C4' B:G34 3.9 49.0 1.0
C5' B:U73 4.2 77.0 1.0
O5' B:G35 4.3 52.5 1.0
OP1 B:G34 4.6 51.9 1.0
O3' B:U72 4.9 74.3 1.0
O3' B:G33 5.0 51.5 1.0
C2' B:G34 5.0 48.7 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: Sat Oct 5 17:53:43 2024

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