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Magnesium in PDB 3iin: Plasticity of the Kink Turn Structural Motif

Protein crystallography data

The structure of Plasticity of the Kink Turn Structural Motif, PDB code: 3iin was solved by S.V.Lipchock, S.A.Strobel, A.H.Antonioli, J.C.Cochrane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.18
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.826, 109.826, 250.218, 90.00, 90.00, 90.00
R / Rfree (%) 29 / 32.3

Other elements in 3iin:

The structure of Plasticity of the Kink Turn Structural Motif also contains other interesting chemical elements:

Potassium (K) 5 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Plasticity of the Kink Turn Structural Motif (pdb code 3iin). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Plasticity of the Kink Turn Structural Motif, PDB code: 3iin:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 3iin

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Magnesium binding site 1 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:87.6
occ:1.00
OP1 B:G170 1.9 87.9 1.0
O3' D:DT3 2.2 84.9 1.0
OP1 B:A172 2.2 86.5 1.0
OP2 C:DA207 2.2 94.0 1.0
OP1 B:C88 2.2 84.9 1.0
OP2 B:C88 2.9 84.6 1.0
P B:C88 2.9 84.9 1.0
P B:A172 3.1 86.8 1.0
P B:G170 3.2 88.3 1.0
C3' D:DT3 3.5 85.8 1.0
P C:DA207 3.5 96.1 1.0
OP2 B:A172 3.5 86.9 1.0
O3' B:C171 3.7 86.1 1.0
C3' B:C171 3.9 87.0 1.0
OP2 B:G170 3.9 87.5 1.0
O5' B:G170 4.0 88.9 1.0
O3' B:A87 4.0 85.3 1.0
K B:K2 4.0 0.9 1.0
C4' D:DT3 4.1 86.3 1.0
OP1 C:DA207 4.1 96.2 1.0
O5' B:C88 4.2 86.6 1.0
C2' D:DT3 4.2 85.5 1.0
O3' C:DG206 4.2 97.0 1.0
O3' B:G169 4.3 87.0 1.0
C5' B:G170 4.4 89.6 1.0
O5' B:A172 4.6 86.9 1.0
O5' C:DA207 4.6 96.8 1.0
O2' B:C171 4.7 87.0 1.0
OP1 B:U173 4.8 85.0 1.0
C2' B:C171 4.8 87.3 1.0
C5' B:C88 4.9 88.3 1.0
C5' D:DT3 4.9 87.2 1.0
C1' D:DT3 4.9 85.6 1.0
C5' B:A172 5.0 87.5 1.0

Magnesium binding site 2 out of 13 in 3iin

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Magnesium binding site 2 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3

b:85.7
occ:1.00
OP2 B:A174 2.2 92.0 1.0
OP2 B:U173 2.2 85.8 1.0
P B:U173 3.3 85.9 1.0
O3' B:A172 3.4 85.8 1.0
P B:A174 3.6 94.7 1.0
C3' B:U173 4.1 91.8 1.0
O2' B:A172 4.1 88.6 1.0
N7 C:DG206 4.1 0.5 1.0
O5' B:U173 4.2 87.1 1.0
O3' B:U173 4.3 93.4 1.0
C8 C:DG206 4.4 0.7 1.0
N7 B:A174 4.5 0.4 1.0
O5' B:A174 4.5 96.4 1.0
OP1 B:U173 4.6 85.0 1.0
OP1 B:A174 4.6 94.9 1.0
N7 B:G175 4.6 0.1 1.0
C3' B:A172 4.7 87.4 1.0
C6 B:U173 4.8 89.1 1.0
C8 B:A174 4.8 0.7 1.0
C5' B:U173 4.9 89.2 1.0
C5 C:DG206 4.9 99.6 1.0
C5 B:U173 4.9 89.6 1.0
C2' B:A172 4.9 88.4 1.0

Magnesium binding site 3 out of 13 in 3iin

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Magnesium binding site 3 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1019

b:89.3
occ:1.00
OP1 B:U126 2.2 94.9 1.0
O6 B:G53 3.3 0.8 1.0
N7 B:G53 3.3 0.5 1.0
P B:U126 3.6 97.3 1.0
C6 B:G53 3.7 0.5 1.0
C5 B:G53 3.7 0.0 1.0
O2' B:G125 3.7 0.0 1.0
O6 B:G54 3.9 0.3 1.0
N7 B:G54 4.0 0.6 1.0
O3' B:G125 4.2 98.1 1.0
C2' B:G125 4.3 0.3 1.0
C8 B:G53 4.3 0.5 1.0
OP2 B:U126 4.4 97.2 1.0
O5' B:U126 4.6 97.2 1.0
C6 B:G54 4.7 0.2 1.0
C5 B:G54 4.7 0.3 1.0
C3' B:G125 4.8 99.5 1.0
C4 B:G53 4.8 0.0 1.0
N1 B:G53 4.9 0.1 1.0

Magnesium binding site 4 out of 13 in 3iin

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Magnesium binding site 4 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1020

b:84.5
occ:1.00
OP1 B:U80 4.6 0.8 1.0
O4 B:U62 4.7 0.1 1.0
OP2 B:U80 4.8 0.6 1.0
OP2 B:A81 4.9 0.6 1.0

Magnesium binding site 5 out of 13 in 3iin

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Magnesium binding site 5 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1021

b:54.5
occ:1.00
N4 B:C66 4.2 0.5 1.0
N4 B:C68 4.3 0.8 1.0
O6 B:G67 4.3 0.1 1.0
C5 B:C66 4.5 0.2 1.0
C4 B:C66 4.8 0.1 1.0
O6 B:G77 4.9 0.3 1.0
N4 B:C78 5.0 0.2 1.0

Magnesium binding site 6 out of 13 in 3iin

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Magnesium binding site 6 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1022

b:66.6
occ:1.00
O6 B:G84 4.3 89.5 1.0
OP2 B:A58 4.3 99.0 1.0
N7 B:G84 4.5 90.7 1.0
O2' B:A81 4.6 1.0 1.0
O6 B:G83 4.6 97.7 1.0
C2' B:A81 4.7 0.5 1.0
N7 B:G83 4.8 98.4 1.0
N4 B:C60 5.0 92.7 1.0

Magnesium binding site 7 out of 13 in 3iin

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Magnesium binding site 7 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1023

b:96.7
occ:1.00
OP2 B:C171 2.2 92.6 1.0
OP1 B:U124 2.2 0.8 1.0
P B:C171 3.5 91.0 1.0
P B:U124 3.6 0.6 1.0
OP2 B:A127 3.6 97.2 1.0
O5' B:C171 3.9 90.8 1.0
OP2 B:G125 4.0 0.6 1.0
C5' B:U124 4.0 0.3 1.0
O3' B:G170 4.1 91.0 1.0
O5' B:U124 4.1 0.9 1.0
K B:K1016 4.3 0.7 1.0
O2' B:U126 4.4 96.2 1.0
O2' B:G170 4.5 93.9 1.0
OP2 B:U124 4.5 0.8 1.0
O3' B:G123 4.6 0.2 1.0
OP1 B:C171 4.7 91.0 1.0
P B:A127 4.9 97.5 1.0

Magnesium binding site 8 out of 13 in 3iin

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Magnesium binding site 8 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1024

b:97.3
occ:1.00
OP2 B:G38 2.2 0.7 1.0
OP2 B:A39 2.5 0.8 1.0
O2' B:G37 3.0 0.4 1.0
P B:G38 3.2 0.8 1.0
N7 B:A39 3.4 0.3 1.0
OP1 B:G38 3.4 0.9 1.0
O4' D:C1 3.7 78.2 1.0
P B:A39 3.9 0.7 1.0
C8 B:A39 4.0 0.4 1.0
C4' D:C1 4.1 78.8 1.0
O3' B:G37 4.1 0.6 1.0
C2' B:G37 4.2 0.4 1.0
C5' D:C1 4.2 78.7 1.0
N6 B:A167 4.4 93.3 1.0
C5 B:A39 4.4 0.5 1.0
O5' B:G38 4.5 0.4 1.0
O5' B:A39 4.5 0.9 1.0
C3' B:G38 4.6 0.9 1.0
C1' B:G37 4.6 0.4 1.0
C3' B:G37 4.7 0.6 1.0
N6 B:A39 4.7 0.3 1.0
O3' B:G38 4.8 0.7 1.0
N1 B:A167 4.8 92.2 1.0
C1' D:C1 4.8 77.5 1.0
OP1 B:A39 4.9 0.3 1.0

Magnesium binding site 9 out of 13 in 3iin

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Magnesium binding site 9 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1025

b:78.8
occ:1.00
OP2 B:A48 2.1 0.1 1.0
OP2 B:U133 3.1 0.8 1.0
P B:A48 3.6 0.7 1.0
OP2 B:A134 3.8 0.3 1.0
P B:U133 3.9 0.1 1.0
OP1 B:U133 3.9 0.8 1.0
O2' B:A47 4.0 0.6 1.0
O5' B:A48 4.3 0.8 1.0
OP1 B:A48 4.3 0.9 1.0
O5' B:U133 4.5 0.9 1.0
O3' B:A47 4.6 0.7 1.0

Magnesium binding site 10 out of 13 in 3iin

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Magnesium binding site 10 out of 13 in the Plasticity of the Kink Turn Structural Motif


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Plasticity of the Kink Turn Structural Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1026

b:0.2
occ:1.00
OP2 B:C74 2.2 0.9 1.0
P B:C74 3.6 0.9 1.0
N7 B:G75 4.1 0.5 1.0
O5' B:C73 4.1 0.8 1.0
OP1 B:C73 4.2 0.8 1.0
O5' B:C74 4.3 0.6 1.0
OP1 B:C74 4.5 0.8 1.0
P B:C73 4.5 0.5 1.0
O3' B:C73 4.6 0.7 1.0
OP2 B:C73 4.6 0.3 1.0
O6 B:G75 4.7 0.8 1.0
C3' B:C73 4.8 0.7 1.0
C8 B:G75 5.0 0.5 1.0

Reference:

A.H.Antonioli, J.C.Cochrane, S.V.Lipchock, S.A.Strobel. Plasticity of the Rna Kink Turn Structural Motif. Rna V. 16 762 2010.
ISSN: ISSN 1355-8382
PubMed: 20145044
DOI: 10.1261/RNA.1883810
Page generated: Mon Dec 14 08:17:01 2020

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