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Manganese in PDB 3pdr: Crystal Structure of Manganese Bound M-Box Rna

Protein crystallography data

The structure of Crystal Structure of Manganese Bound M-Box Rna, PDB code: 3pdr was solved by A.Ramesh, W.C.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.49 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.780, 102.487, 126.375, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.8

Other elements in 3pdr:

The structure of Crystal Structure of Manganese Bound M-Box Rna also contains other interesting chemical elements:

Potassium (K) 6 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Manganese Bound M-Box Rna (pdb code 3pdr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 25 binding sites of Manganese where determined in the Crystal Structure of Manganese Bound M-Box Rna, PDB code: 3pdr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 25 in 3pdr

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Manganese binding site 1 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn176

b:20.7
occ:1.00
 OP2 X:A103 2.2 19.8 1.0
O4 X:U104 2.2 18.6 1.0
OP2 X:G100 2.2 16.6 1.0
OP2 X:C102 2.2 21.2 1.0
O X:HOH497 2.3 21.0 1.0
O X:HOH187 2.4 18.6 1.0
C4 X:U104 3.2 18.1 1.0
P X:A103 3.5 24.9 1.0
P X:C102 3.6 22.9 1.0
P X:G100 3.6 18.5 1.0
C5 X:U104 3.7 18.2 1.0
OP1 X:A103 4.0 29.6 1.0
O5' X:G100 4.1 17.6 1.0
O5' X:C102 4.1 25.1 1.0
O X:HOH297 4.2 27.0 1.0
O3' X:C102 4.3 26.0 1.0
O X:HOH222 4.3 27.5 1.0
C3' X:A101 4.4 20.1 1.0
N3 X:U104 4.4 19.4 1.0
N7 X:G100 4.4 18.0 1.0
O3' X:A101 4.5 24.2 1.0
C8 X:G100 4.5 15.9 1.0
O3' X:C99 4.5 16.2 1.0
C5' X:A101 4.6 20.7 1.0
O5' X:A103 4.6 23.4 1.0
C5' X:C102 4.6 24.6 1.0
OP1 X:C102 4.6 26.8 1.0
C3' X:C99 4.6 15.4 1.0
OP1 X:G100 4.6 17.1 1.0
OP2 X:C99 4.8 23.9 1.0
O5' X:C99 4.8 19.4 1.0
C4' X:A101 4.8 21.8 1.0
C3' X:C102 4.8 21.5 1.0
O5' X:A101 4.9 18.7 1.0

Manganese binding site 2 out of 25 in 3pdr

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Manganese binding site 2 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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 Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn177

b:19.2
occ:1.00
 OP1 X:U23 2.0 21.0 1.0
OP1 X:G100 2.1 17.1 1.0
O X:HOH209 2.3 17.9 1.0
O X:HOH327 2.3 16.9 1.0
O X:HOH203 2.3 20.4 1.0
O X:HOH316 2.4 23.6 1.0
P X:U23 3.3 20.2 1.0
P X:G100 3.3 18.5 1.0
O3' X:C99 3.5 16.2 1.0
O X:HOH518 3.7 21.5 1.0
OP2 X:U23 3.8 20.9 1.0
O3' X:G22 3.8 21.0 1.0
C5' X:G100 3.9 17.5 1.0
O5' X:G100 4.1 17.6 1.0
O X:HOH297 4.2 27.0 1.0
OP2 X:G157 4.3 18.1 1.0
O X:HOH246 4.3 32.4 1.0
OP1 X:G157 4.3 17.4 1.0
O X:HOH304 4.4 15.5 1.0
OP2 X:G100 4.5 16.6 1.0
OP1 X:G22 4.6 23.3 1.0
O5' X:U23 4.6 19.2 1.0
P X:G157 4.9 19.4 1.0
O2' X:C99 4.9 17.9 1.0
C3' X:C99 4.9 15.4 1.0

Manganese binding site 3 out of 25 in 3pdr

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Manganese binding site 3 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn178

b:22.4
occ:1.00
 OP1 X:A25 2.1 19.7 1.0
OP2 X:U24 2.1 21.3 1.0
O X:HOH498 2.2 23.0 1.0
O X:HOH272 2.2 19.8 1.0
O X:HOH247 2.3 24.8 1.0
O X:HOH279 2.4 21.9 1.0
P X:A25 3.4 20.0 1.0
P X:U24 3.5 21.2 1.0
O3' X:U24 3.8 20.7 1.0
O X:HOH211 3.9 25.2 1.0
N7 X:G26 4.1 25.8 1.0
O X:HOH332 4.1 23.7 1.0
O5' X:A25 4.2 22.9 1.0
OP1 X:U24 4.3 21.0 1.0
O6 X:G26 4.3 23.6 1.0
C2' X:U23 4.3 19.8 1.0
O X:HOH266 4.3 27.8 1.0
C3' X:U24 4.3 20.0 1.0
N3 X:C160 4.3 28.6 1.0
C5' X:U24 4.3 21.6 1.0
O3' X:U23 4.4 18.8 1.0
N7 X:A25 4.4 29.1 1.0
O5' X:U24 4.4 20.5 1.0
O X:HOH342 4.5 27.1 1.0
C3' X:U23 4.5 20.9 1.0
OP2 X:A25 4.5 22.1 1.0
O4 X:U161 4.6 27.6 1.0
C8 X:A25 4.6 26.8 1.0
C4' X:U24 4.8 20.0 1.0
C5 X:G26 4.9 22.6 1.0
N3 X:U161 4.9 28.8 1.0
O X:HOH328 4.9 26.3 1.0
N4 X:C160 4.9 26.4 1.0
C6 X:G26 4.9 23.3 1.0
O2 X:C160 5.0 29.6 1.0
O4 X:U159 5.0 23.4 1.0
C4 X:U161 5.0 27.2 1.0

Manganese binding site 4 out of 25 in 3pdr

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Manganese binding site 4 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn4

b:37.4
occ:0.85
 OP2 X:A72 2.0 28.9 1.0
O X:HOH299 2.3 23.6 1.0
O X:HOH471 2.4 36.6 1.0
O X:HOH288 2.6 32.0 1.0
P X:A72 3.5 27.9 1.0
N3 X:C69 4.1 30.8 1.0
N7 X:G73 4.1 26.6 1.0
O3' X:A71 4.3 27.6 1.0
O6 X:G73 4.3 25.5 1.0
O2 X:C69 4.3 28.5 1.0
O5' X:A72 4.4 24.9 1.0
OP1 X:A72 4.4 32.3 1.0
C3' X:A71 4.5 27.8 1.0
C5 X:G73 4.5 24.0 1.0
O5' X:A71 4.5 29.6 1.0
C6 X:G73 4.6 25.8 1.0
N7 X:A72 4.6 25.0 1.0
C2 X:C69 4.7 29.7 1.0
C8 X:A72 4.7 24.8 1.0
O X:HOH298 4.8 36.9 1.0
OP2 X:A71 4.8 29.7 1.0
C8 X:G73 4.9 26.5 1.0
P X:A71 5.0 30.7 1.0

Manganese binding site 5 out of 25 in 3pdr

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Manganese binding site 5 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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 Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn7

b:68.9
occ:1.00
 OP2 X:U119 2.1 52.7 1.0
OP1 X:A118 2.3 39.0 1.0
O X:HOH547 2.4 41.7 1.0
OP1 X:A117 3.0 50.0 1.0
P X:U119 3.5 59.3 1.0
OP2 X:A117 3.5 39.8 1.0
O X:HOH499 3.5 42.4 1.0
P X:A117 3.6 42.3 1.0
P X:A118 3.7 37.8 1.0
C5' X:U119 3.9 53.7 1.0
OP1 X:U119 4.2 63.9 1.0
O5' X:U119 4.2 55.3 1.0
O5' X:A117 4.3 35.1 1.0
O4' X:U119 4.3 65.8 1.0
O5' X:A118 4.4 35.3 1.0
OP2 X:A118 4.4 35.1 1.0
O3' X:A118 4.5 46.0 1.0
C5' X:A118 4.6 41.2 1.0
O2 X:U119 4.6 71.0 1.0
C4' X:U119 4.7 63.0 1.0
C3' X:A118 4.8 44.3 1.0
O3' X:A117 4.8 33.9 1.0

Manganese binding site 6 out of 25 in 3pdr

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Manganese binding site 6 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn9

b:36.1
occ:0.79
 OP2 X:C36 2.1 36.8 1.0
O X:HOH504 2.2 38.8 1.0
OP2 X:C35 2.2 34.8 1.0
O X:HOH523 2.3 40.0 1.0
O X:HOH524 2.3 43.4 1.0
O X:HOH522 2.4 42.5 1.0
P X:C35 3.4 35.9 1.0
P X:C36 3.5 37.1 1.0
OP1 X:C35 3.9 32.6 1.0
O3' X:C35 4.2 35.8 1.0
O5' X:C35 4.2 29.2 1.0
C5' X:C35 4.3 32.8 1.0
OP1 X:C36 4.3 44.4 1.0
OP2 X:C143 4.4 30.9 1.0
O5' X:C36 4.5 38.5 1.0
O3' X:U34 4.5 31.5 1.0
C3' X:C35 4.6 34.3 1.0
C5 X:C36 4.9 34.1 1.0

Manganese binding site 7 out of 25 in 3pdr

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Manganese binding site 7 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn10

b:23.4
occ:0.88
 O X:HOH501 2.2 20.6 1.0
O X:HOH502 2.2 22.9 1.0
OP2 X:A106 2.2 26.0 1.0
O X:HOH500 2.3 22.7 1.0
N7 X:G107 2.3 19.4 1.0
O X:HOH503 2.4 24.6 1.0
C8 X:G107 3.1 17.3 1.0
C5 X:G107 3.5 18.2 1.0
P X:A106 3.5 25.6 1.0
O6 X:G107 3.9 19.6 1.0
C6 X:G107 4.1 18.7 1.0
OP1 X:A106 4.1 24.3 1.0
O5' X:A106 4.2 22.0 1.0
N9 X:G107 4.4 18.7 1.0
N2 X:G100 4.4 17.0 1.0
OP2 X:A105 4.6 21.6 1.0
C4 X:G107 4.6 16.2 1.0
OP2 X:G107 4.6 25.2 1.0
O X:HOH280 4.6 26.6 1.0
O3' X:A105 4.7 24.9 1.0

Manganese binding site 8 out of 25 in 3pdr

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Manganese binding site 8 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn12

b:51.4
occ:1.00
 O X:HOH526 2.4 43.2 1.0
O X:HOH525 2.5 42.8 1.0
N7 X:G45 2.5 34.8 1.0
O X:HOH551 2.5 44.3 1.0
C8 X:G45 3.4 31.1 1.0
O X:HOH552 3.4 38.1 1.0
C5 X:G45 3.5 29.3 1.0
O6 X:G45 3.6 29.9 1.0
OP2 X:A44 3.7 36.0 1.0
C6 X:G45 4.0 31.9 1.0
C5 X:U138 4.1 34.4 1.0
O4 X:U138 4.3 34.0 1.0
C4 X:U138 4.6 33.5 1.0
N9 X:G45 4.6 28.6 1.0
C4 X:G45 4.7 28.7 1.0
O X:HOH423 4.8 43.3 1.0
OP2 X:G45 4.8 38.6 1.0
N7 X:A44 4.9 31.2 1.0
P X:A44 4.9 39.0 1.0

Manganese binding site 9 out of 25 in 3pdr

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Manganese binding site 9 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn13

b:41.0
occ:1.00
 O X:HOH506 2.1 30.5 1.0
OP1 X:U129 2.2 31.8 1.0
OP2 X:A128 2.2 27.8 1.0
OP1 X:G127 2.3 25.8 1.0
O X:HOH505 3.0 37.7 1.0
P X:G127 3.5 28.3 1.0
P X:U129 3.6 33.0 1.0
P X:A128 3.7 32.2 1.0
C3' X:A128 3.9 26.9 1.0
O5' X:G127 3.9 24.8 1.0
C5' X:G127 4.1 26.4 1.0
O3' X:A128 4.2 27.3 1.0
OP2 X:G127 4.4 27.4 1.0
C5' X:A128 4.4 30.3 1.0
O5' X:A128 4.4 27.3 1.0
OP1 X:A128 4.5 34.5 1.0
OP2 X:U129 4.5 30.9 1.0
C4' X:A128 4.6 30.3 1.0
O5' X:U129 4.7 32.2 1.0
O3' X:G127 4.7 30.8 1.0
O3' X:G126 4.7 24.2 1.0

Manganese binding site 10 out of 25 in 3pdr

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Manganese binding site 10 out of 25 in the Crystal Structure of Manganese Bound M-Box Rna


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 Manganese Bound M-Box Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mn14

b:23.5
occ:1.00
 OP2 X:G31 2.1 18.1 1.0
OP2 X:A30 2.2 20.7 1.0
O X:HOH507 2.2 28.4 1.0
O X:HOH510 2.2 28.5 1.0
O X:HOH509 2.3 22.3 1.0
O X:HOH508 2.4 26.3 1.0
P X:A30 3.4 22.8 1.0
P X:G31 3.6 16.7 1.0
O5' X:A30 3.7 20.9 1.0
O3' X:G29 4.0 21.2 1.0
O2' X:G29 4.3 19.6 1.0
OP1 X:G31 4.3 18.3 1.0
N7 X:G31 4.3 17.0 1.0
O5' X:G31 4.4 17.4 1.0
O A:HOH316 4.4 22.9 1.0
O X:HOH313 4.4 26.1 1.0
O3' X:A30 4.4 19.5 1.0
C5' X:A30 4.5 18.1 1.0
C8 X:G31 4.5 18.1 1.0
O X:HOH250 4.5 29.4 1.0
C3' X:A30 4.6 16.8 1.0
O X:HOH242 4.6 28.2 1.0
C3' X:G29 4.7 18.2 1.0
OP1 X:A30 4.7 22.6 1.0

Reference:

A.Ramesh, C.A.Wakeman, W.C.Winkler. Insights Into Metalloregulation By M-Box Riboswitch Rnas Via Structural Analysis of Manganese-Bound Complexes. J.Mol.Biol. V. 407 556 2011.
ISSN: ISSN 0022-2836
PubMed: 21315082
DOI: 10.1016/J.JMB.2011.01.049
Page generated: Sat Oct 5 17:29:39 2024

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