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Strontium in PDB 1nuv: The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution

Protein crystallography data

The structure of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution, PDB code: 1nuv was solved by J.E.Wedekind, D.B.Mckay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.10 / 1.81
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.600, 60.600, 133.100, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 21.9

Other elements in 1nuv:

The structure of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution (pdb code 1nuv). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 6 binding sites of Strontium where determined in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution, PDB code: 1nuv:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 1nuv

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Strontium binding site 1 out of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr424

b:68.9
occ:1.00
O B:HOH466 2.2 41.3 1.0
O B:HOH467 2.2 43.5 1.0
O B:HOH465 2.3 38.8 1.0
O B:HOH456 2.8 26.3 1.0
N7 B:G44 4.0 27.5 1.0
O B:HOH457 4.1 28.5 1.0
N6 B:A45 4.2 30.3 1.0
O A:HOH424 4.2 40.0 1.0
O B:HOH461 4.3 49.1 1.0
O A:HOH449 4.3 43.8 1.0
N3 A:C23 4.5 29.8 1.0
O6 B:G44 4.5 27.8 1.0
N7 B:G43 4.5 20.6 1.0
OP2 B:G43 4.6 26.7 1.0
N4 A:C23 4.6 32.2 1.0
O A:HOH422 4.7 33.4 1.0
C5 B:G44 5.0 26.3 1.0
C8 B:G44 5.0 28.6 1.0
C8 B:G43 5.0 21.8 1.0

Strontium binding site 2 out of 6 in 1nuv

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Strontium binding site 2 out of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr420

b:57.2
occ:1.00
O C:HOH157 2.3 45.7 1.0
O C:HOH147 2.7 55.5 1.0
O C:HOH325 2.8 43.6 1.0
N1 D:A45 2.9 25.9 1.0
OP1 C:A25 2.9 20.9 1.0
O C:HOH395 3.0 33.0 1.0
C2 D:A45 3.1 22.8 1.0
O2 C:C23 3.4 38.0 1.0
O2' C:C23 3.8 37.4 1.0
P C:A25 3.9 20.9 1.0
OP2 C:A25 3.9 21.3 1.0
C6 D:A45 4.1 25.4 1.0
N3 D:A45 4.4 26.6 1.0
C2 C:C23 4.4 35.1 1.0
N6 D:A45 4.5 26.0 1.0
O C:HOH244 4.8 40.2 1.0
C1' C:C23 4.8 36.0 1.0
O6 D:G44 4.8 26.1 1.0
C2' C:C23 4.8 37.1 1.0
O5' C:A25 4.8 20.0 1.0

Strontium binding site 3 out of 6 in 1nuv

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Strontium binding site 3 out of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr422

b:85.1
occ:1.00
O D:HOH123 2.3 28.3 1.0
O D:HOH192 2.5 44.1 1.0
O D:HOH121 2.6 48.2 1.0
O D:HOH186 4.1 48.9 1.0
O C:HOH197 4.3 56.3 1.0
O D:HOH183 4.4 32.0 1.0
O D:HOH135 4.6 42.9 1.0
O D:HOH139 4.9 27.8 1.0
O6 D:G43 5.0 18.7 1.0
N7 D:G42 5.0 23.3 1.0
O6 D:G42 5.0 19.5 1.0

Strontium binding site 4 out of 6 in 1nuv

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Strontium binding site 4 out of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr421

b:53.6
occ:1.00
O E:HOH82 2.4 42.0 1.0
O F:HOH114 2.5 50.7 1.0
N1 F:A45 2.8 23.8 1.0
OP1 E:A25 2.8 21.3 1.0
O E:HOH329 2.9 46.9 1.0
O E:HOH83 3.1 34.2 1.0
C2 F:A45 3.2 22.8 1.0
O2 E:C23 3.4 35.0 1.0
O2' E:C23 3.8 41.3 1.0
P E:A25 3.9 20.6 1.0
OP2 E:A25 3.9 19.4 1.0
C6 F:A45 4.0 22.9 1.0
N6 F:A45 4.4 23.4 1.0
C2 E:C23 4.4 32.8 1.0
N3 F:A45 4.5 26.8 1.0
O C:HOH393 4.8 34.2 1.0
O E:HOH340 4.8 35.6 1.0
O6 F:G44 4.8 27.1 1.0
C1' E:C23 4.8 35.7 1.0
O5' E:A25 4.8 18.4 1.0
C2' E:C23 4.8 39.5 1.0

Strontium binding site 5 out of 6 in 1nuv

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Strontium binding site 5 out of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr425

b:84.6
occ:1.00
O F:HOH331 2.2 29.6 1.0
O F:HOH330 2.3 44.4 1.0
O F:HOH392 2.4 48.0 1.0
O F:HOH397 4.2 58.5 1.0
O F:HOH387 4.5 32.7 1.0
O F:HOH92 4.6 36.1 1.0
O6 F:G42 4.9 19.3 1.0
O6 F:G43 4.9 20.3 1.0
N7 F:G42 4.9 24.0 1.0
O F:HOH396 5.0 30.0 1.0

Strontium binding site 6 out of 6 in 1nuv

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Strontium binding site 6 out of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sr423

b:65.4
occ:1.00
O H:HOH236 2.1 48.0 1.0
O H:HOH243 2.2 35.2 1.0
O H:HOH270 2.3 31.4 1.0
O G:HOH284 2.4 31.1 1.0
O H:HOH283 2.7 25.6 1.0
N7 H:G44 4.1 28.6 1.0
O G:HOH234 4.2 39.1 1.0
N6 H:A45 4.2 28.5 1.0
O H:HOH358 4.2 27.5 1.0
O H:HOH354 4.3 49.1 1.0
O G:HOH261 4.4 43.0 1.0
N3 G:C23 4.5 30.7 1.0
N7 H:G43 4.5 22.0 1.0
OP2 H:G43 4.5 28.7 1.0
O6 H:G44 4.6 28.2 1.0
N4 G:C23 4.6 32.6 1.0
O G:HOH229 4.7 36.3 1.0
O G:HOH403 4.9 51.7 1.0
C8 H:G43 4.9 23.0 1.0

Reference:

J.E.Wedekind, D.B.Mckay. Crystal Structure of the Leadzyme at 1.8 A Resolution: Metal Ion Binding and the Implications For Catalytic Mechanism and Allo Site Ion Regulation. Biochemistry V. 42 9554 2003.
ISSN: ISSN 0006-2960
PubMed: 12911297
DOI: 10.1021/BI0300783
Page generated: Wed Dec 16 02:10:36 2020

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