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Magnesium 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:

Strontium (Sr) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 10 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1nuv

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Magnesium binding site 1 out of 10 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 Magnesium with other atoms in the Mg 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
A:Mg410

b:38.6
occ:1.00
 O A:HOH412 2.0 28.4 1.0
O A:HOH413 2.0 29.3 1.0
O A:HOH415 2.0 27.8 1.0
O A:HOH416 2.2 32.7 1.0
O B:HOH425 2.2 39.2 1.0
O A:HOH414 2.2 40.5 1.0
O B:HOH458 3.9 23.5 1.0
O A:HOH464 4.0 36.8 1.0
O B:HOH431 4.1 39.7 1.0
O4 B:U47 4.2 24.7 1.0
O6 A:G19 4.2 23.5 1.0
O B:HOH443 4.3 39.1 1.0
O6 A:G20 4.3 25.4 1.0
N7 A:G19 4.3 23.1 1.0
O B:HOH445 4.4 38.3 1.0
O A:HOH425 4.5 54.8 1.0
O A:HOH440 4.5 38.9 1.0
N6 A:A21 4.7 26.4 1.0
N4 B:C48 4.7 23.5 1.0
N4 A:C18 4.8 23.6 1.0
C6 A:G19 4.9 22.3 1.0
C5 A:G19 5.0 23.0 1.0

Magnesium binding site 2 out of 10 in 1nuv

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Magnesium binding site 2 out of 10 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 Magnesium with other atoms in the Mg 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
A:Mg411

b:27.5
occ:1.00
 O B:HOH426 2.0 29.8 1.0
O A:HOH420 2.2 25.9 1.0
O A:HOH418 2.2 25.7 1.0
O A:HOH419 2.2 20.1 1.0
O A:HOH417 2.2 25.8 1.0
O B:HOH427 2.3 29.4 1.0
O A:HOH457 4.1 22.9 1.0
O B:HOH454 4.1 20.6 1.0
N6 A:A29 4.2 19.6 1.0
O6 B:G39 4.2 22.9 1.0
O A:HOH431 4.2 29.9 1.0
O A:HOH430 4.3 27.5 1.0
O B:HOH434 4.3 27.6 1.0
N7 A:A29 4.4 23.0 1.0
O A:HOH451 4.5 28.3 1.0
O6 A:G30 4.6 20.6 1.0
C6 A:A29 5.0 17.9 1.0

Magnesium binding site 3 out of 10 in 1nuv

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Magnesium binding site 3 out of 10 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 Magnesium with other atoms in the Mg 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
B:Mg412

b:26.8
occ:1.00
 O A:HOH422 2.0 33.4 1.0
O B:HOH430 2.1 27.4 1.0
O B:HOH429 2.2 19.8 1.0
O A:HOH421 2.2 24.3 1.0
O B:HOH428 2.3 27.4 1.0
O A:HOH423 2.4 41.8 1.0
OP1 A:A25 4.0 28.2 1.0
O B:HOH441 4.2 26.6 1.0
O B:HOH455 4.2 24.7 1.0
O4 B:U41 4.3 19.8 1.0
O B:HOH456 4.3 26.3 1.0
O B:HOH442 4.4 50.7 1.0
O B:HOH433 4.4 25.9 1.0
O6 B:G42 4.4 21.1 1.0
O6 B:G43 4.6 20.8 1.0
OP2 A:G26 4.6 22.7 1.0
N7 B:G42 4.6 21.6 1.0
C5 B:U41 4.6 19.1 1.0
O A:HOH469 4.7 44.9 1.0
C4 B:U41 4.7 19.5 1.0

Magnesium binding site 4 out of 10 in 1nuv

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Magnesium binding site 4 out of 10 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 Magnesium with other atoms in the Mg 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
C:Mg418

b:34.0
occ:1.00
 O C:HOH371 2.3 42.9 1.0
O D:HOH372 2.4 42.5 1.0
O C:HOH286 2.4 31.7 1.0
O C:HOH198 2.4 30.8 1.0
O C:HOH180 2.6 27.5 1.0
O C:HOH151 3.1 31.1 1.0
O C:HOH132 4.0 29.9 1.0
O C:HOH124 4.4 22.9 1.0
N6 C:A29 4.5 21.4 1.0
N7 C:A29 4.5 24.8 1.0
O D:HOH181 4.7 33.5 1.0
O D:HOH150 4.7 29.8 1.0
O C:HOH190 4.7 34.5 1.0
O6 C:G30 4.8 25.6 1.0
O C:HOH167 4.9 32.5 1.0

Magnesium binding site 5 out of 10 in 1nuv

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Magnesium binding site 5 out of 10 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 Magnesium with other atoms in the Mg 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
C:Mg419

b:74.8
occ:1.00
 O C:HOH136 2.1 29.3 1.0
O D:HOH348 2.2 32.5 1.0
O C:HOH130 2.5 31.1 1.0
O D:HOH158 2.7 30.3 1.0
O D:HOH173 3.5 47.0 1.0
O C:HOH142 3.5 40.6 1.0
O C:HOH137 3.7 48.2 1.0
O D:HOH185 4.3 42.8 1.0
O6 C:G19 4.4 21.4 1.0
O4 D:U47 4.4 22.3 1.0
O6 C:G20 4.6 25.9 1.0
N7 C:G19 4.6 20.1 1.0
O D:HOH131 4.7 26.7 1.0
N6 C:A21 5.0 21.1 1.0
OP2 D:A45 5.0 26.9 1.0

Magnesium binding site 6 out of 10 in 1nuv

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Magnesium binding site 6 out of 10 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 Magnesium with other atoms in the Mg 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
E:Mg416

b:56.1
occ:1.00
 O F:HOH294 2.1 34.4 1.0
O E:HOH112 2.2 34.4 1.0
O E:HOH93 2.2 26.7 1.0
O E:HOH305 2.2 48.4 1.0
O E:HOH117 2.5 32.6 1.0
O E:HOH90 2.6 33.6 1.0
O F:HOH390 3.8 37.0 1.0
O F:HOH377 3.8 31.2 1.0
O E:HOH99 4.1 44.9 1.0
O6 E:G19 4.2 21.5 1.0
O E:HOH94 4.2 50.9 1.0
O4 F:U47 4.3 21.5 1.0
O F:HOH91 4.3 27.8 1.0
O F:HOH375 4.5 33.0 1.0
O E:HOH292 4.7 37.4 1.0
O6 E:G20 4.7 25.4 1.0
N7 E:G19 4.7 22.2 1.0
O E:HOH164 4.7 52.7 1.0
C6 E:G19 5.0 21.2 1.0

Magnesium binding site 7 out of 10 in 1nuv

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Magnesium binding site 7 out of 10 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 Magnesium with other atoms in the Mg binding site number 7 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:Mg417

b:30.2
occ:1.00
 O F:HOH293 2.1 34.7 1.0
O E:HOH302 2.1 36.0 1.0
O E:HOH370 2.1 45.3 1.0
O E:HOH367 2.3 45.2 1.0
O E:HOH287 2.5 29.1 1.0
O E:HOH285 2.5 31.2 1.0
O E:HOH291 4.1 34.3 1.0
O F:HOH295 4.4 34.6 1.0
O E:HOH85 4.4 23.7 1.0
O F:HOH106 4.5 30.4 1.0
N6 E:A29 4.5 20.5 1.0
O6 E:G30 4.7 25.1 1.0
N7 E:A29 4.8 25.9 1.0
O6 F:G39 4.8 22.4 1.0
O E:HOH389 4.9 36.4 1.0

Magnesium binding site 8 out of 10 in 1nuv

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Magnesium binding site 8 out of 10 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 Magnesium with other atoms in the Mg binding site number 8 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
G:Mg413

b:45.8
occ:1.00
 O H:HOH223 1.9 31.0 1.0
O G:HOH225 2.0 35.4 1.0
O G:HOH222 2.0 26.1 1.0
O H:HOH226 2.2 28.9 1.0
O G:HOH224 2.2 38.2 1.0
O H:HOH221 2.3 37.9 1.0
O H:HOH233 3.9 46.2 1.0
O H:HOH96 3.9 23.6 1.0
O6 G:G19 4.2 25.2 1.0
O4 H:U47 4.3 24.9 1.0
O6 G:G20 4.3 25.5 1.0
O G:HOH399 4.3 42.6 1.0
N7 G:G19 4.3 27.4 1.0
O H:HOH246 4.4 42.3 1.0
O G:HOH239 4.6 58.7 1.0
N6 G:A21 4.7 26.7 1.0
N4 H:C48 4.8 23.5 1.0
C6 G:G19 4.9 25.5 1.0
N4 G:C18 4.9 23.9 1.0
C5 G:G19 5.0 26.3 1.0

Magnesium binding site 9 out of 10 in 1nuv

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Magnesium binding site 9 out of 10 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 Magnesium with other atoms in the Mg binding site number 9 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
G:Mg414

b:26.4
occ:1.00
 O G:HOH206 2.1 26.1 1.0
O H:HOH201 2.1 26.3 1.0
O G:HOH205 2.1 22.6 1.0
O G:HOH203 2.2 24.6 1.0
O H:HOH204 2.3 23.7 1.0
O G:HOH202 2.3 29.4 1.0
O G:HOH280 4.1 18.8 1.0
O H:HOH281 4.2 25.0 1.0
O6 H:G39 4.2 23.3 1.0
N6 G:A29 4.2 18.4 1.0
O G:HOH212 4.3 24.9 1.0
O G:HOH213 4.3 29.1 1.0
O H:HOH209 4.4 30.6 1.0
N7 G:A29 4.4 22.7 1.0
O G:HOH264 4.5 28.9 1.0
O G:HOH381 4.5 39.8 1.0
O6 G:G30 4.6 22.4 1.0

Magnesium binding site 10 out of 10 in 1nuv

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Magnesium binding site 10 out of 10 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 Magnesium with other atoms in the Mg binding site number 10 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:Mg415

b:24.4
occ:1.00
 O G:HOH229 2.0 36.3 1.0
O H:HOH232 2.1 29.1 1.0
O H:HOH230 2.2 17.4 1.0
O G:HOH231 2.2 37.3 1.0
O G:HOH228 2.2 23.8 1.0
O H:HOH227 2.3 25.6 1.0
OP1 G:A25 4.0 27.7 1.0
O H:HOH357 4.1 31.6 1.0
O4 H:U41 4.2 19.0 1.0
O H:HOH282 4.4 24.7 1.0
O6 H:G42 4.4 20.8 1.0
O H:HOH283 4.4 25.6 1.0
O H:HOH369 4.4 25.3 1.0
O H:HOH245 4.4 42.4 1.0
O G:HOH402 4.5 39.2 1.0
O6 H:G43 4.5 21.0 1.0
OP2 G:G26 4.6 23.3 1.0
N7 H:G42 4.6 21.1 1.0
C5 H:U41 4.6 17.8 1.0
C4 H:U41 4.7 18.8 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: Tue Aug 13 10:23:46 2024

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