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Magnesium in PDB 1nuj: The Leadzyme Structure Bound to Mg(H20)6(II) at 1.8 A Resolution

Protein crystallography data

The structure of The Leadzyme Structure Bound to Mg(H20)6(II) at 1.8 A Resolution, PDB code: 1nuj 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) 29.31 / 1.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.100, 60.100, 133.100, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Leadzyme Structure Bound to Mg(H20)6(II) at 1.8 A Resolution (pdb code 1nuj). 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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution, PDB code: 1nuj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1nuj

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Magnesium binding site 1 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg417

b:35.1
occ:1.00
 O A:HOH419 2.1 24.2 1.0
O B:HOH420 2.1 25.9 1.0
O B:HOH421 2.2 25.0 1.0
O A:HOH420 2.2 30.2 1.0
O B:HOH422 2.2 38.2 1.0
O A:HOH421 2.2 30.8 1.0
O B:HOH461 3.6 60.9 1.0
O B:HOH429 4.0 34.8 1.0
O4 B:U47 4.1 29.1 1.0
O6 A:G19 4.2 25.5 1.0
O B:HOH440 4.3 31.9 1.0
N7 A:G19 4.3 23.3 1.0
O6 A:G20 4.3 25.9 1.0
O A:HOH440 4.4 50.4 1.0
O B:HOH430 4.5 55.7 1.0
N4 B:C48 4.7 24.9 1.0
N4 A:C18 4.7 20.4 1.0
N6 A:A21 4.8 22.9 1.0
C6 A:G19 4.9 22.6 1.0
C5 A:G19 4.9 23.9 1.0

Magnesium binding site 2 out of 10 in 1nuj

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Magnesium binding site 2 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg418

b:30.1
occ:1.00
 O A:HOH423 2.2 24.9 1.0
O A:HOH425 2.2 24.5 1.0
O B:HOH423 2.2 24.0 1.0
O B:HOH424 2.2 26.1 1.0
O A:HOH422 2.2 23.7 1.0
O A:HOH424 2.3 20.6 1.0
O A:HOH454 4.0 25.7 1.0
N6 A:A29 4.1 22.3 1.0
O B:HOH451 4.2 23.9 1.0
O A:HOH433 4.2 37.5 1.0
O6 B:G39 4.3 24.0 1.0
O A:HOH468 4.3 32.2 1.0
N7 A:A29 4.4 24.8 1.0
O A:HOH432 4.4 27.6 1.0
O B:HOH432 4.5 26.7 1.0
O6 A:G30 4.5 19.9 1.0
C6 A:A29 4.9 22.9 1.0
C5 A:A29 5.0 23.2 1.0

Magnesium binding site 3 out of 10 in 1nuj

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Magnesium binding site 3 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg419

b:28.3
occ:1.00
 O B:HOH428 2.1 46.4 1.0
O B:HOH426 2.2 37.9 1.0
O B:HOH427 2.2 23.8 1.0
O A:HOH426 2.2 27.5 1.0
O B:HOH425 2.2 31.9 1.0
O A:HOH427 2.3 37.7 1.0
OP1 A:A25 4.1 33.1 1.0
O4 B:U41 4.1 22.1 1.0
O6 B:G42 4.2 24.4 1.0
O B:HOH452 4.2 24.6 1.0
O B:HOH437 4.2 36.3 1.0
O B:HOH453 4.3 26.1 1.0
O B:HOH431 4.3 27.1 1.0
O6 B:G43 4.4 25.2 1.0
O A:HOH428 4.4 27.9 1.0
OP2 A:G26 4.5 29.0 1.0
N7 B:G42 4.6 25.1 1.0
C4 B:U41 4.6 20.9 1.0
C5 B:U41 4.6 21.7 1.0
O B:HOH439 4.7 44.8 1.0
O A:HOH461 4.9 48.0 1.0
N4 A:C27 4.9 23.3 1.0

Magnesium binding site 4 out of 10 in 1nuj

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Magnesium binding site 4 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg425

b:64.9
occ:1.00
 O C:HOH391 2.0 45.3 1.0
O C:HOH363 2.1 35.7 1.0
O C:HOH184 2.1 34.9 1.0
O C:HOH307 2.3 33.0 1.0
O C:HOH392 2.4 53.6 1.0
O D:HOH364 2.4 32.6 1.0
O C:HOH393 3.6 44.4 1.0
O6 C:G30 3.7 28.7 1.0
N6 C:A29 3.8 21.9 1.0
O C:HOH133 4.0 44.3 1.0
O C:HOH124 4.3 23.2 1.0
N7 C:A29 4.3 26.4 1.0
O D:HOH185 4.4 43.7 1.0
N4 D:C40 4.6 26.0 1.0
O C:HOH200 4.6 44.8 1.0
C6 C:A29 4.6 25.0 1.0
O D:HOH152 4.7 31.8 1.0
O6 D:G39 4.7 25.9 1.0
C5 C:A29 4.8 25.6 1.0
C6 C:G30 4.8 31.1 1.0

Magnesium binding site 5 out of 10 in 1nuj

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Magnesium binding site 5 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg426

b:41.8
occ:1.00
 O D:HOH371 2.1 29.3 1.0
O C:HOH131 2.2 27.2 1.0
O C:HOH137 2.2 28.6 1.0
O C:HOH166 2.2 35.5 1.0
O D:HOH160 2.3 32.9 1.0
O D:HOH178 2.5 41.4 1.0
O6 C:G19 3.9 21.2 1.0
O C:HOH138 4.1 56.4 1.0
O D:HOH189 4.1 34.3 1.0
O C:HOH145 4.2 44.5 1.0
N7 C:G19 4.2 24.0 1.0
O C:HOH271 4.3 38.3 1.0
O6 C:G20 4.3 22.4 1.0
O D:HOH132 4.3 25.3 1.0
O D:HOH127 4.4 44.1 1.0
O4 D:U47 4.4 24.2 1.0
C6 C:G19 4.6 21.8 1.0
C5 C:G19 4.7 23.4 1.0
N4 D:C48 4.9 19.5 1.0

Magnesium binding site 6 out of 10 in 1nuj

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Magnesium binding site 6 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg423

b:38.9
occ:1.00
 O E:HOH443 2.1 30.8 1.0
O F:HOH82 2.2 27.1 1.0
O E:HOH431 2.2 29.3 1.0
O E:HOH432 2.2 26.9 1.0
O F:HOH99 2.2 35.5 1.0
O F:HOH68 2.3 35.6 1.0
O6 E:G19 3.8 21.9 1.0
O E:HOH451 4.1 39.8 1.0
N7 E:G19 4.2 24.5 1.0
O E:HOH436 4.2 42.5 1.0
O F:HOH88 4.2 38.4 1.0
O F:HOH56 4.2 23.8 1.0
O6 E:G20 4.3 21.2 1.0
O E:HOH433 4.3 51.3 1.0
O4 F:U47 4.4 23.1 1.0
C6 E:G19 4.5 22.8 1.0
C5 E:G19 4.7 23.3 1.0
O E:HOH476 4.8 53.6 1.0
N4 F:C48 4.8 20.5 1.0

Magnesium binding site 7 out of 10 in 1nuj

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Magnesium binding site 7 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg424

b:66.4
occ:1.00
 O E:HOH477 2.0 57.0 1.0
O E:HOH469 2.1 37.4 1.0
O F:HOH81 2.1 36.1 1.0
O E:HOH453 2.2 37.5 1.0
O E:HOH459 2.3 48.5 1.0
O E:HOH454 2.6 29.9 1.0
O E:HOH448 4.0 42.9 1.0
O F:HOH83 4.1 45.5 1.0
O E:HOH430 4.2 25.4 1.0
O F:HOH90 4.3 59.2 1.0
O F:HOH64 4.3 27.0 1.0
O6 E:G30 4.4 31.9 1.0
N6 E:A29 4.5 20.8 1.0
O E:HOH471 4.7 33.7 1.0
O6 F:G39 4.8 23.1 1.0
N4 F:C40 4.9 24.6 1.0
N7 E:A29 4.9 27.1 1.0

Magnesium binding site 8 out of 10 in 1nuj

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Magnesium binding site 8 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg420

b:33.5
occ:1.00
 O G:HOH232 2.1 29.5 1.0
O G:HOH231 2.1 26.8 1.0
O G:HOH229 2.1 22.7 1.0
O G:HOH230 2.2 23.2 1.0
O H:HOH228 2.2 26.0 1.0
O G:HOH233 2.2 40.9 1.0
O6 G:G19 4.1 24.1 1.0
O H:HOH240 4.2 35.4 1.0
N7 G:G19 4.2 23.4 1.0
O4 H:U47 4.2 28.0 1.0
O G:HOH261 4.3 57.2 1.0
O H:HOH255 4.3 35.3 1.0
O G:HOH259 4.3 46.0 1.0
O6 G:G20 4.3 24.9 1.0
N4 G:C18 4.7 23.0 1.0
N4 H:C48 4.8 24.1 1.0
C6 G:G19 4.8 20.2 1.0
C5 G:G19 4.8 22.7 1.0
C5 G:C18 4.9 24.6 1.0
N6 G:A21 4.9 24.8 1.0
C4 G:C18 4.9 23.2 1.0

Magnesium binding site 9 out of 10 in 1nuj

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Magnesium binding site 9 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg421

b:30.7
occ:1.00
 O G:HOH211 2.1 26.7 1.0
O G:HOH210 2.2 23.4 1.0
O H:HOH209 2.2 25.8 1.0
O G:HOH212 2.2 27.0 1.0
O G:HOH213 2.2 18.8 1.0
O G:HOH214 2.3 24.4 1.0
O G:HOH298 4.1 21.7 1.0
N6 G:A29 4.2 21.3 1.0
O H:HOH299 4.2 23.7 1.0
O6 H:G39 4.2 24.2 1.0
O G:HOH219 4.3 26.6 1.0
O G:HOH220 4.3 33.2 1.0
O G:HOH277 4.4 32.4 1.0
N7 G:A29 4.4 24.5 1.0
O H:HOH216 4.5 24.9 1.0
O6 G:G30 4.6 20.2 1.0
C6 G:A29 5.0 21.8 1.0
O G:HOH370 5.0 55.2 1.0

Magnesium binding site 10 out of 10 in 1nuj

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Magnesium binding site 10 out of 10 in the The Leadzyme Structure Bound to Mg(H20)6(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 Structure Bound to Mg(H20)6(II) at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg422

b:29.8
occ:1.00
 O H:HOH239 2.1 38.3 1.0
O H:HOH234 2.2 28.7 1.0
O G:HOH235 2.2 30.9 1.0
O H:HOH237 2.2 23.4 1.0
O G:HOH238 2.3 35.7 1.0
O H:HOH236 2.3 32.2 1.0
O4 H:U41 4.1 22.0 1.0
OP1 G:A25 4.1 33.9 1.0
O6 H:G42 4.2 21.5 1.0
O G:HOH351 4.2 35.4 1.0
O H:HOH300 4.2 25.3 1.0
O H:HOH254 4.4 46.2 1.0
O6 H:G43 4.4 26.3 1.0
O H:HOH368 4.4 26.9 1.0
O G:HOH215 4.5 32.6 1.0
O H:HOH301 4.5 27.8 1.0
OP2 G:G26 4.5 28.8 1.0
N7 H:G42 4.6 24.4 1.0
C4 H:U41 4.6 20.8 1.0
C5 H:U41 4.6 21.7 1.0
N4 G:C27 4.9 22.0 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: Tue Aug 13 10:23:02 2024

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