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Magnesium in PDB 3nkb: A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage

Protein crystallography data

The structure of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage, PDB code: 3nkb was solved by J.-H.Chen, R.Yajima, D.M.Chadalavada, E.Chase, P.C.Bevilacqua, B.L.Golden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.36 / 1.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 64.837, 84.107, 102.020, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage (pdb code 3nkb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage, PDB code: 3nkb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3nkb

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Magnesium binding site 1 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:58.5
occ:1.00
O B:HOH661 2.4 39.9 1.0
O B:HOH656 2.5 54.5 1.0
OP1 B:G35 2.6 31.1 1.0
O B:HOH615 2.6 48.5 1.0
O B:HOH635 2.6 48.7 1.0
O B:HOH663 3.0 49.5 1.0
P B:G35 3.7 33.0 1.0
O6 B:G63 3.7 36.3 1.0
O B:HOH577 3.8 35.3 1.0
OP2 B:G35 4.0 33.4 1.0
N1 B:G63 4.5 31.9 1.0
C6 B:G63 4.5 37.9 1.0
O5' B:G35 4.7 33.6 1.0
O3' B:A34 4.8 30.4 1.0

Magnesium binding site 2 out of 10 in 3nkb

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Magnesium binding site 2 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:53.4
occ:1.00
O B:HOH570 2.6 40.4 1.0
O B:HOH651 2.7 39.5 1.0
O B:HOH652 3.4 46.0 1.0
O B:HOH639 4.2 39.1 1.0
OP2 B:C25 4.3 27.9 1.0
O B:HOH628 4.3 36.9 1.0
O B:HOH618 4.5 40.8 1.0
OP1 B:C25 4.6 32.3 1.0
O B:HOH557 4.8 26.7 1.0
O B:HOH548 4.8 29.5 1.0
P B:C25 4.9 31.8 1.0

Magnesium binding site 3 out of 10 in 3nkb

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Magnesium binding site 3 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:41.9
occ:1.00
O B:HOH514 2.3 29.8 1.0
O B:HOH515 2.4 40.9 1.0
O B:HOH555 2.4 35.2 1.0
O B:HOH511 2.4 40.9 1.0
O B:HOH513 2.5 30.9 1.0
O B:HOH510 2.6 47.9 1.0
OP1 B:A52 3.9 34.2 1.0
N7 B:G50 4.1 28.1 1.0
O B:HOH519 4.1 33.9 1.0
O B:HOH518 4.1 35.6 1.0
O B:HOH581 4.2 32.7 1.0
OP2 B:A52 4.2 29.5 1.0
O6 B:G50 4.5 36.3 1.0
P B:A52 4.6 34.0 1.0
O B:HOH512 4.7 38.2 1.0
C5 B:G50 4.7 31.1 1.0
C8 B:G50 4.9 31.2 1.0
C6 B:G50 4.9 33.0 1.0

Magnesium binding site 4 out of 10 in 3nkb

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Magnesium binding site 4 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:42.7
occ:1.00
O4 B:U56 2.3 36.2 1.0
OP2 B:G55 2.4 36.1 1.0
O B:HOH509 2.4 47.3 1.0
O B:HOH516 2.5 42.9 1.0
O B:HOH508 2.5 49.1 1.0
O B:HOH507 2.5 41.2 1.0
C4 B:U56 3.2 38.2 1.0
C5 B:U56 3.6 35.1 1.0
P B:G55 3.8 41.3 1.0
O B:HOH520 4.3 37.8 1.0
O B:HOH585 4.3 44.0 1.0
O B:HOH586 4.4 45.5 1.0
O B:HOH608 4.5 44.1 1.0
N3 B:U56 4.5 33.5 1.0
OP1 B:G55 4.6 42.4 1.0
O3' B:G54 4.6 39.1 1.0
C3' B:G54 4.6 37.7 1.0
O5' B:G55 4.6 35.8 1.0
O B:HOH606 4.7 43.3 1.0
C5' B:G54 4.9 36.7 1.0
C6 B:U56 5.0 33.1 1.0

Magnesium binding site 5 out of 10 in 3nkb

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Magnesium binding site 5 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:39.1
occ:1.00
OP2 B:A58 2.2 32.2 1.0
O B:HOH506 2.2 35.4 1.0
OP2 B:A57 2.3 34.5 1.0
O B:HOH543 2.3 27.2 1.0
O B:HOH502 2.4 34.0 1.0
O B:HOH504 2.5 36.4 1.0
P B:A57 3.4 33.3 1.0
O3' B:U56 3.4 31.7 1.0
P B:A58 3.6 33.9 1.0
O B:HOH505 3.9 36.4 1.0
N7 B:A58 4.0 31.2 1.0
O B:HOH503 4.1 32.8 1.0
C3' B:A57 4.1 35.8 1.0
O5' B:A57 4.1 34.1 1.0
O B:HOH559 4.2 32.5 1.0
O3' B:A57 4.2 35.5 1.0
C8 B:A58 4.3 27.9 1.0
O2' B:U56 4.3 34.0 1.0
O5' B:A58 4.4 31.9 1.0
O B:HOH535 4.5 43.7 1.0
C2' B:C41 4.5 31.0 1.0
OP1 B:A57 4.6 33.9 1.0
OP1 B:A58 4.6 34.9 1.0
C3' B:U56 4.7 31.0 1.0
O B:HOH582 4.8 45.8 1.0
O2' B:C41 4.8 35.4 1.0
C5' B:A57 4.8 35.2 1.0
C8 B:A57 4.8 30.3 1.0
C2' B:A57 5.0 35.8 1.0

Magnesium binding site 6 out of 10 in 3nkb

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Magnesium binding site 6 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:42.7
occ:1.00
O B:HOH536 2.4 39.0 1.0
O B:HOH528 2.4 36.8 1.0
O B:HOH566 2.4 33.0 1.0
O B:HOH563 2.4 33.4 1.0
O B:HOH524 2.4 37.2 1.0
O B:HOH532 2.5 35.6 1.0
N7 B:A34 4.0 37.3 1.0
N3 B:G63 4.1 35.6 1.0
O B:HOH564 4.1 33.7 1.0
O4' B:G63 4.2 33.0 1.0
O B:HOH534 4.3 35.6 1.0
N2 B:G63 4.3 34.1 1.0
N6 B:A34 4.3 42.5 1.0
O B:HOH567 4.3 36.3 1.0
O6 B:G35 4.4 44.4 1.0
C2 B:G63 4.4 36.6 1.0
O B:HOH527 4.5 34.1 1.0
N7 B:G35 4.5 40.7 1.0
C5 B:A34 4.7 38.3 1.0
C4 B:G63 4.9 38.2 1.0
C6 B:A34 4.9 44.6 1.0
C8 B:A34 4.9 36.6 1.0
N4 B:C36 5.0 48.2 1.0

Magnesium binding site 7 out of 10 in 3nkb

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Magnesium binding site 7 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg207

b:55.2
occ:1.00
OP1 B:A64 2.6 37.9 1.0
O B:HOH600 2.7 39.5 1.0
O B:HOH613 2.7 46.2 1.0
OP2 B:A65 2.8 32.3 1.0
OP1 B:C32 3.1 41.9 1.0
O B:HOH601 3.8 42.3 1.0
OP2 B:A33 3.8 40.4 1.0
P B:A64 4.0 34.8 1.0
P B:A65 4.0 40.2 1.0
P B:C32 4.0 48.0 1.0
O B:HOH655 4.1 46.5 1.0
O B:HOH533 4.2 36.0 1.0
O B:HOH567 4.2 36.3 1.0
OP2 B:C32 4.3 38.2 1.0
OP1 B:A65 4.4 31.8 1.0
OP2 B:A64 4.5 30.6 1.0
O5' B:C32 4.6 41.0 1.0
P B:A33 4.7 40.4 1.0
OP1 B:A33 4.8 33.7 1.0
O3' B:G63 4.9 35.3 1.0
O5' B:A64 5.0 33.4 1.0
O5' B:A65 5.0 32.9 1.0

Magnesium binding site 8 out of 10 in 3nkb

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Magnesium binding site 8 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg208

b:37.5
occ:1.00
OP1 B:U24 2.2 28.7 1.0
O B:HOH645 2.3 29.7 1.0
O B:HOH647 2.4 35.2 1.0
O B:HOH604 2.4 32.0 1.0
O B:HOH596 2.4 33.9 1.0
O B:HOH657 2.6 44.5 1.0
P B:U24 3.5 28.6 1.0
O5' B:U24 3.8 27.8 1.0
O B:HOH644 4.1 32.0 1.0
N7 B:G26 4.1 26.5 1.0
O6 B:G26 4.1 28.4 1.0
C3' B:C23 4.3 27.4 1.0
O2' B:C23 4.3 30.1 1.0
N4 B:C62 4.3 26.8 1.0
O3' B:C23 4.4 24.3 1.0
O B:HOH648 4.5 28.3 1.0
O2 B:U21 4.6 26.9 1.0
C2' B:C23 4.6 28.9 1.0
OP2 B:U24 4.7 31.0 1.0
N3 B:G28 4.8 25.9 1.0
C6 B:G26 4.8 28.6 1.0
C5 B:G26 4.8 28.9 1.0
O5' A:DG2 4.9 60.8 1.0
C5' B:U24 4.9 30.1 1.0
O B:HOH597 5.0 41.5 1.0
O2' B:G28 5.0 36.1 1.0

Magnesium binding site 9 out of 10 in 3nkb

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Magnesium binding site 9 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg209

b:51.6
occ:1.00
O B:HOH544 1.9 40.1 1.0
O B:HOH623 2.0 43.3 1.0
O B:HOH650 2.3 31.7 1.0
O2 B:C25 2.4 30.3 1.0
O B:HOH573 3.0 35.2 1.0
C2 B:C25 3.6 29.8 1.0
O B:HOH643 4.0 44.5 1.0
N2 B:G26 4.1 26.7 1.0
N3 B:C25 4.1 28.3 1.0
O B:HOH592 4.1 37.6 1.0
N1 B:C25 4.7 31.1 1.0
O4 B:U21 4.7 26.5 1.0
O B:HOH542 4.7 32.4 1.0
C1' B:C25 4.8 26.9 1.0
O B:HOH541 4.9 37.7 1.0

Magnesium binding site 10 out of 10 in 3nkb

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Magnesium binding site 10 out of 10 in the A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of A 1.9A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg210

b:54.7
occ:1.00
O B:HOH630 2.6 53.1 1.0
O B:HOH631 2.8 47.8 1.0
N7 B:G40 2.8 32.5 1.0
O B:HOH530 2.9 57.1 1.0
C8 B:G40 3.7 32.8 1.0
C5 B:G40 3.9 29.5 1.0
O6 B:G40 3.9 34.2 1.0
N7 B:G39 4.1 34.9 1.0
C6 B:G40 4.3 31.8 1.0
C8 B:G39 4.4 36.4 1.0
OP2 B:G40 4.6 44.8 1.0
OP2 B:G39 4.7 46.2 1.0
C5 B:G39 4.7 34.3 1.0
N9 B:G40 5.0 31.0 1.0

Reference:

J.H.Chen, R.Yajima, D.M.Chadalavada, E.Chase, P.C.Bevilacqua, B.L.Golden. A 1.9 A Crystal Structure of the Hdv Ribozyme Precleavage Suggests Both Lewis Acid and General Acid Mechanisms Contribute to Phosphodiester Cleavage. Biochemistry V. 49 6508 2010.
ISSN: ISSN 0006-2960
PubMed: 20677830
DOI: 10.1021/BI100670P
Page generated: Mon Dec 14 08:28:54 2020

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