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Magnesium in PDB 5ded: Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp

Enzymatic activity of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp

All present enzymatic activity of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp:
2.7.6.5;

Protein crystallography data

The structure of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp, PDB code: 5ded was solved by W.Steinchen, J.S.Schuhmacher, F.Altegoer, G.Bange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.57 / 2.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.869, 113.492, 139.848, 90.00, 127.17, 90.00
R / Rfree (%) 18.1 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp (pdb code 5ded). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp, PDB code: 5ded:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ded

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:18.4
occ:1.00
O3B A:0O2302 2.1 19.4 1.0
O1D A:0O2302 2.2 13.8 1.0
O2C A:0O2302 2.4 20.8 1.0
O2G A:0O2302 2.8 26.1 1.0
PG A:0O2302 3.1 17.8 1.0
PB A:0O2302 3.3 13.2 1.0
PD A:0O2302 3.5 17.0 1.0
PC A:0O2302 3.6 18.9 1.0
O2B A:0O2302 3.7 18.0 1.0
O3C A:0O2302 3.8 17.1 1.0
O3A A:0O2302 3.9 24.7 1.0
NZ A:LYS25 4.0 16.0 1.0
O3G A:0O2302 4.1 12.4 1.0
O1G A:0O2302 4.2 22.1 1.0
NZ C:LYS25 4.2 15.7 1.0
O2D A:0O2302 4.3 16.9 1.0
O3' A:0O2302 4.4 20.1 1.0
O1B A:0O2302 4.5 16.5 1.0
O3D A:0O2302 4.7 17.7 1.0
O1C A:0O2302 4.8 13.6 1.0
C5' A:0O2302 5.0 18.7 1.0

Magnesium binding site 2 out of 4 in 5ded

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:22.0
occ:1.00
O3G D:0O2302 2.0 19.1 1.0
O3D D:0O2302 2.2 15.4 1.0
O1B D:0O2302 2.3 13.3 1.0
O1C D:0O2302 2.6 15.0 1.0
PD D:0O2302 3.3 24.3 1.0
PG D:0O2302 3.4 16.6 1.0
O3C D:0O2302 3.4 30.2 1.0
PB D:0O2302 3.5 13.6 1.0
PC D:0O2302 3.5 19.7 1.0
O3B D:0O2302 3.7 16.3 1.0
NZ D:LYS25 4.0 21.9 1.0
O1D D:0O2302 4.0 30.9 1.0
O2B D:0O2302 4.1 16.8 1.0
NZ B:LYS25 4.3 9.5 1.0
O2G D:0O2302 4.3 22.5 1.0
O1G D:0O2302 4.3 16.9 1.0
O3' D:0O2302 4.3 21.6 1.0
C5' D:0O2302 4.4 24.7 1.0
O2D D:0O2302 4.5 27.1 1.0
O2C D:0O2302 4.8 18.8 1.0
O3A D:0O2302 4.8 19.3 1.0
C3' D:0O2302 4.9 22.4 1.0
C4' D:0O2302 5.0 23.1 1.0

Magnesium binding site 3 out of 4 in 5ded

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:26.1
occ:1.00
O1C H:0O2302 2.2 37.2 1.0
O3B H:0O2302 2.3 27.2 1.0
O2D H:0O2302 2.5 25.5 1.0
O3D H:0O2302 3.2 43.7 1.0
O3G H:0O2302 3.2 33.1 1.0
PC H:0O2302 3.3 28.1 1.0
PG H:0O2302 3.3 26.4 1.0
PD H:0O2302 3.3 26.4 1.0
O3' H:0O2302 3.4 35.5 1.0
PB H:0O2302 3.5 25.3 1.0
O1B H:0O2302 3.6 27.8 1.0
O3C H:0O2302 3.9 25.1 1.0
NZ H:LYS25 4.0 27.5 1.0
NZ E:LYS25 4.1 24.0 1.0
O3A H:0O2302 4.2 39.9 1.0
O1G H:0O2302 4.2 25.3 1.0
O2G H:0O2302 4.5 36.2 1.0
O2C H:0O2302 4.6 26.3 1.0
C3' H:0O2302 4.7 36.1 1.0
O1D H:0O2302 4.7 25.4 1.0
O2B H:0O2302 4.7 21.0 1.0

Magnesium binding site 4 out of 4 in 5ded

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Small Alarmone Synthethase 1 From Bacillus Subtilis Bound to Its Product Pppgpp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg303

b:10.1
occ:1.00
O1D G:0O2302 1.6 31.1 1.0
O2G G:0O2302 2.4 28.9 1.0
PD G:0O2302 2.9 30.2 1.0
O3C G:0O2302 3.2 42.1 1.0
O3D G:0O2302 3.8 24.6 1.0
CE G:LYS21 3.8 20.2 1.0
PG G:0O2302 3.8 50.2 1.0
O2D G:0O2302 4.0 25.6 1.0
O1G G:0O2302 4.1 41.2 1.0
NZ G:LYS21 4.1 23.6 1.0
NZ G:LYS25 4.2 19.3 1.0
CD G:LYS21 4.5 18.2 1.0
O3G G:0O2302 4.5 40.7 1.0
O2A G:0O2302 4.7 26.2 1.0
PC G:0O2302 4.8 35.7 1.0
CG G:LYS21 4.9 19.1 1.0
CE G:LYS25 4.9 21.1 1.0
O3B G:0O2302 5.0 37.6 1.0

Reference:

W.Steinchen, J.S.Schuhmacher, F.Altegoer, C.D.Fage, V.Srinivasan, U.Linne, M.A.Marahiel, G.Bange. Catalytic Mechanism and Allosteric Regulation of An Oligomeric (P)Ppgpp Synthetase By An Alarmone. Proc.Natl.Acad.Sci.Usa V. 112 13348 2015.
ISSN: ESSN 1091-6490
PubMed: 26460002
DOI: 10.1073/PNAS.1505271112
Page generated: Sun Sep 29 02:42:54 2024

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