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Magnesium in PDB 5udg: Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99

Enzymatic activity of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99

All present enzymatic activity of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99:
1.7.1.13;

Protein crystallography data

The structure of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99, PDB code: 5udg was solved by A.Mohammad, M.K.Kiani, D.Iwata-Reuyl, B.Stec, M.Swairjo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.61 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 87.308, 87.308, 196.734, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 29.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 (pdb code 5udg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99, PDB code: 5udg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5udg

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Magnesium binding site 1 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:94.4
occ:1.00
 OD2 A:ASP162 2.2 70.2 1.0
O A:HOH340 2.3 60.4 1.0
OXT A:ARG164 2.9 88.8 1.0
CG A:ASP162 3.2 78.2 1.0
C A:ARG164 3.7 86.9 1.0
OD1 A:ASP162 3.8 76.9 1.0
N A:ASP162 3.9 75.3 1.0
N A:ARG164 3.9 72.9 1.0
CA A:ARG164 4.3 78.0 1.0
CB A:ASP162 4.4 73.3 1.0
CA A:ASP162 4.5 75.2 1.0
O A:THR160 4.5 57.3 1.0
CB A:ARG164 4.5 78.6 1.0
N A:ASN163 4.6 77.2 1.0
O A:ARG164 4.6 87.8 1.0
C A:ASP162 4.8 74.8 1.0
C A:ILE161 4.9 76.9 1.0

Magnesium binding site 2 out of 7 in 5udg

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Magnesium binding site 2 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:64.8
occ:1.00
 OD1 A:ASP106 2.5 52.2 1.0
OE1 A:GLU109 2.6 63.1 1.0
O A:HOH339 2.7 40.9 1.0
O A:HOH329 3.6 53.2 1.0
CG A:ASP106 3.7 47.3 1.0
CD A:GLU109 3.8 56.5 1.0
OH A:TYR25 4.1 44.1 1.0
OD2 A:ASP106 4.2 51.5 1.0
OE2 A:GLU109 4.5 57.7 1.0
CA A:ASP106 4.7 39.7 1.0
CG A:GLU109 4.7 49.8 1.0
CB A:ASP106 4.8 41.6 1.0
N A:ASP106 4.8 39.0 1.0

Magnesium binding site 3 out of 7 in 5udg

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Magnesium binding site 3 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:0.6
occ:1.00
 OXT B:ARG164 2.5 83.6 1.0
O B:HOH363 2.8 62.3 1.0
O B:HOH335 3.3 58.4 1.0
C B:ARG164 3.6 85.8 1.0
O B:HOH305 3.7 39.4 1.0
O B:ARG164 3.9 87.7 1.0
OD2 B:ASP162 4.5 64.3 1.0
CA B:ARG164 4.9 86.7 1.0

Magnesium binding site 4 out of 7 in 5udg

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Magnesium binding site 4 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:20.7
occ:1.00
 O D:HOH319 2.0 40.2 1.0
O D:HOH308 2.2 28.4 1.0
O D:HOH301 2.4 37.9 1.0
OD2 D:ASP73 2.4 40.1 1.0
OE2 D:GLU74 2.5 62.4 1.0
CG D:ASP73 3.5 39.5 1.0
CD D:GLU74 3.5 65.0 1.0
OD1 D:ASP73 3.8 42.0 1.0
OE1 D:GLU74 3.8 70.7 1.0
O D:HOH322 4.6 44.5 1.0
CB D:ASP73 4.8 37.3 1.0
NZ D:LYS138 4.8 39.3 1.0
CG D:GLU74 4.8 55.5 1.0

Magnesium binding site 5 out of 7 in 5udg

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Magnesium binding site 5 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:73.8
occ:1.00
 O D:HOH311 2.4 56.3 1.0
OD2 D:ASP162 2.5 69.5 1.0
OXT D:ARG164 2.8 79.1 1.0
CG D:ASP162 3.2 74.2 1.0
N D:ASP162 3.5 76.1 1.0
O D:THR160 3.8 93.8 1.0
OD1 D:ASP162 3.8 77.9 1.0
C D:ARG164 3.9 75.9 1.0
CA D:ASP162 4.2 75.8 1.0
N D:ARG164 4.2 67.8 1.0
CB D:ASP162 4.2 74.3 1.0
C D:ILE161 4.4 74.2 1.0
CA D:ILE161 4.4 70.1 1.0
N D:ASN163 4.5 80.6 1.0
CA D:ARG164 4.6 74.0 1.0
C D:ASP162 4.6 81.2 1.0
C D:THR160 4.7 83.6 1.0
O D:ARG164 4.8 76.0 1.0
CB D:ARG164 4.9 76.8 1.0
N D:ILE161 5.0 72.8 1.0

Magnesium binding site 6 out of 7 in 5udg

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Magnesium binding site 6 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:64.3
occ:1.00
 O E:HOH328 2.1 65.9 1.0
OD1 E:ASP162 2.6 75.3 1.0
OD2 E:ASP162 2.7 52.0 1.0
OXT E:ARG164 2.7 77.6 1.0
CG E:ASP162 2.9 68.8 1.0
O E:HOH355 3.1 63.1 1.0
O E:HOH321 3.2 79.6 1.0
C E:ARG164 3.9 83.9 1.0
CB E:ASP162 4.3 67.5 1.0
CB E:ARG164 4.6 80.1 1.0
O E:HOH339 4.6 57.1 1.0
O E:ARG164 4.7 86.2 1.0
CA E:ARG164 4.7 78.7 1.0
N E:ARG164 4.9 78.0 1.0
N E:ASP162 5.0 69.7 1.0

Magnesium binding site 7 out of 7 in 5udg

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Magnesium binding site 7 out of 7 in the Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mutant E97Q Crystal Structure of Bacillus Subtilis Quef with A Disulfide Cys 55-99 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:29.7
occ:1.00
 O E:HOH331 2.4 53.8 1.0
OE2 E:GLU74 2.5 61.1 1.0
OD2 E:ASP73 2.5 40.6 1.0
O E:HOH308 2.6 65.6 1.0
CG E:ASP73 3.6 42.5 1.0
CD E:GLU74 3.7 61.9 1.0
OD1 E:ASP73 3.9 45.6 1.0
NZ E:LYS138 4.0 45.9 1.0
CG E:GLU74 4.3 57.4 1.0
O E:HOH344 4.4 33.4 1.0
OE1 E:GLU74 4.7 66.5 1.0
CB E:ASP73 4.9 42.4 1.0

Reference:

A.Mohammad, A.Bon Ramos, B.W.Lee, S.W.Cohen, M.K.Kiani, D.Iwata-Reuyl, B.Stec, M.A.Swairjo. Protection of the Queuosine Biosynthesis Enzyme Quef From Irreversible Oxidation By A Conserved Intramolecular Disulfide. Biomolecules V. 7 2017.
ISSN: ISSN 2218-273X
PubMed: 28300774
DOI: 10.3390/BIOM7010030
Page generated: Mon Sep 30 05:16:54 2024

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