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Magnesium in PDB 2gqs: Saicar Synthetase Complexed with Cair-MG2+ and Adp

Enzymatic activity of Saicar Synthetase Complexed with Cair-MG2+ and Adp

All present enzymatic activity of Saicar Synthetase Complexed with Cair-MG2+ and Adp:
6.3.2.6;

Protein crystallography data

The structure of Saicar Synthetase Complexed with Cair-MG2+ and Adp, PDB code: 2gqs was solved by N.D.Ginder, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.96 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.430, 67.120, 149.310, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Saicar Synthetase Complexed with Cair-MG2+ and Adp (pdb code 2gqs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Saicar Synthetase Complexed with Cair-MG2+ and Adp, PDB code: 2gqs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2gqs

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Magnesium binding site 1 out of 6 in the Saicar Synthetase Complexed with Cair-MG2+ and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Saicar Synthetase Complexed with Cair-MG2+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg239

b:27.7
occ:1.00
 O1 A:FMT243 2.0 31.6 1.0
O3B A:ADP238 2.1 38.5 1.0
O A:HOH244 2.1 21.8 1.0
O2A A:ADP238 2.2 27.1 1.0
O A:HOH245 2.2 23.0 1.0
O A:HOH246 2.2 19.3 1.0
C A:FMT243 3.1 32.2 1.0
PB A:ADP238 3.3 32.6 1.0
PA A:ADP238 3.4 23.8 1.0
O3A A:ADP238 3.5 32.2 1.0
O2 A:FMT243 3.5 29.9 1.0
NZ A:LYS13 3.9 20.1 1.0
O2B A:ADP238 4.0 37.1 1.0
OD1 A:ASP191 4.0 19.4 1.0
OD2 A:ASP191 4.1 23.1 1.0
OE1 A:GLU179 4.1 23.6 1.0
NZ A:LYS177 4.2 22.3 1.0
O1A A:ADP238 4.3 30.8 1.0
O A:HOH295 4.3 29.3 1.0
NZ A:LYS123 4.4 23.9 1.0
O1B A:ADP238 4.5 35.5 1.0
CG A:ASP191 4.5 21.4 1.0
O5' A:ADP238 4.6 31.3 1.0
NZ A:LYS11 4.7 34.1 1.0
C5' A:ADP238 4.8 24.7 1.0

Magnesium binding site 2 out of 6 in 2gqs

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Magnesium binding site 2 out of 6 in the Saicar Synthetase Complexed with Cair-MG2+ and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Saicar Synthetase Complexed with Cair-MG2+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg240

b:27.4
occ:1.00
 O A:HOH249 2.0 20.0 1.0
OE1 A:GLU90 2.1 24.5 1.0
O8 A:C2R242 2.1 28.0 1.0
OD2 A:ASP129 2.1 28.6 1.0
O A:HOH248 2.1 20.7 1.0
N3 A:C2R242 2.2 28.0 1.0
C4 A:C2R242 2.8 28.3 1.0
C6 A:C2R242 2.8 28.2 1.0
CD A:GLU90 2.9 26.5 1.0
OE2 A:GLU90 3.1 23.9 1.0
CG A:ASP129 3.1 27.0 1.0
MG A:MG241 3.2 26.2 1.0
C2 A:C2R242 3.4 27.8 1.0
CB A:ASP129 3.5 25.9 1.0
OD1 A:ASP36 3.9 33.2 1.0
O A:HOH281 3.9 25.6 1.0
O7 A:C2R242 4.0 29.0 1.0
C5 A:C2R242 4.1 28.4 1.0
O A:HOH250 4.2 21.4 1.0
OD1 A:ASP129 4.2 27.1 1.0
CG A:GLU90 4.3 25.1 1.0
N1 A:C2R242 4.4 26.6 1.0
O2 A:FMT243 4.7 29.9 1.0
CB A:GLU90 4.8 25.6 1.0
O A:HOH251 4.8 19.8 1.0
C A:FMT243 4.9 32.2 1.0

Magnesium binding site 3 out of 6 in 2gqs

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Magnesium binding site 3 out of 6 in the Saicar Synthetase Complexed with Cair-MG2+ and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Saicar Synthetase Complexed with Cair-MG2+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg241

b:26.2
occ:1.00
 O A:HOH251 2.0 19.8 1.0
O8 A:C2R242 2.1 28.0 1.0
OD2 A:ASP129 2.2 28.6 1.0
OE2 A:GLU90 2.2 23.9 1.0
O A:HOH250 2.2 21.4 1.0
O2 A:FMT243 2.2 29.9 1.0
C A:FMT243 3.0 32.2 1.0
CG A:ASP129 3.0 27.0 1.0
OD1 A:ASP129 3.1 27.1 1.0
MG A:MG240 3.2 27.4 1.0
C6 A:C2R242 3.2 28.2 1.0
CD A:GLU90 3.2 26.5 1.0
OE1 A:GLU90 3.6 24.5 1.0
O7 A:C2R242 3.7 29.0 1.0
NZ A:LYS11 4.0 34.1 1.0
O A:HOH311 4.1 39.2 1.0
OD1 A:ASP125 4.1 34.8 1.0
OD1 A:ASP36 4.1 33.2 1.0
O1 A:FMT243 4.2 31.6 1.0
NZ A:LYS123 4.3 23.9 1.0
C4 A:C2R242 4.4 28.3 1.0
O A:HOH248 4.4 20.7 1.0
CB A:ASP129 4.4 25.9 1.0
CG A:GLU90 4.5 25.1 1.0
N3 A:C2R242 4.7 28.0 1.0
CE A:LYS11 4.8 35.6 1.0
CG A:LYS123 4.8 26.8 1.0
O A:HOH249 4.9 20.0 1.0

Magnesium binding site 4 out of 6 in 2gqs

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Magnesium binding site 4 out of 6 in the Saicar Synthetase Complexed with Cair-MG2+ and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Saicar Synthetase Complexed with Cair-MG2+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg239

b:34.9
occ:1.00
 O2A B:ADP238 2.1 28.9 1.0
O2 B:FMT243 2.1 30.3 1.0
O B:HOH244 2.2 28.3 1.0
O B:HOH246 2.2 24.0 1.0
O B:HOH245 2.3 32.6 1.0
O3B B:ADP238 2.4 44.7 1.0
C B:FMT243 3.2 33.8 1.0
PA B:ADP238 3.3 28.1 1.0
O3A B:ADP238 3.5 36.0 1.0
PB B:ADP238 3.6 39.3 1.0
O1 B:FMT243 3.8 35.1 1.0
NZ B:LYS13 3.9 25.7 1.0
OD1 B:ASP191 4.0 31.6 1.0
NZ B:LYS123 4.1 32.8 1.0
OE1 B:GLU179 4.2 28.7 1.0
OD2 B:ASP191 4.2 30.0 1.0
O1A B:ADP238 4.3 29.6 1.0
NZ B:LYS177 4.3 25.6 1.0
O1B B:ADP238 4.4 44.6 1.0
CG B:ASP191 4.5 31.3 1.0
O5' B:ADP238 4.5 31.8 1.0
O B:HOH329 4.5 38.1 1.0
NZ B:LYS11 4.7 30.3 1.0
O2B B:ADP238 4.7 44.5 1.0
O B:HOH262 4.8 31.3 1.0
C5' B:ADP238 4.9 29.7 1.0
C3' B:ADP238 4.9 28.7 1.0
OE1 B:GLU192 5.0 32.9 1.0

Magnesium binding site 5 out of 6 in 2gqs

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Magnesium binding site 5 out of 6 in the Saicar Synthetase Complexed with Cair-MG2+ and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Saicar Synthetase Complexed with Cair-MG2+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg240

b:28.3
occ:1.00
 O B:HOH248 2.0 27.8 1.0
OE1 B:GLU90 2.0 26.8 1.0
OD2 B:ASP129 2.1 27.1 1.0
O8 B:C2R242 2.1 30.7 1.0
O B:HOH249 2.1 20.0 1.0
N3 B:C2R242 2.2 29.6 1.0
C6 B:C2R242 2.8 31.8 1.0
C4 B:C2R242 2.9 29.5 1.0
CD B:GLU90 2.9 29.7 1.0
MG B:MG241 3.0 34.5 1.0
CG B:ASP129 3.1 25.9 1.0
OE2 B:GLU90 3.2 27.9 1.0
C2 B:C2R242 3.5 29.1 1.0
CB B:ASP129 3.5 24.6 1.0
OD1 B:ASP36 4.0 39.1 1.0
O7 B:C2R242 4.1 32.4 1.0
O B:HOH264 4.1 30.6 1.0
O B:HOH250 4.2 31.8 1.0
C5 B:C2R242 4.2 27.9 1.0
OD1 B:ASP129 4.2 26.6 1.0
CG B:GLU90 4.3 30.2 1.0
O B:HOH319 4.4 34.3 1.0
N1 B:C2R242 4.5 26.9 1.0
O1 B:FMT243 4.7 35.1 1.0
O B:HOH281 4.7 27.0 1.0
O B:HOH251 4.7 23.3 1.0
CB B:GLU90 4.8 28.6 1.0
C B:FMT243 4.8 33.8 1.0

Magnesium binding site 6 out of 6 in 2gqs

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Magnesium binding site 6 out of 6 in the Saicar Synthetase Complexed with Cair-MG2+ and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Saicar Synthetase Complexed with Cair-MG2+ and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg241

b:34.5
occ:1.00
 O8 B:C2R242 2.0 30.7 1.0
O1 B:FMT243 2.1 35.1 1.0
O B:HOH250 2.1 31.8 1.0
O B:HOH251 2.1 23.3 1.0
OD2 B:ASP129 2.1 27.1 1.0
OE2 B:GLU90 2.2 27.9 1.0
C B:FMT243 2.8 33.8 1.0
MG B:MG240 3.0 28.3 1.0
CG B:ASP129 3.1 25.9 1.0
C6 B:C2R242 3.1 31.8 1.0
CD B:GLU90 3.1 29.7 1.0
OD1 B:ASP129 3.3 26.6 1.0
OE1 B:GLU90 3.5 26.8 1.0
O7 B:C2R242 3.7 32.4 1.0
OD1 B:ASP125 3.9 45.2 1.0
O2 B:FMT243 4.0 30.3 1.0
OD1 B:ASP36 4.0 39.1 1.0
O B:HOH248 4.1 27.8 1.0
NZ B:LYS123 4.1 32.8 1.0
NZ B:LYS11 4.3 30.3 1.0
C4 B:C2R242 4.3 29.5 1.0
CB B:ASP129 4.5 24.6 1.0
CG B:GLU90 4.5 30.2 1.0
N3 B:C2R242 4.6 29.6 1.0
CG B:LYS123 4.6 29.1 1.0
CE B:LYS11 4.7 30.5 1.0
O B:HOH249 4.9 20.0 1.0

Reference:

N.D.Ginder, D.J.Binkowski, H.J.Fromm, R.B.Honzatko. Nucleotide Complexes of Escherichia Coli Phosphoribosylaminoimidazole Succinocarboxamide Synthetase. J.Biol.Chem. V. 281 20680 2006.
ISSN: ISSN 0021-9258
PubMed: 16687397
DOI: 10.1074/JBC.M602109200
Page generated: Tue Aug 13 23:34:53 2024

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