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Magnesium in PDB 1nuw: Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6

Enzymatic activity of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6

All present enzymatic activity of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6:
3.1.3.11;

Protein crystallography data

The structure of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6, PDB code: 1nuw was solved by J.Choe, C.V.Iancu, H.J.Fromm, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 53.600, 83.017, 165.378, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 20.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6 (pdb code 1nuw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6, PDB code: 1nuw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1nuw

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Magnesium binding site 1 out of 4 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2497

b:19.1
occ:1.00
 O2 A:PO32496 2.0 23.8 1.0
OD2 A:ASP1118 2.0 19.4 1.0
O A:LEU1120 2.0 17.2 1.0
OE1 A:GLU1097 2.0 24.2 1.0
O A:HOH3056 2.2 20.1 1.0
O A:HOH3155 2.3 28.2 1.0
CG A:ASP1118 3.0 16.9 1.0
CD A:GLU1097 3.0 27.2 1.0
MG A:MG2498 3.1 25.6 1.0
P A:PO32496 3.1 19.1 1.0
C A:LEU1120 3.1 15.0 1.0
OD1 A:ASP1118 3.3 27.7 1.0
OE2 A:GLU1097 3.4 25.9 1.0
MG A:MG2500 3.7 21.2 0.5
CA A:ASP1121 3.8 18.0 1.0
MG A:MG2499 3.9 22.3 0.5
N A:ASP1121 3.9 15.7 1.0
O3 A:PO32496 3.9 27.4 1.0
N A:LEU1120 4.0 14.6 1.0
OE2 A:GLU1098 4.0 25.4 1.0
OD2 A:ASP1074 4.0 26.0 1.0
OD1 A:ASP1121 4.1 13.4 1.0
O1 A:PO32496 4.1 18.0 1.0
CA A:LEU1120 4.1 14.8 1.0
CB A:ASP1121 4.3 20.7 1.0
O A:HOH3193 4.3 34.1 1.0
CG A:GLU1097 4.4 19.9 1.0
CB A:ASP1118 4.4 15.8 1.0
CG A:ASP1121 4.5 20.0 1.0
CB A:GLU1097 4.6 17.1 1.0
CD A:PRO1119 4.6 18.9 1.0
CB A:LEU1120 4.7 15.8 0.7
CA A:ASP1118 4.8 15.0 1.0
C A:ASP1118 4.8 16.0 1.0
CB A:LEU1120 4.8 15.6 0.3
N A:PRO1119 4.8 16.6 1.0
CG A:ASP1074 5.0 22.9 1.0

Magnesium binding site 2 out of 4 in 1nuw

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Magnesium binding site 2 out of 4 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2498

b:25.6
occ:1.00
 O2 A:PO32496 1.8 23.8 1.0
OD1 A:ASP1121 2.0 13.4 1.0
OE2 A:GLU1097 2.0 25.9 1.0
OD1 A:ASP1118 2.1 27.7 1.0
OE1 A:GLU1280 2.1 28.5 1.0
O3 A:PO32496 2.5 27.4 1.0
P A:PO32496 2.6 19.1 1.0
NH1 A:ARG1276 2.7 36.1 1.0
CG A:ASP1118 3.0 16.9 1.0
CD A:GLU1097 3.0 27.2 1.0
MG A:MG2497 3.1 19.1 1.0
CG A:ASP1121 3.1 20.0 1.0
OE1 A:GLU1097 3.2 24.2 1.0
CD A:GLU1280 3.2 17.6 1.0
OD2 A:ASP1118 3.3 19.4 1.0
CZ A:ARG1276 3.6 33.3 1.0
O1 A:PO32496 3.7 18.0 1.0
CB A:ASP1121 3.9 20.7 1.0
CG A:GLU1280 3.9 17.4 1.0
OE2 A:GLU1280 4.1 17.7 1.0
OD2 A:ASP1121 4.1 18.3 1.0
MG A:MG2500 4.2 21.2 0.5
C1 A:F6P2336 4.2 19.5 1.0
NH2 A:ARG1276 4.2 33.2 1.0
CB A:ASP1118 4.2 15.8 1.0
CA A:ASP1121 4.3 18.0 1.0
NE A:ARG1276 4.3 40.8 1.0
CG A:GLU1097 4.4 19.9 1.0
O1 A:F6P2336 4.4 27.3 1.0
O A:LEU1120 4.4 17.2 1.0
O A:HOH3155 4.5 28.2 1.0
O A:HOH3169 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in 1nuw

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Magnesium binding site 3 out of 4 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2499

b:22.3
occ:0.50
 O A:HOH3193 1.9 34.1 1.0
OE2 A:GLU1098 2.0 25.4 1.0
OD1 A:ASN1064 2.4 45.3 1.0
MG A:MG2500 2.7 21.2 0.5
OE1 A:GLU1097 2.7 24.2 1.0
O A:HOH3155 2.8 28.2 1.0
CD A:GLU1098 2.9 24.3 1.0
OE1 A:GLU1098 3.3 36.7 1.0
CD A:GLU1097 3.3 27.2 1.0
OD2 A:ASP1068 3.5 34.3 1.0
CG A:GLU1097 3.6 19.9 1.0
O A:HOH3056 3.6 20.1 1.0
CG A:ASN1064 3.7 52.4 1.0
MG A:MG2497 3.9 19.1 1.0
O A:HOH3115 4.0 30.8 1.0
O A:HOH3145 4.1 34.9 1.0
OD1 A:ASP1074 4.2 27.1 1.0
CB A:ASP1068 4.2 35.8 1.0
CG A:GLU1098 4.2 24.6 1.0
CG A:ASP1074 4.3 22.9 1.0
OD2 A:ASP1074 4.3 26.0 1.0
OE2 A:GLU1097 4.3 25.9 1.0
CG A:ASP1068 4.4 31.5 1.0
CB A:GLU1097 4.5 17.1 1.0
CB A:ASN1064 4.5 51.5 1.0
ND2 A:ASN1064 4.6 46.9 1.0
P A:PO32496 4.8 19.1 1.0
O A:GLU1097 4.8 19.9 1.0
O2 A:PO32496 4.8 23.8 1.0
O3 A:PO32496 4.9 27.4 1.0
C A:GLU1097 4.9 17.5 1.0
NH2 A:ARG1276 4.9 33.2 1.0
CB A:ASP1074 5.0 23.4 1.0

Magnesium binding site 4 out of 4 in 1nuw

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Magnesium binding site 4 out of 4 in the Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fructose-1,6-Bisphosphatase Complex with Magnesium, Fructose-6- Phosphate and Phosphate at pH 9.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2500

b:21.2
occ:0.50
 OD2 A:ASP1068 1.9 34.3 1.0
O A:HOH3193 2.0 34.1 1.0
O A:HOH3115 2.0 30.8 1.0
O A:HOH3155 2.4 28.2 1.0
O3 A:PO32496 2.6 27.4 1.0
P A:PO32496 2.6 19.1 1.0
MG A:MG2499 2.7 22.3 0.5
CG A:ASP1068 3.0 31.5 1.0
OE1 A:GLU1097 3.3 24.2 1.0
O2 A:PO32496 3.4 23.8 1.0
CB A:ASP1068 3.6 35.8 1.0
O A:HOH3145 3.6 34.9 1.0
CD A:GLU1097 3.6 27.2 1.0
MG A:MG2497 3.7 19.1 1.0
O1 A:PO32496 3.8 18.0 1.0
OE2 A:GLU1097 3.9 25.9 1.0
OD1 A:ASN1064 4.0 45.3 1.0
NH2 A:ARG1276 4.0 33.2 1.0
OD1 A:ASP1068 4.1 35.5 1.0
OG A:SER1123 4.1 44.1 1.0
MG A:MG2498 4.2 25.6 1.0
NH1 A:ARG1276 4.3 36.1 1.0
CB A:SER1123 4.4 29.5 1.0
OE2 A:GLU1098 4.4 25.4 1.0
CG A:GLU1097 4.6 19.9 1.0
CZ A:ARG1276 4.6 33.3 1.0
O A:HOH3056 4.6 20.1 1.0
O1 A:F6P2336 4.8 27.3 1.0
OD2 A:ASP1074 4.9 26.0 1.0
OD1 A:ASP1074 4.9 27.1 1.0

Reference:

J.Y.Choe, C.V.Iancu, H.J.Fromm, R.B.Honzatko. Metaphosphate in the Active Site of Fructose-1,6-Bisphosphatase J.Biol.Chem. V. 278 16015 2003.
ISSN: ISSN 0021-9258
PubMed: 12595528
DOI: 10.1074/JBC.M212395200
Page generated: Tue Aug 13 10:23:49 2024

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