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Magnesium in PDB 3t2d: Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form

Enzymatic activity of Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form

All present enzymatic activity of Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form:
3.1.3.11; 4.1.2.13;

Protein crystallography data

The structure of Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form, PDB code: 3t2d was solved by J.Du, R.Say, W.Lue, G.Fuchs, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.78 / 1.36
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 112.291, 112.291, 151.348, 90.00, 90.00, 90.00
R / Rfree (%) 10.4 / 12.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form (pdb code 3t2d). 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-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form, PDB code: 3t2d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3t2d

Go back to Magnesium Binding Sites List in 3t2d
Magnesium binding site 1 out of 4 in the Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form


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-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:7.3
occ:1.00
 OD1 A:ASP132 2.0 8.6 1.0
O3P A:P6F412 2.1 8.8 1.0
O A:HOH474 2.1 10.3 1.0
OD1 A:ASP52 2.1 8.5 1.0
OD2 A:ASP53 2.1 10.4 1.0
OD2 A:ASP234 2.1 9.2 1.0
CG A:ASP132 3.1 7.0 1.0
CG A:ASP53 3.1 10.4 1.0
CG A:ASP234 3.1 8.4 1.0
CG A:ASP52 3.1 8.0 1.0
P1 A:P6F412 3.2 11.6 1.0
OD1 A:ASP53 3.4 11.6 1.0
MG A:MG410 3.5 15.1 1.0
NZ A:LYS133 3.6 8.5 1.0
OD2 A:ASP132 3.6 7.9 1.0
OD2 A:ASP52 3.7 9.4 1.0
O1P A:P6F412 3.7 15.0 1.0
O2P A:P6F412 3.8 9.3 1.0
OD1 A:ASP234 3.8 9.0 1.0
O A:HOH482 3.9 10.5 1.0
CB A:ASP234 4.0 8.5 1.0
OD2 A:ASP11 4.0 9.4 1.0
CB A:ASP132 4.2 7.8 1.0
CB A:ASP53 4.4 9.3 1.0
CB A:ASP52 4.4 7.9 1.0
C A:ASP52 4.5 7.8 1.0
N A:LYS133 4.5 6.0 1.0
N A:ASP53 4.5 7.4 1.0
N A:ASP52 4.6 7.1 1.0
MG A:MG409 4.6 8.7 1.0
O1 A:P6F412 4.6 15.6 1.0
O A:HOH484 4.6 17.5 1.0
CA A:ASP132 4.6 5.8 1.0
CA A:ASP52 4.7 7.9 1.0
CE A:LYS133 4.8 8.6 1.0
O A:ASP52 4.9 9.4 1.0
CA A:ASP53 4.9 8.2 1.0
CG A:ASP11 4.9 9.7 1.0
CD A:LYS133 4.9 8.1 1.0
CB A:ASP11 4.9 9.2 1.0
MG A:MG411 5.0 12.4 1.0

Magnesium binding site 2 out of 4 in 3t2d

Go back to Magnesium Binding Sites List in 3t2d
Magnesium binding site 2 out of 4 in the Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form


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-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:8.7
occ:1.00
 O2P A:P6F412 2.0 9.3 1.0
OD2 A:ASP52 2.0 9.4 1.0
OD2 A:ASP11 2.1 9.4 1.0
O A:HOH506 2.2 10.2 1.0
OE1 A:GLN95 2.2 9.9 1.0
ND1 A:HIS18 2.2 8.6 1.0
CE1 A:HIS18 3.1 8.9 1.0
CG A:ASP52 3.1 8.0 1.0
CD A:GLN95 3.2 12.8 1.0
CG A:ASP11 3.2 9.7 1.0
CG A:HIS18 3.3 7.8 1.0
P1 A:P6F412 3.4 11.6 1.0
NE2 A:GLN95 3.5 12.9 1.0
OD1 A:ASP11 3.5 10.0 1.0
CB A:HIS18 3.7 7.8 1.0
OD1 A:ASP52 3.8 8.5 1.0
O A:HOH474 3.9 10.3 1.0
O3P A:P6F412 3.9 8.8 1.0
CB A:ASP52 4.0 7.9 1.0
CA A:HIS18 4.2 8.0 1.0
OD1 A:ASN105 4.3 16.1 1.0
NE2 A:HIS18 4.3 9.4 1.0
O1 A:P6F412 4.4 15.6 1.0
CD2 A:HIS18 4.4 8.4 1.0
CB A:ASP11 4.4 9.2 1.0
C1 A:P6F412 4.5 15.7 1.0
O1P A:P6F412 4.5 15.0 1.0
CG A:GLN95 4.5 12.9 1.0
MG A:MG408 4.6 7.3 1.0
CB A:GLN95 4.9 11.9 1.0
NZ A:LYS133 4.9 8.5 1.0

Magnesium binding site 3 out of 4 in 3t2d

Go back to Magnesium Binding Sites List in 3t2d
Magnesium binding site 3 out of 4 in the Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form


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-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:15.1
occ:1.00
 OD1 A:ASP233 2.3 13.6 1.0
OD2 A:ASP234 2.3 9.2 1.0
O A:HOH478 2.4 15.3 1.0
O1P A:P6F412 2.4 15.0 1.0
O A:HOH474 2.5 10.3 1.0
O A:HOH484 2.6 17.5 1.0
CG A:ASP234 3.2 8.4 1.0
CG A:ASP233 3.4 12.6 1.0
P1 A:P6F412 3.5 11.6 1.0
MG A:MG408 3.5 7.3 1.0
MG A:MG411 3.6 12.4 1.0
CB A:ASP234 3.8 8.5 1.0
O3P A:P6F412 3.8 8.8 1.0
OD1 A:ASP53 3.8 11.6 1.0
OD2 A:ASP233 3.9 16.5 1.0
O A:HOH479 4.0 16.9 1.0
OD1 A:ASP234 4.0 9.0 1.0
NE2 A:GLN95 4.0 12.9 1.0
O A:HOH475 4.0 17.2 1.0
O A:ASP233 4.0 13.7 1.0
O A:HOH482 4.0 10.5 1.0
O2P A:P6F412 4.1 9.3 1.0
C A:ASP233 4.2 10.1 1.0
NZ A:LYS9 4.2 12.4 0.5
O A:HOH483 4.3 15.6 1.0
OD2 A:ASP53 4.4 10.4 1.0
OD1 A:ASP96 4.5 13.9 1.0
CG A:ASP53 4.5 10.4 1.0
OD2 A:ASP96 4.6 12.7 1.0
N A:ASP234 4.6 10.3 1.0
CB A:ASP233 4.6 12.4 1.0
O1 A:P6F412 4.7 15.6 1.0
OD2 A:ASP11 4.7 9.4 1.0
CA A:ASP234 4.8 9.1 1.0
CA A:ASP233 4.8 12.2 1.0
CB A:ASP11 4.9 9.2 1.0
N A:ASP233 4.9 13.0 1.0
NZ A:LYS9 4.9 10.0 0.5

Magnesium binding site 4 out of 4 in 3t2d

Go back to Magnesium Binding Sites List in 3t2d
Magnesium binding site 4 out of 4 in the Fructose-1,6-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form


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-Bisphosphate Aldolase/Phosphatase From Thermoproteus Neutrophilus, Fbp-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:12.4
occ:1.00
 OD2 A:ASP233 1.9 16.5 1.0
O1P A:P6F412 2.0 15.0 1.0
O A:HOH510 2.0 13.5 1.0
O A:HOH483 2.0 15.6 1.0
O A:HOH482 2.2 10.5 1.0
O1 A:P6F412 2.6 15.6 1.0
CG A:ASP233 2.8 12.6 1.0
P1 A:P6F412 3.0 11.6 1.0
OD1 A:ASP233 3.0 13.6 1.0
MG A:MG410 3.6 15.1 1.0
O3P A:P6F412 3.7 8.8 1.0
OE1 A:GLU357 3.9 17.0 1.0
O A:HOH480 4.0 21.4 1.0
O A:HOH479 4.0 16.9 1.0
OD2 A:ASP234 4.0 9.2 1.0
O2 A:P6F412 4.1 16.3 1.0
C1 A:P6F412 4.1 15.7 1.0
O A:HOH481 4.1 11.2 1.0
O2P A:P6F412 4.2 9.3 1.0
CB A:ASP233 4.2 12.4 1.0
OD1 A:ASN105 4.2 16.1 1.0
OD1 A:ASP234 4.3 9.0 1.0
OE2 A:GLU357 4.3 14.6 1.0
O A:HOH509 4.4 28.9 1.0
CG A:ASP234 4.5 8.4 1.0
CD A:GLU357 4.6 12.6 1.0
C2 A:P6F412 4.6 11.9 1.0
O A:HOH476 4.7 18.9 1.0
O A:HOH478 4.8 15.3 1.0
O A:HOH474 4.9 10.3 1.0
MG A:MG408 5.0 7.3 1.0

Reference:

J.Du, R.F.Say, W.Lu, G.Fuchs, O.Einsle. Active-Site Remodelling in the Bifunctional Fructose-1,6-Bisphosphate Aldolase/Phosphatase. Nature V. 478 534 2011.
ISSN: ISSN 0028-0836
PubMed: 21983965
DOI: 10.1038/NATURE10458
Page generated: Thu Aug 15 11:49:32 2024

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