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Manganese in PDB 4gbw: Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant

Enzymatic activity of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant

All present enzymatic activity of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant:
3.1.3.11;

Protein crystallography data

The structure of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant, PDB code: 4gbw was solved by R.B.Honzatko, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.41 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 53.381, 82.718, 165.165, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant (pdb code 4gbw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant, PDB code: 4gbw:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4gbw

Go back to Manganese Binding Sites List in 4gbw
Manganese binding site 1 out of 3 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:10.9
occ:1.00
 OD2 A:ASP118 2.0 24.9 1.0
OE1 A:GLU97 2.2 27.0 1.0
O1 A:PO4405 2.2 28.0 1.0
O A:LEU120 2.2 19.7 1.0
O3 A:PO4405 2.6 37.6 1.0
P A:PO4405 3.0 42.0 1.0
CG A:ASP118 3.1 30.7 1.0
CD A:GLU97 3.1 39.2 1.0
C A:LEU120 3.3 23.7 1.0
OD1 A:ASP118 3.5 33.2 1.0
OE2 A:GLU97 3.6 43.0 1.0
MN A:MN403 3.7 25.8 1.0
O2 A:PO4405 3.9 32.5 1.0
CA A:ASP121 3.9 26.0 1.0
N A:ASP121 4.0 22.5 1.0
N A:LEU120 4.1 21.6 1.0
OD2 A:ASP74 4.1 35.2 1.0
OE2 A:GLU98 4.1 32.1 1.0
MN A:MN404 4.2 38.0 1.0
O4 A:PO4405 4.2 32.7 1.0
CA A:LEU120 4.2 22.1 1.0
CG A:GLU97 4.3 28.3 1.0
CD A:PRO119 4.4 21.9 1.0
CB A:ASP118 4.5 23.7 1.0
CB A:GLU97 4.6 27.0 1.0
N A:PRO119 4.8 24.2 1.0
CB A:ASP121 4.8 27.3 1.0
C A:ASP118 4.8 25.2 1.0
CA A:ASP118 4.8 24.2 1.0
CB A:LEU120 4.9 23.9 1.0
OG A:SER123 4.9 37.0 1.0

Manganese binding site 2 out of 3 in 4gbw

Go back to Manganese Binding Sites List in 4gbw
Manganese binding site 2 out of 3 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:25.8
occ:1.00
 O2 A:PO4405 2.1 32.5 1.0
OD2 A:ASP68 2.2 49.9 1.0
O1 A:PO4405 2.3 28.0 1.0
OE1 A:GLU97 2.8 27.0 1.0
P A:PO4405 2.8 42.0 1.0
CG A:ASP68 3.0 57.3 1.0
CB A:ASP68 3.3 56.3 1.0
CD A:GLU97 3.5 39.2 1.0
NH2 A:ARG276 3.6 40.8 1.0
O3 A:PO4405 3.6 37.6 1.0
MN A:MN402 3.7 10.9 1.0
O A:HOH569 3.7 40.4 1.0
O A:HOH591 3.9 49.7 1.0
ND2 A:ASN64 3.9 44.8 1.0
O4 A:PO4405 3.9 32.7 1.0
OG A:SER123 4.0 37.0 1.0
OE2 A:GLU97 4.1 43.0 1.0
NH1 A:ARG276 4.2 42.4 1.0
OD1 A:ASP68 4.2 55.8 1.0
CZ A:ARG276 4.3 38.1 1.0
OE2 A:GLU98 4.4 32.1 1.0
CG A:GLU97 4.5 28.3 1.0
CB A:SER123 4.7 26.7 1.0
O1 A:F6P401 4.8 36.2 1.0
CA A:ASP68 4.8 56.9 1.0
CG A:ASN64 5.0 54.4 1.0
OD2 A:ASP74 5.0 35.2 1.0

Manganese binding site 3 out of 3 in 4gbw

Go back to Manganese Binding Sites List in 4gbw
Manganese binding site 3 out of 3 in the Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Amp Complexes of Porcine Liver Fructose-1,6- Bisphosphatase Mutant A54L with 1,2-Propanediol As Cryo-Protectant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:38.0
occ:1.00
 OD1 A:ASP121 2.0 23.7 1.0
O3 A:PO4405 2.2 37.6 1.0
OD1 A:ASP118 2.4 33.2 1.0
OE1 A:GLU280 2.6 30.0 1.0
CG A:ASP121 2.9 33.3 1.0
CB A:ASP121 2.9 27.3 1.0
P A:PO4405 3.1 42.0 1.0
C1 A:F6P401 3.2 26.8 1.0
CA A:ASP121 3.3 26.0 1.0
O4 A:PO4405 3.4 32.7 1.0
CG A:ASP118 3.5 30.7 1.0
CD A:GLU280 3.6 26.5 1.0
O3 A:F6P401 3.8 21.6 1.0
N A:GLY122 3.9 25.2 1.0
CG A:GLU280 3.9 21.3 1.0
O2 A:PO4405 4.0 32.5 1.0
OD2 A:ASP118 4.1 24.9 1.0
C A:ASP121 4.1 26.0 1.0
OE2 A:GLU97 4.1 43.0 1.0
OD2 A:ASP121 4.2 30.5 1.0
MN A:MN402 4.2 10.9 1.0
O1 A:PO4405 4.2 28.0 1.0
C3 A:F6P401 4.2 23.5 1.0
O1 A:F6P401 4.2 36.2 1.0
C2 A:F6P401 4.2 25.7 1.0
NH1 A:ARG276 4.3 42.4 1.0
CD1 A:ILE135 4.4 16.0 1.0
O2 A:F6P401 4.5 23.5 1.0
N A:ASP121 4.5 22.5 1.0
OE2 A:GLU280 4.7 25.4 1.0
CB A:ASP118 4.7 23.7 1.0
O A:LEU120 4.8 19.7 1.0
OE1 A:GLU97 4.9 27.0 1.0
CD A:GLU97 5.0 39.2 1.0

Reference:

R.B.Honzatko, Y.Gao, N.D.Ginder. Water Structure of the Central Hydrophobic Cavity of Mammalian Fructose-1,6-Bisphosphatase: A Potential Thermodynamic Determinant of Allowed Quaternary States To Be Published.
Page generated: Sat Oct 5 19:29:48 2024

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