Zinc in PDB 2f3d: Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase

All present enzymatic activity of Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase:
3.1.3.11;

The structure of Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase, PDB code: 2f3d was solved by C.V.Iancu, S.Mukund, J.-Y.Choe, 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)	5.00 / 1.83
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.840, 82.502, 165.025, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.6

The binding sites of Zinc atom in the Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase (pdb code 2f3d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase, PDB code: 2f3d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn340 b:30.6 occ:1.00 OE1 A:GLU97 2.1 27.6 1.0 OD2 A:ASP118 2.2 13.8 1.0 O4 A:PO4434 2.4 14.5 1.0 O A:HOH511 2.4 20.4 1.0 O A:LEU120 2.4 14.8 1.0 O2 A:PO4434 2.4 14.7 1.0 P A:PO4434 2.9 13.7 1.0 CD A:GLU97 3.2 26.7 1.0 CG A:ASP118 3.3 14.4 1.0 C A:LEU120 3.3 15.2 1.0 ZN A:ZN341 3.7 15.2 1.0 OD1 A:ASP118 3.7 14.2 1.0 OE2 A:GLU98 3.9 34.5 1.0 ZN A:ZN342 3.9 36.7 1.0 O3 A:PO4434 3.9 14.8 1.0 O A:HOH519 3.9 27.3 1.0 O1 A:PO4434 4.0 14.1 1.0 OE2 A:GLU97 4.0 26.2 1.0 CA A:ASP121 4.0 13.9 1.0 N A:ASP121 4.0 14.8 1.0 CG A:GLU97 4.1 26.7 1.0 N A:LEU120 4.1 15.3 1.0 O A:HOH624 4.2 25.2 1.0 CB A:GLU97 4.3 26.1 1.0 CA A:LEU120 4.3 15.6 1.0 CB A:ASP118 4.6 14.4 1.0 CA A:ASP118 4.8 15.5 1.0 CD A:PRO119 4.8 16.8 1.0 NH2 A:ARG276 4.8 18.8 1.0 CB A:ASP121 4.8 13.8 1.0 C A:ASP118 4.9 15.8 1.0 CB A:LEU120 4.9 17.1 1.0 OD2 A:ASP74 4.9 31.1 1.0 N A:PRO119 4.9 16.4 1.0 CG A:PRO119 5.0 17.1 1.0 CD A:GLU98 5.0 33.8 1.0

Zinc binding site 2 out of 3 in the Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn341 b:15.2 occ:1.00 O2 A:PO4434 1.9 14.7 1.0 OD1 A:ASP118 1.9 14.2 1.0 OD1 A:ASP121 2.0 14.2 1.0 OE1 A:GLU280 2.0 14.4 1.0 CG A:ASP121 2.9 14.0 1.0 CG A:ASP118 2.9 14.4 1.0 CD A:GLU280 3.1 14.6 1.0 CB A:ASP121 3.2 13.8 1.0 P A:PO4434 3.2 13.7 1.0 OD2 A:ASP118 3.3 13.8 1.0 CG A:GLU280 3.5 14.5 1.0 CA A:ASP121 3.5 13.9 1.0 O1 A:PO4434 3.6 14.1 1.0 ZN A:ZN340 3.7 30.6 1.0 NH2 A:ARG276 3.8 18.8 1.0 O3 A:PO4434 3.9 14.8 1.0 OD2 A:ASP121 4.1 12.9 1.0 C1 A:F6P339 4.1 14.7 1.0 O3 A:F6P339 4.2 13.3 1.0 OE2 A:GLU280 4.2 15.4 1.0 CB A:ASP118 4.2 14.4 1.0 O4 A:PO4434 4.3 14.5 1.0 N A:GLY122 4.4 14.4 1.0 C A:ASP121 4.5 14.0 1.0 N A:ASP121 4.5 14.8 1.0 O A:LEU120 4.6 14.8 1.0 C3 A:F6P339 4.7 14.7 1.0 CD1 A:ILE135 4.7 12.1 1.0 OE1 A:GLU97 4.7 27.6 1.0 C2 A:F6P339 4.8 14.3 1.0 O2 A:F6P339 4.9 14.1 1.0 O1 A:F6P339 4.9 14.2 1.0 C A:LEU120 4.9 15.2 1.0 CZ A:ARG276 5.0 19.3 1.0 CB A:GLU280 5.0 14.4 1.0

Zinc binding site 3 out of 3 in the Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Fructose-1,6-Bisphosphatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn342 b:36.7 occ:1.00 O3 A:PO4434 2.1 14.8 1.0 O A:HOH624 2.1 25.2 1.0 OE2 A:GLU97 2.4 26.2 1.0 O4 A:PO4434 2.5 14.5 1.0 OD2 A:ASP68 2.5 39.9 1.0 P A:PO4434 2.8 13.7 1.0 CD A:GLU97 3.1 26.7 1.0 OE1 A:GLU97 3.2 27.6 1.0 CG A:ASP68 3.2 40.0 1.0 CB A:ASP68 3.4 40.1 1.0 O2 A:PO4434 3.7 14.7 1.0 NH2 A:ARG276 3.8 18.8 1.0 O A:HOH680 3.8 19.9 1.0 ZN A:ZN340 3.9 30.6 1.0 ND2 A:ASN64 4.0 44.9 1.0 O1 A:PO4434 4.0 14.1 1.0 OE2 A:GLU98 4.2 34.5 1.0 NH1 A:ARG276 4.2 19.1 1.0 OD1 A:ASP68 4.3 39.9 1.0 O1 A:F6P339 4.3 14.2 1.0 CG A:GLU97 4.5 26.7 1.0 CZ A:ARG276 4.5 19.3 1.0 CB A:SER123 4.6 19.4 1.0 O A:HOH681 4.6 20.3 1.0 O A:HOH519 4.8 27.3 1.0 CA A:ASP68 4.9 40.3 1.0

Y.Gao, C.V.Iancu, S.Mukind, J.Y.Choe, R.B.Honzatko. Mechanism of Displacement of A Catalytically Essential Loop From the Active Site of Mammalian Fructose-1,6-Bisphosphatase. Biochemistry V. 52 5206 2013.
ISSN: ISSN 0006-2960
PubMed: 23844654
DOI: 10.1021/BI400532N