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Iron in PDB 2zoa: Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom

Enzymatic activity of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom

All present enzymatic activity of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom:
3.1.4.46;

Protein crystallography data

The structure of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom, PDB code: 2zoa was solved by D.L.Ollis, C.J.Jackson, P.D.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.50 / 2.40
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 164.343, 164.343, 164.343, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.9

Iron Binding Sites:

The binding sites of Iron atom in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom (pdb code 2zoa). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom, PDB code: 2zoa:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2zoa

Go back to Iron Binding Sites List in 2zoa
Iron binding site 1 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe275

b:46.3
occ:0.80
 OD1 A:ASP8 2.1 50.2 1.0
NE2 A:HIS10 2.4 41.0 1.0
O8 A:MLI277 2.4 66.8 0.6
NE2 A:HIS197 2.4 44.6 1.0
OD2 A:ASP50 2.5 48.7 1.0
O9 A:MLI277 2.7 65.8 0.6
C3 A:MLI277 2.9 67.5 0.6
CG A:ASP8 3.2 47.6 1.0
CE1 A:HIS10 3.2 42.0 1.0
CE1 A:HIS197 3.3 45.5 1.0
CG A:ASP50 3.3 46.5 1.0
CB A:ASP50 3.4 45.3 1.0
CD2 A:HIS10 3.5 41.8 1.0
CD2 A:HIS197 3.5 46.5 1.0
FE A:FE2276 3.6 50.0 0.6
CB A:ASP8 3.8 45.1 1.0
OD2 A:ASP8 4.2 50.6 1.0
O A:HIS195 4.4 50.6 1.0
C1 A:MLI277 4.4 68.0 0.6
ND1 A:HIS10 4.4 42.5 1.0
CD2 A:HIS81 4.5 43.9 1.0
ND1 A:HIS197 4.5 47.0 1.0
OD1 A:ASP50 4.5 46.0 1.0
CE1 A:HIS156 4.5 43.0 1.0
CG A:HIS10 4.5 42.6 1.0
CG A:HIS197 4.6 46.8 1.0
CA A:ASP8 4.6 44.8 1.0
NE2 A:HIS156 4.7 43.9 1.0
NE2 A:HIS81 4.8 45.8 1.0
CA A:HIS195 4.8 50.2 1.0
CA A:ASP50 4.9 45.4 1.0
C A:HIS195 4.9 50.4 1.0

Iron binding site 2 out of 4 in 2zoa

Go back to Iron Binding Sites List in 2zoa
Iron binding site 2 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe276

b:50.0
occ:0.60
 OD2 A:ASP50 2.2 48.7 1.0
OD1 A:ASN80 2.3 49.5 1.0
NE2 A:HIS156 2.4 43.9 1.0
ND1 A:HIS195 2.5 51.6 1.0
O8 A:MLI277 2.5 66.8 0.6
CG A:ASP50 3.2 46.5 1.0
CE1 A:HIS195 3.2 52.8 1.0
CG A:ASN80 3.3 46.5 1.0
CE1 A:HIS156 3.3 43.0 1.0
C3 A:MLI277 3.4 67.5 0.6
CD2 A:HIS156 3.5 43.3 1.0
O7 A:MLI277 3.6 67.0 0.6
OD1 A:ASP50 3.6 46.0 1.0
CG A:HIS195 3.6 51.1 1.0
FE A:FE2275 3.6 46.3 0.8
ND2 A:ASN80 3.7 48.7 1.0
CA A:HIS195 3.7 50.2 1.0
CB A:HIS195 4.0 50.0 1.0
C1 A:MLI277 4.1 68.0 0.6
O9 A:MLI277 4.1 65.8 0.6
OD1 A:ASP8 4.2 50.2 1.0
CD2 A:HIS81 4.2 43.9 1.0
C2 A:MLI277 4.3 68.5 0.6
O A:HIS195 4.3 50.6 1.0
CB A:ASP50 4.4 45.3 1.0
NE2 A:HIS195 4.4 55.6 1.0
N A:ASN80 4.5 43.6 1.0
ND1 A:HIS156 4.5 44.0 1.0
C A:HIS195 4.6 50.4 1.0
N A:HIS195 4.6 50.3 1.0
CG A:HIS156 4.6 43.3 1.0
CD2 A:HIS195 4.6 52.8 1.0
CB A:ASN80 4.7 45.4 1.0
NE2 A:HIS81 4.9 45.8 1.0

Iron binding site 3 out of 4 in 2zoa

Go back to Iron Binding Sites List in 2zoa
Iron binding site 3 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe275

b:48.6
occ:0.80
 OD1 B:ASP8 2.3 51.7 1.0
NE2 B:HIS197 2.4 50.0 1.0
OD2 B:ASP50 2.4 52.7 1.0
NE2 B:HIS10 2.5 42.0 1.0
O8 B:MLI277 2.6 62.7 0.6
O9 B:MLI277 2.6 61.5 0.6
C3 B:MLI277 3.0 62.8 0.6
CG B:ASP8 3.2 48.1 1.0
CD2 B:HIS197 3.3 50.6 1.0
CE1 B:HIS197 3.4 49.7 1.0
CG B:ASP50 3.4 49.1 1.0
CE1 B:HIS10 3.4 41.0 1.0
CD2 B:HIS10 3.5 40.5 1.0
FE B:FE2276 3.5 53.7 0.6
CB B:ASP50 3.6 47.0 1.0
CB B:ASP8 3.7 45.7 1.0
OD2 B:ASP8 4.2 52.5 1.0
O B:HIS195 4.3 51.5 1.0
ND1 B:HIS197 4.5 50.3 1.0
CG B:HIS197 4.5 50.4 1.0
C1 B:MLI277 4.5 63.5 0.6
CA B:ASP8 4.5 45.4 1.0
CE1 B:HIS156 4.5 43.3 1.0
OD1 B:ASP50 4.5 48.5 1.0
ND1 B:HIS10 4.6 41.9 1.0
CA B:HIS195 4.6 50.5 1.0
CG B:HIS10 4.6 40.5 1.0
CD2 B:HIS81 4.6 48.4 1.0
NE2 B:HIS156 4.7 44.7 1.0
C B:HIS195 4.8 50.7 1.0
NE2 B:HIS81 4.9 51.1 1.0
N B:HIS195 4.9 50.7 1.0

Iron binding site 4 out of 4 in 2zoa

Go back to Iron Binding Sites List in 2zoa
Iron binding site 4 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) Collected at 1.280 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe276

b:53.7
occ:0.60
 OD1 B:ASN80 2.3 50.8 1.0
NE2 B:HIS156 2.3 44.7 1.0
OD2 B:ASP50 2.3 52.7 1.0
ND1 B:HIS195 2.6 51.4 1.0
O8 B:MLI277 2.6 62.7 0.6
CE1 B:HIS156 3.2 43.3 1.0
CG B:ASP50 3.2 49.1 1.0
CG B:ASN80 3.4 47.4 1.0
CE1 B:HIS195 3.4 52.7 1.0
CD2 B:HIS156 3.4 43.9 1.0
C3 B:MLI277 3.5 62.8 0.6
OD1 B:ASP50 3.5 48.5 1.0
FE B:FE2275 3.5 48.6 0.8
CG B:HIS195 3.6 50.1 1.0
O7 B:MLI277 3.6 63.0 0.6
CA B:HIS195 3.7 50.5 1.0
ND2 B:ASN80 3.8 47.9 1.0
CB B:HIS195 3.9 50.7 1.0
OD1 B:ASP8 4.1 51.7 1.0
O9 B:MLI277 4.1 61.5 0.6
CD2 B:HIS81 4.3 48.4 1.0
O B:HIS195 4.3 51.5 1.0
ND1 B:HIS156 4.4 44.0 1.0
C1 B:MLI277 4.4 63.5 0.6
N B:ASN80 4.4 44.5 1.0
C2 B:MLI277 4.4 64.6 0.6
CB B:ASP50 4.5 47.0 1.0
CG B:HIS156 4.5 43.1 1.0
NE2 B:HIS195 4.5 54.4 1.0
C B:HIS195 4.5 50.7 1.0
N B:HIS195 4.5 50.7 1.0
CD2 B:HIS195 4.6 51.6 1.0
CB B:ASN80 4.7 46.3 1.0
NE2 B:HIS81 4.9 51.1 1.0

Reference:

C.J.Jackson, K.S.Hadler, P.D.Carr, A.J.Oakley, S.Yip, G.Schenk, D.L.Ollis. Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal-Ion Preference. Acta Crystallogr.,Sect.F V. 64 681 2008.
ISSN: ESSN 1744-3091
PubMed: 18678932
DOI: 10.1107/S1744309108017600
Page generated: Mon Aug 4 22:48:58 2025

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