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Iron in PDB 2zo9: Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference

Enzymatic activity of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference

All present enzymatic activity of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference:
3.1.4.46;

Protein crystallography data

The structure of Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference, PDB code: 2zo9 was solved by C.J.Jackson, P.D.Carr, D.L.Ollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.03 / 2.20
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 164.159, 164.159, 164.159, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 18.9

Iron Binding Sites:

The binding sites of Iron atom in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference (pdb code 2zo9). 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) and Characterization of the Native FE2+ Metal Ion Preference, PDB code: 2zo9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2zo9

Go back to Iron Binding Sites List in 2zo9
Iron binding site 1 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference


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) and Characterization of the Native FE2+ Metal Ion Preference within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe275

b:44.9
occ:0.75
 OD1 B:ASP8 2.1 52.5 1.0
OD2 B:ASP50 2.3 55.8 1.0
NE2 B:HIS10 2.4 49.1 1.0
NE2 B:HIS197 2.4 50.3 1.0
O8 B:MLI277 2.4 64.9 0.7
O9 B:MLI277 2.6 64.4 0.7
C3 B:MLI277 2.8 66.3 0.7
CG B:ASP8 3.2 51.1 1.0
CE1 B:HIS10 3.2 47.4 1.0
CG B:ASP50 3.2 52.1 1.0
CE1 B:HIS197 3.2 48.1 1.0
CB B:ASP50 3.4 51.1 1.0
CD2 B:HIS197 3.4 50.3 1.0
CD2 B:HIS10 3.5 48.5 1.0
FE B:FE2276 3.5 47.1 0.6
CB B:ASP8 3.8 49.1 1.0
OD2 B:ASP8 4.2 53.4 1.0
O B:HIS195 4.3 53.2 1.0
C1 B:MLI277 4.4 67.0 0.7
ND1 B:HIS10 4.4 49.0 1.0
OD1 B:ASP50 4.4 51.7 1.0
ND1 B:HIS197 4.4 49.9 1.0
CD2 B:HIS81 4.5 47.4 1.0
CE1 B:HIS156 4.5 48.4 1.0
CG B:HIS197 4.5 50.8 1.0
CG B:HIS10 4.5 48.7 1.0
CA B:ASP8 4.6 49.4 1.0
NE2 B:HIS156 4.7 49.1 1.0
CA B:HIS195 4.8 53.6 1.0
NE2 B:HIS81 4.9 48.7 1.0
O7 B:MLI277 4.9 66.0 0.7
CA B:ASP50 4.9 50.6 1.0
C B:HIS195 4.9 53.2 1.0

Iron binding site 2 out of 4 in 2zo9

Go back to Iron Binding Sites List in 2zo9
Iron binding site 2 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference


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) and Characterization of the Native FE2+ Metal Ion Preference within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe276

b:47.1
occ:0.55
 OD1 B:ASN80 2.3 56.0 1.0
OD2 B:ASP50 2.3 55.8 1.0
NE2 B:HIS156 2.4 49.1 1.0
ND1 B:HIS195 2.5 54.6 1.0
O8 B:MLI277 2.5 64.9 0.7
CG B:ASP50 3.1 52.1 1.0
CE1 B:HIS195 3.2 54.9 1.0
CE1 B:HIS156 3.2 48.4 1.0
O7 B:MLI277 3.3 66.0 0.7
CG B:ASN80 3.3 52.1 1.0
C3 B:MLI277 3.4 66.3 0.7
OD1 B:ASP50 3.4 51.7 1.0
CD2 B:HIS156 3.4 47.3 1.0
FE B:FE2275 3.5 44.9 0.8
CG B:HIS195 3.7 54.0 1.0
ND2 B:ASN80 3.7 53.4 1.0
CA B:HIS195 3.8 53.6 1.0
OD1 B:ASP8 4.1 52.5 1.0
C1 B:MLI277 4.1 67.0 0.7
O9 B:MLI277 4.1 64.4 0.7
C2 B:MLI277 4.1 67.2 0.7
CB B:HIS195 4.1 53.5 1.0
CD2 B:HIS81 4.2 47.4 1.0
O B:HIS195 4.3 53.2 1.0
CB B:ASP50 4.4 51.1 1.0
N B:ASN80 4.4 49.5 1.0
ND1 B:HIS156 4.4 47.9 1.0
NE2 B:HIS195 4.5 57.0 1.0
CG B:HIS156 4.5 49.2 1.0
C B:HIS195 4.6 53.2 1.0
CB B:ASN80 4.6 50.5 1.0
N B:HIS195 4.7 53.8 1.0
CD2 B:HIS195 4.7 55.0 1.0
NE2 B:HIS81 4.9 48.7 1.0

Iron binding site 3 out of 4 in 2zo9

Go back to Iron Binding Sites List in 2zo9
Iron binding site 3 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference


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) and Characterization of the Native FE2+ Metal Ion Preference within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe275

b:45.7
occ:0.75
 OD1 C:ASP8 2.3 55.7 1.0
OD2 C:ASP50 2.3 54.1 1.0
NE2 C:HIS197 2.3 53.4 1.0
O8 C:MLI277 2.3 63.4 0.7
NE2 C:HIS10 2.4 47.8 1.0
O9 C:MLI277 2.7 61.4 0.7
C3 C:MLI277 2.8 63.7 0.7
CE1 C:HIS10 3.2 42.5 1.0
CD2 C:HIS197 3.2 54.0 1.0
CG C:ASP8 3.2 51.5 1.0
CG C:ASP50 3.3 52.1 1.0
CE1 C:HIS197 3.3 52.3 1.0
CB C:ASP50 3.6 51.0 1.0
CD2 C:HIS10 3.6 43.6 1.0
FE C:FE2276 3.6 47.6 0.6
CB C:ASP8 3.7 48.7 1.0
OD2 C:ASP8 4.3 54.0 1.0
O C:HIS195 4.3 52.6 1.0
C1 C:MLI277 4.3 62.9 0.7
ND1 C:HIS10 4.4 47.8 1.0
CG C:HIS197 4.4 52.9 1.0
ND1 C:HIS197 4.4 53.8 1.0
OD1 C:ASP50 4.4 49.6 1.0
CE1 C:HIS156 4.5 49.8 1.0
CA C:ASP8 4.5 49.1 1.0
CG C:HIS10 4.6 45.9 1.0
CD2 C:HIS81 4.6 50.9 1.0
CA C:HIS195 4.7 52.6 1.0
NE2 C:HIS156 4.7 51.0 1.0
C C:HIS195 4.9 52.4 1.0
NE2 C:HIS81 4.9 52.5 1.0

Iron binding site 4 out of 4 in 2zo9

Go back to Iron Binding Sites List in 2zo9
Iron binding site 4 out of 4 in the Malonate-Bound Structure of the Glycerophosphodiesterase From Enterobacter Aerogenes (Gpdq) and Characterization of the Native FE2+ Metal Ion Preference


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) and Characterization of the Native FE2+ Metal Ion Preference within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe276

b:47.6
occ:0.55
 NE2 C:HIS156 2.3 51.0 1.0
OD1 C:ASN80 2.3 56.0 1.0
OD2 C:ASP50 2.4 54.1 1.0
O8 C:MLI277 2.5 63.4 0.7
ND1 C:HIS195 2.5 55.5 1.0
CG C:ASP50 3.1 52.1 1.0
CE1 C:HIS156 3.1 49.8 1.0
OD1 C:ASP50 3.3 49.6 1.0
CG C:ASN80 3.3 51.9 1.0
CD2 C:HIS156 3.3 50.0 1.0
C3 C:MLI277 3.4 63.7 0.7
CE1 C:HIS195 3.4 55.1 1.0
FE C:FE2275 3.6 45.7 0.8
CG C:HIS195 3.6 53.3 1.0
ND2 C:ASN80 3.7 52.2 1.0
O7 C:MLI277 3.7 61.9 0.7
CA C:HIS195 3.8 52.6 1.0
CB C:HIS195 3.9 53.2 1.0
OD1 C:ASP8 4.1 55.7 1.0
O9 C:MLI277 4.1 61.4 0.7
C1 C:MLI277 4.1 62.9 0.7
CD2 C:HIS81 4.2 50.9 1.0
ND1 C:HIS156 4.3 49.2 1.0
O C:HIS195 4.3 52.6 1.0
N C:ASN80 4.4 49.6 1.0
C2 C:MLI277 4.4 63.5 0.7
CB C:ASP50 4.4 51.0 1.0
CG C:HIS156 4.4 50.3 1.0
NE2 C:HIS195 4.6 55.6 1.0
C C:HIS195 4.6 52.4 1.0
N C:HIS195 4.6 52.5 1.0
CB C:ASN80 4.6 50.9 1.0
CD2 C:HIS195 4.7 54.1 1.0
NE2 C:HIS81 4.9 52.5 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: Sun Aug 4 06:02:23 2024

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