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Iron in PDB 4pgi: Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound

Enzymatic activity of Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound

All present enzymatic activity of Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound:
4.1.99.5;

Protein crystallography data

The structure of Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound, PDB code: 4pgi was solved by B.C.Buer, B.Paul, D.Das, J.A.Stuckey, E.N.G.Marsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.48 / 2.08
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.071, 77.071, 117.259, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.2

Iron Binding Sites:

The binding sites of Iron atom in the Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound (pdb code 4pgi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound, PDB code: 4pgi:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 4pgi

Go back to Iron Binding Sites List in 4pgi
Iron binding site 1 out of 2 in the Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.0
occ:0.36
 O A:HOH536 1.9 17.6 0.5
OE1 A:GLU45 2.2 30.4 1.0
OE1 A:GLU73 2.3 68.8 1.0
OE2 A:GLU45 2.6 52.8 1.0
CD A:GLU45 2.7 46.0 1.0
CD A:GLU73 2.8 63.4 1.0
CAC A:Y69303 2.8 27.6 0.5
OAB A:Y69303 2.8 44.0 0.5
OE2 A:GLU73 2.9 40.8 1.0
CAE A:Y69303 3.0 43.3 0.5
ND1 A:HIS76 3.2 39.5 1.0
CAC A:Y69303 3.2 44.2 0.5
FE A:FE302 3.3 28.4 0.4
OAB A:Y69303 3.5 24.4 0.5
CAG A:Y69303 3.9 41.4 0.5
CAE A:Y69303 3.9 29.5 0.5
CAF A:Y69303 3.9 43.2 0.5
CG A:GLU73 4.1 41.6 1.0
CE1 A:HIS76 4.1 38.8 1.0
CG A:GLU45 4.2 29.1 1.0
CG A:HIS76 4.2 37.6 1.0
CAF A:Y69303 4.2 35.3 0.5
OH A:TYR135 4.3 45.8 1.0
CB A:HIS76 4.4 33.9 1.0
CG A:GLU157 4.4 41.9 0.5
CB A:GLU73 4.5 30.2 1.0
CA A:GLU73 4.6 29.2 1.0
OE1 A:GLU128 4.9 34.8 0.5
CB A:GLU45 5.0 26.3 1.0

Iron binding site 2 out of 2 in 4pgi

Go back to Iron Binding Sites List in 4pgi
Iron binding site 2 out of 2 in the Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Analogs Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:28.4
occ:0.36
 OAB A:Y69303 1.4 44.0 0.5
CAC A:Y69303 1.8 44.2 0.5
OE1 A:GLU73 2.2 68.8 1.0
OE2 A:GLU128 2.2 41.1 0.5
OE1 A:GLU128 2.4 34.8 0.5
CAE A:Y69303 2.4 43.3 0.5
OAB A:Y69303 2.4 24.4 0.5
CD A:GLU128 2.6 46.7 0.5
ND1 A:HIS160 2.7 31.9 0.5
OH A:TYR52 2.9 39.8 0.5
CD A:GLU73 3.1 63.4 1.0
CAC A:Y69303 3.2 27.6 0.5
FE A:FE301 3.3 30.0 0.4
CE1 A:HIS160 3.5 30.9 0.5
OE2 A:GLU73 3.5 40.8 1.0
CG A:HIS160 3.6 30.6 0.5
CB A:HIS160 3.8 27.6 0.5
CAF A:Y69303 3.9 43.2 0.5
OE2 A:GLU128 4.0 33.9 0.5
CG A:GLU128 4.1 31.3 0.5
CG A:GLU128 4.1 31.7 0.5
CZ A:TYR52 4.2 36.5 0.5
CG A:GLU73 4.2 41.6 1.0
NE2 A:GLN123 4.3 22.0 0.5
OH A:TYR52 4.3 17.9 0.5
CG A:GLU157 4.4 41.9 0.5
CE2 A:TYR52 4.4 28.6 0.5
CD A:GLU128 4.4 39.4 0.5
O A:HOH536 4.4 17.6 0.5
NE2 A:HIS160 4.6 32.0 0.5
CA A:GLU157 4.6 30.7 0.5
CD2 A:HIS160 4.6 32.6 0.5
CAE A:Y69303 4.7 29.5 0.5
CB A:ALA48 4.7 27.0 1.0
CE2 A:TYR52 4.8 32.8 0.5
CZ A:TYR52 4.8 30.7 0.5
CB A:GLU157 4.9 31.4 0.5
CAG A:Y69303 4.9 41.4 0.5
OE1 A:GLU45 5.0 30.4 1.0

Reference:

B.C.Buer, B.Paul, D.Das, J.A.Stuckey, E.N.Marsh. Insights Into Substrate and Metal Binding From the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound. Acs Chem.Biol. V. 9 2584 2014.
ISSN: ESSN 1554-8937
PubMed: 25222710
DOI: 10.1021/CB500343J
Page generated: Mon Aug 5 08:24:58 2024

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