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Iron in PDB 3bu7: Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi

Enzymatic activity of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi

All present enzymatic activity of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi:
1.13.11.4;

Protein crystallography data

The structure of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi, PDB code: 3bu7 was solved by J.Chen, M.Z.Wang, G.Y.Zhu, X.C.Zhang, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.93 / 2.80
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 129.999, 129.999, 246.255, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 24.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi (pdb code 3bu7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi, PDB code: 3bu7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3bu7

Go back to Iron Binding Sites List in 3bu7
Iron binding site 1 out of 4 in the Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:29.2
occ:1.00
 NE2 A:HIS121 2.2 23.8 1.0
NE2 A:HIS160 2.2 20.6 1.0
NE2 A:HIS119 2.4 26.3 1.0
O A:HOH501 2.5 20.0 1.0
O A:HOH502 2.6 14.3 1.0
CE1 A:HIS160 3.1 21.1 1.0
CD2 A:HIS121 3.2 24.0 1.0
CE1 A:HIS121 3.2 24.5 1.0
CD2 A:HIS160 3.3 20.5 1.0
CE1 A:HIS119 3.3 26.2 1.0
CD2 A:HIS119 3.3 26.1 1.0
ND1 A:HIS121 4.3 23.9 1.0
ND1 A:HIS160 4.3 20.8 1.0
CG A:HIS121 4.3 24.2 1.0
CG A:HIS160 4.4 20.7 1.0
ND1 A:HIS119 4.5 27.1 1.0
CG A:HIS119 4.5 26.3 1.0

Iron binding site 2 out of 4 in 3bu7

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Iron binding site 2 out of 4 in the Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:36.7
occ:1.00
 NE2 A:HIS330 2.2 29.6 1.0
NE2 A:HIS292 2.3 28.1 1.0
NE2 A:HIS290 2.4 30.8 1.0
CE1 A:HIS330 3.1 29.8 1.0
CD2 A:HIS330 3.2 29.4 1.0
CE1 A:HIS290 3.2 30.8 1.0
CD2 A:HIS292 3.2 27.9 1.0
CD2 A:HIS290 3.4 31.2 1.0
CE1 A:HIS292 3.4 28.3 1.0
OH A:TYR298 4.0 25.4 1.0
OD2 A:ASP255 4.0 30.9 1.0
OD1 A:ASP255 4.0 30.8 1.0
ND1 A:HIS330 4.3 29.8 1.0
CG A:HIS330 4.3 29.3 1.0
ND1 A:HIS290 4.4 31.4 1.0
CG A:HIS292 4.4 28.6 1.0
CG A:ASP255 4.4 31.3 1.0
ND1 A:HIS292 4.5 28.6 1.0
CG A:HIS290 4.5 31.9 1.0

Iron binding site 3 out of 4 in 3bu7

Go back to Iron Binding Sites List in 3bu7
Iron binding site 3 out of 4 in the Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:46.3
occ:1.00
 NE2 B:HIS160 2.2 37.0 1.0
NE2 B:HIS119 2.2 41.7 1.0
NE2 B:HIS121 2.4 32.8 1.0
CE1 B:HIS160 3.1 36.9 1.0
CD2 B:HIS119 3.1 41.3 1.0
CD2 B:HIS121 3.3 32.9 1.0
CE1 B:HIS119 3.3 41.7 1.0
CD2 B:HIS160 3.3 37.5 1.0
CE1 B:HIS121 3.4 33.1 1.0
ND1 B:HIS160 4.3 37.3 1.0
CG B:HIS119 4.3 40.9 1.0
ND1 B:HIS119 4.4 41.8 1.0
CG B:HIS160 4.4 37.4 1.0
CG B:HIS121 4.5 32.7 1.0
ND1 B:HIS121 4.5 32.4 1.0
NE2 B:HIS162 5.0 46.9 1.0

Iron binding site 4 out of 4 in 3bu7

Go back to Iron Binding Sites List in 3bu7
Iron binding site 4 out of 4 in the Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure and Biochemical Characterization of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:22.1
occ:1.00
 NE2 B:HIS330 2.1 20.1 1.0
O B:HOH501 2.2 2.0 1.0
NE2 B:HIS292 2.3 22.7 1.0
O B:HOH502 2.3 14.0 1.0
NE2 B:HIS290 2.4 25.6 1.0
CD2 B:HIS330 3.1 20.3 1.0
CE1 B:HIS330 3.1 20.4 1.0
CE1 B:HIS290 3.2 25.5 1.0
CD2 B:HIS292 3.2 22.9 1.0
CE1 B:HIS292 3.3 23.0 1.0
CD2 B:HIS290 3.4 26.5 1.0
OH B:TYR298 3.9 26.1 1.0
OD2 B:ASP255 4.1 21.3 1.0
OD1 B:ASP255 4.1 22.5 1.0
ND1 B:HIS330 4.2 20.4 1.0
CG B:HIS330 4.2 20.6 1.0
ND1 B:HIS290 4.3 25.8 1.0
ND1 B:HIS292 4.4 23.2 1.0
CG B:HIS292 4.4 23.6 1.0
CG B:HIS290 4.5 26.6 1.0
CG B:ASP255 4.5 22.2 1.0

Reference:

J.Chen, W.Li, M.Wang, G.Zhu, D.Liu, F.Sun, N.Hao, X.Li, Z.Rao, X.C.Zhang. Crystal Structure and Mutagenic Analysis of Gdosp, A Gentisate 1,2-Dioxygenase From Silicibacter Pomeroyi. Protein Sci. V. 17 1362 2008.
ISSN: ISSN 0961-8368
PubMed: 18505738
DOI: 10.1110/PS.035881.108
Page generated: Sun Aug 4 08:00:52 2024

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