Iron in PDB 1iw0: Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State
Enzymatic activity of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State
All present enzymatic activity of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State:
1.14.99.3;
Protein crystallography data
The structure of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State, PDB code: 1iw0
was solved by
S.Hirotsu,
M.Unno,
G.C.Chu,
D.S.Lee,
S.Y.Park,
Y.Shiro,
M.Ikeda-Saito,
Riken Structural Genomics/Proteomics Initiative (Rsgi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
12.00 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.559,
62.838,
107.661,
90.00,
100.86,
90.00
|
R / Rfree (%)
|
16.5 /
19.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State
(pdb code 1iw0). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the
Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State, PDB code: 1iw0:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 1iw0
Go back to
Iron Binding Sites List in 1iw0
Iron binding site 1 out
of 3 in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe901
b:15.1
occ:1.00
|
FE
|
A:HEM901
|
0.0
|
15.1
|
1.0
|
NE2
|
A:HIS20
|
2.0
|
17.4
|
1.0
|
NC
|
A:HEM901
|
2.0
|
16.6
|
1.0
|
NA
|
A:HEM901
|
2.0
|
13.9
|
1.0
|
ND
|
A:HEM901
|
2.0
|
17.5
|
1.0
|
NB
|
A:HEM901
|
2.0
|
12.7
|
1.0
|
O
|
A:HOH1001
|
2.1
|
15.9
|
1.0
|
C4B
|
A:HEM901
|
2.9
|
14.9
|
1.0
|
C1C
|
A:HEM901
|
2.9
|
17.2
|
1.0
|
CE1
|
A:HIS20
|
2.9
|
20.0
|
1.0
|
C4D
|
A:HEM901
|
3.0
|
18.8
|
1.0
|
C4C
|
A:HEM901
|
3.0
|
18.5
|
1.0
|
CD2
|
A:HIS20
|
3.0
|
17.2
|
1.0
|
C1A
|
A:HEM901
|
3.0
|
14.8
|
1.0
|
C1D
|
A:HEM901
|
3.1
|
20.2
|
1.0
|
C4A
|
A:HEM901
|
3.1
|
12.8
|
1.0
|
C1B
|
A:HEM901
|
3.1
|
11.9
|
1.0
|
CHC
|
A:HEM901
|
3.3
|
16.8
|
1.0
|
CHD
|
A:HEM901
|
3.4
|
19.2
|
1.0
|
CHB
|
A:HEM901
|
3.4
|
12.0
|
1.0
|
CHA
|
A:HEM901
|
3.5
|
17.0
|
1.0
|
ND1
|
A:HIS20
|
4.1
|
20.4
|
1.0
|
CG
|
A:HIS20
|
4.1
|
18.1
|
1.0
|
C3C
|
A:HEM901
|
4.2
|
18.4
|
1.0
|
C2C
|
A:HEM901
|
4.2
|
18.4
|
1.0
|
C3B
|
A:HEM901
|
4.2
|
14.3
|
1.0
|
O
|
A:HOH1377
|
4.2
|
42.1
|
1.0
|
C3A
|
A:HEM901
|
4.2
|
12.5
|
1.0
|
C2D
|
A:HEM901
|
4.3
|
23.2
|
1.0
|
C2B
|
A:HEM901
|
4.3
|
13.0
|
1.0
|
O
|
A:HOH1042
|
4.3
|
15.6
|
1.0
|
C2A
|
A:HEM901
|
4.3
|
14.4
|
1.0
|
C3D
|
A:HEM901
|
4.3
|
23.4
|
1.0
|
CA
|
A:GLY135
|
4.7
|
13.5
|
1.0
|
O
|
A:GLY135
|
4.7
|
14.4
|
1.0
|
|
Iron binding site 2 out
of 3 in 1iw0
Go back to
Iron Binding Sites List in 1iw0
Iron binding site 2 out
of 3 in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe902
b:13.1
occ:1.00
|
FE
|
B:HEM902
|
0.0
|
13.1
|
1.0
|
NB
|
B:HEM902
|
2.0
|
11.4
|
1.0
|
NA
|
B:HEM902
|
2.0
|
11.4
|
1.0
|
NE2
|
B:HIS320
|
2.0
|
12.4
|
1.0
|
ND
|
B:HEM902
|
2.1
|
14.2
|
1.0
|
NC
|
B:HEM902
|
2.1
|
13.9
|
1.0
|
O
|
B:HOH1002
|
2.1
|
14.4
|
1.0
|
C4B
|
B:HEM902
|
2.9
|
12.0
|
1.0
|
C4D
|
B:HEM902
|
3.0
|
14.3
|
1.0
|
CD2
|
B:HIS320
|
3.0
|
11.0
|
1.0
|
CE1
|
B:HIS320
|
3.0
|
14.2
|
1.0
|
C1A
|
B:HEM902
|
3.0
|
12.5
|
1.0
|
C1C
|
B:HEM902
|
3.0
|
14.6
|
1.0
|
C4A
|
B:HEM902
|
3.1
|
10.2
|
1.0
|
C1B
|
B:HEM902
|
3.1
|
10.0
|
1.0
|
C1D
|
B:HEM902
|
3.1
|
15.1
|
1.0
|
C4C
|
B:HEM902
|
3.1
|
15.6
|
1.0
|
CHD
|
B:HEM902
|
3.4
|
15.0
|
1.0
|
CHB
|
B:HEM902
|
3.4
|
10.1
|
1.0
|
CHA
|
B:HEM902
|
3.4
|
12.9
|
1.0
|
CHC
|
B:HEM902
|
3.4
|
13.6
|
1.0
|
ND1
|
B:HIS320
|
4.1
|
14.9
|
1.0
|
CG
|
B:HIS320
|
4.1
|
13.0
|
1.0
|
C2D
|
B:HEM902
|
4.2
|
16.5
|
1.0
|
C3B
|
B:HEM902
|
4.2
|
12.3
|
1.0
|
O
|
B:HOH1443
|
4.2
|
15.4
|
1.0
|
C3C
|
B:HEM902
|
4.2
|
16.3
|
1.0
|
C3A
|
B:HEM902
|
4.2
|
11.2
|
1.0
|
C3D
|
B:HEM902
|
4.3
|
17.0
|
1.0
|
C2C
|
B:HEM902
|
4.3
|
16.6
|
1.0
|
C2B
|
B:HEM902
|
4.3
|
10.9
|
1.0
|
C2A
|
B:HEM902
|
4.3
|
11.8
|
1.0
|
CA
|
B:GLY435
|
4.7
|
12.1
|
1.0
|
CA
|
B:GLY439
|
4.7
|
22.7
|
0.5
|
CA
|
B:GLY439
|
4.7
|
22.6
|
0.5
|
O
|
B:GLY435
|
4.7
|
13.1
|
1.0
|
N
|
B:GLY439
|
4.9
|
22.1
|
0.5
|
|
Iron binding site 3 out
of 3 in 1iw0
Go back to
Iron Binding Sites List in 1iw0
Iron binding site 3 out
of 3 in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferric State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe903
b:12.7
occ:1.00
|
FE
|
C:HEM903
|
0.0
|
12.7
|
1.0
|
NE2
|
C:HIS620
|
2.0
|
13.8
|
1.0
|
NA
|
C:HEM903
|
2.0
|
12.1
|
1.0
|
NB
|
C:HEM903
|
2.0
|
12.0
|
1.0
|
ND
|
C:HEM903
|
2.0
|
11.9
|
1.0
|
NC
|
C:HEM903
|
2.0
|
13.6
|
1.0
|
O
|
C:HOH1003
|
2.1
|
15.7
|
1.0
|
CD2
|
C:HIS620
|
3.0
|
14.9
|
1.0
|
C1A
|
C:HEM903
|
3.0
|
11.8
|
1.0
|
CE1
|
C:HIS620
|
3.0
|
15.9
|
1.0
|
C1C
|
C:HEM903
|
3.0
|
15.0
|
1.0
|
C4B
|
C:HEM903
|
3.0
|
12.8
|
1.0
|
C4D
|
C:HEM903
|
3.0
|
12.2
|
1.0
|
C1D
|
C:HEM903
|
3.0
|
12.1
|
1.0
|
C1B
|
C:HEM903
|
3.1
|
11.0
|
1.0
|
C4A
|
C:HEM903
|
3.1
|
10.7
|
1.0
|
C4C
|
C:HEM903
|
3.1
|
13.9
|
1.0
|
CHC
|
C:HEM903
|
3.4
|
15.2
|
1.0
|
CHA
|
C:HEM903
|
3.4
|
12.5
|
1.0
|
CHD
|
C:HEM903
|
3.4
|
11.8
|
1.0
|
CHB
|
C:HEM903
|
3.4
|
10.6
|
1.0
|
ND1
|
C:HIS620
|
4.1
|
16.6
|
1.0
|
CG
|
C:HIS620
|
4.1
|
16.3
|
1.0
|
O
|
C:HOH1370
|
4.2
|
17.9
|
1.0
|
C2D
|
C:HEM903
|
4.2
|
12.4
|
1.0
|
C3B
|
C:HEM903
|
4.2
|
13.7
|
1.0
|
C2B
|
C:HEM903
|
4.2
|
12.6
|
1.0
|
C2C
|
C:HEM903
|
4.2
|
15.7
|
1.0
|
C2A
|
C:HEM903
|
4.3
|
11.8
|
1.0
|
C3D
|
C:HEM903
|
4.3
|
12.8
|
1.0
|
C3A
|
C:HEM903
|
4.3
|
10.7
|
1.0
|
C3C
|
C:HEM903
|
4.3
|
15.6
|
1.0
|
CA
|
C:GLY735
|
4.5
|
11.5
|
1.0
|
O
|
C:GLY735
|
4.7
|
11.6
|
1.0
|
|
Reference:
S.Hirotsu,
G.C.Chu,
M.Unno,
D.S.Lee,
T.Yoshida,
S.Y.Park,
Y.Shiro,
M.Ikeda-Saito.
The Crystal Structures of the Ferric and Ferrous Forms of the Heme Complex of Hmuo, A Heme Oxygenase of Corynebacterium Diphtheriae. J.Biol.Chem. V. 279 11937 2004.
ISSN: ISSN 0021-9258
PubMed: 14645223
DOI: 10.1074/JBC.M311631200
Page generated: Sat Aug 3 08:15:37 2024
|