Iron in PDB 1iw1: Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferrous State
Enzymatic activity of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferrous State
All present enzymatic activity of Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferrous 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 Ferrous State, PDB code: 1iw1
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 /
1.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.865,
62.837,
107.208,
90.00,
101.02,
90.00
|
R / Rfree (%)
|
17.7 /
20.2
|
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 Ferrous State
(pdb code 1iw1). 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 Ferrous State, PDB code: 1iw1:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 1iw1
Go back to
Iron Binding Sites List in 1iw1
Iron binding site 1 out
of 3 in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferrous 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 Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe901
b:9.4
occ:1.00
|
FE
|
A:HEM901
|
0.0
|
9.4
|
1.0
|
NC
|
A:HEM901
|
2.0
|
11.8
|
1.0
|
ND
|
A:HEM901
|
2.0
|
9.6
|
1.0
|
NA
|
A:HEM901
|
2.1
|
8.2
|
1.0
|
NB
|
A:HEM901
|
2.1
|
8.0
|
1.0
|
NE2
|
A:HIS20
|
2.2
|
10.1
|
1.0
|
C4D
|
A:HEM901
|
3.0
|
9.7
|
1.0
|
C1C
|
A:HEM901
|
3.1
|
8.9
|
1.0
|
C4B
|
A:HEM901
|
3.1
|
9.0
|
1.0
|
C1A
|
A:HEM901
|
3.1
|
7.4
|
1.0
|
C1D
|
A:HEM901
|
3.1
|
11.3
|
1.0
|
C4C
|
A:HEM901
|
3.1
|
11.9
|
1.0
|
CD2
|
A:HIS20
|
3.1
|
10.1
|
1.0
|
C4A
|
A:HEM901
|
3.1
|
6.5
|
1.0
|
C1B
|
A:HEM901
|
3.2
|
6.9
|
1.0
|
CE1
|
A:HIS20
|
3.2
|
11.4
|
1.0
|
CHB
|
A:HEM901
|
3.4
|
7.5
|
1.0
|
CHC
|
A:HEM901
|
3.4
|
10.9
|
1.0
|
CHD
|
A:HEM901
|
3.4
|
13.8
|
1.0
|
CHA
|
A:HEM901
|
3.4
|
9.2
|
1.0
|
C2D
|
A:HEM901
|
4.2
|
11.6
|
1.0
|
N
|
A:GLY139
|
4.2
|
12.1
|
1.0
|
C3C
|
A:HEM901
|
4.3
|
13.8
|
1.0
|
C2C
|
A:HEM901
|
4.3
|
12.7
|
1.0
|
CG
|
A:HIS20
|
4.3
|
10.6
|
1.0
|
C3A
|
A:HEM901
|
4.3
|
7.3
|
1.0
|
C3D
|
A:HEM901
|
4.3
|
10.5
|
1.0
|
ND1
|
A:HIS20
|
4.3
|
12.0
|
1.0
|
C2B
|
A:HEM901
|
4.3
|
8.7
|
1.0
|
C2A
|
A:HEM901
|
4.3
|
7.8
|
1.0
|
CA
|
A:GLY139
|
4.4
|
12.9
|
1.0
|
C3B
|
A:HEM901
|
4.4
|
10.8
|
1.0
|
CA
|
A:GLY135
|
4.7
|
9.2
|
1.0
|
CB
|
A:SER138
|
4.9
|
10.9
|
1.0
|
O
|
A:GLY135
|
5.0
|
10.4
|
1.0
|
|
Iron binding site 2 out
of 3 in 1iw1
Go back to
Iron Binding Sites List in 1iw1
Iron binding site 2 out
of 3 in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferrous 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 Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe902
b:19.0
occ:1.00
|
FE
|
B:HEM902
|
0.0
|
19.0
|
1.0
|
ND
|
B:HEM902
|
1.9
|
19.6
|
1.0
|
NB
|
B:HEM902
|
2.0
|
17.6
|
1.0
|
NA
|
B:HEM902
|
2.1
|
15.3
|
1.0
|
NE2
|
B:HIS320
|
2.1
|
19.2
|
1.0
|
NC
|
B:HEM902
|
2.2
|
16.8
|
1.0
|
C4D
|
B:HEM902
|
2.9
|
15.8
|
1.0
|
C1D
|
B:HEM902
|
2.9
|
18.8
|
1.0
|
C1A
|
B:HEM902
|
3.0
|
14.0
|
1.0
|
C4B
|
B:HEM902
|
3.0
|
18.1
|
1.0
|
CD2
|
B:HIS320
|
3.0
|
19.5
|
1.0
|
C1C
|
B:HEM902
|
3.1
|
19.6
|
1.0
|
CE1
|
B:HIS320
|
3.1
|
21.0
|
1.0
|
C1B
|
B:HEM902
|
3.1
|
15.3
|
1.0
|
C4A
|
B:HEM902
|
3.2
|
11.8
|
1.0
|
CHA
|
B:HEM902
|
3.2
|
17.5
|
1.0
|
C4C
|
B:HEM902
|
3.3
|
17.7
|
1.0
|
CHB
|
B:HEM902
|
3.3
|
13.5
|
1.0
|
CHD
|
B:HEM902
|
3.4
|
17.1
|
1.0
|
CHC
|
B:HEM902
|
3.4
|
20.0
|
1.0
|
C2D
|
B:HEM902
|
4.0
|
19.3
|
1.0
|
ND1
|
B:HIS320
|
4.2
|
21.9
|
1.0
|
CG
|
B:HIS320
|
4.2
|
19.6
|
1.0
|
CA
|
B:GLY439
|
4.2
|
15.1
|
1.0
|
C3A
|
B:HEM902
|
4.2
|
12.8
|
1.0
|
C3D
|
B:HEM902
|
4.2
|
21.0
|
1.0
|
C2B
|
B:HEM902
|
4.3
|
16.2
|
1.0
|
C2A
|
B:HEM902
|
4.3
|
13.9
|
1.0
|
C3B
|
B:HEM902
|
4.3
|
17.5
|
1.0
|
N
|
B:GLY439
|
4.4
|
15.0
|
1.0
|
C3C
|
B:HEM902
|
4.4
|
18.3
|
1.0
|
C2C
|
B:HEM902
|
4.4
|
20.7
|
1.0
|
O
|
B:HOH2056
|
4.7
|
14.8
|
1.0
|
CA
|
B:GLY435
|
4.7
|
10.6
|
1.0
|
O
|
B:GLY435
|
4.9
|
11.4
|
1.0
|
|
Iron binding site 3 out
of 3 in 1iw1
Go back to
Iron Binding Sites List in 1iw1
Iron binding site 3 out
of 3 in the Crystal Structure of A Heme Oxygenase (Hmuo) From Corynebacterium Diphtheriae Complexed with Heme in the Ferrous 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 Ferrous State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe903
b:18.1
occ:1.00
|
FE
|
C:HEM903
|
0.0
|
18.1
|
1.0
|
NB
|
C:HEM903
|
2.0
|
15.9
|
1.0
|
ND
|
C:HEM903
|
2.0
|
18.5
|
1.0
|
NA
|
C:HEM903
|
2.0
|
17.7
|
1.0
|
NC
|
C:HEM903
|
2.1
|
19.0
|
1.0
|
NE2
|
C:HIS620
|
2.2
|
30.3
|
1.0
|
C4D
|
C:HEM903
|
3.0
|
20.4
|
1.0
|
C1A
|
C:HEM903
|
3.0
|
19.2
|
1.0
|
C4B
|
C:HEM903
|
3.0
|
17.5
|
1.0
|
C4A
|
C:HEM903
|
3.0
|
17.2
|
1.0
|
CD2
|
C:HIS620
|
3.1
|
30.9
|
1.0
|
C1D
|
C:HEM903
|
3.1
|
20.4
|
1.0
|
C1C
|
C:HEM903
|
3.1
|
20.2
|
1.0
|
C1B
|
C:HEM903
|
3.1
|
16.0
|
1.0
|
C4C
|
C:HEM903
|
3.1
|
20.7
|
1.0
|
CE1
|
C:HIS620
|
3.3
|
31.0
|
1.0
|
CHB
|
C:HEM903
|
3.3
|
16.1
|
1.0
|
CHA
|
C:HEM903
|
3.4
|
20.4
|
1.0
|
CHC
|
C:HEM903
|
3.4
|
19.1
|
1.0
|
CHD
|
C:HEM903
|
3.4
|
20.4
|
1.0
|
C2D
|
C:HEM903
|
4.2
|
22.4
|
1.0
|
C3A
|
C:HEM903
|
4.2
|
18.1
|
1.0
|
C2B
|
C:HEM903
|
4.2
|
16.4
|
1.0
|
CG
|
C:HIS620
|
4.2
|
31.1
|
1.0
|
C3B
|
C:HEM903
|
4.3
|
19.6
|
1.0
|
C2A
|
C:HEM903
|
4.3
|
19.9
|
1.0
|
C3C
|
C:HEM903
|
4.3
|
22.2
|
1.0
|
ND1
|
C:HIS620
|
4.3
|
32.5
|
1.0
|
C2C
|
C:HEM903
|
4.3
|
21.7
|
1.0
|
C3D
|
C:HEM903
|
4.3
|
24.0
|
1.0
|
CA
|
C:GLY735
|
4.7
|
19.0
|
1.0
|
O
|
C:HOH2074
|
4.7
|
23.5
|
1.0
|
O
|
C:GLY735
|
4.8
|
19.6
|
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 08:15:47 2024
|