Iron in PDB 1olt: Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme.
Protein crystallography data
The structure of Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme., PDB code: 1olt
was solved by
G.Layer,
J.Moser,
D.W.Heinz,
D.Jahn,
W.-D.Schubert,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
100.00 /
2.07
|
Space group
|
P 63
|
Cell size a, b, c (Å), α, β, γ (°)
|
114.036,
114.036,
76.459,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.4 /
18.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme.
(pdb code 1olt). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme., PDB code: 1olt:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1olt
Go back to
Iron Binding Sites List in 1olt
Iron binding site 1 out
of 4 in the Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:23.8
occ:1.00
|
FE1
|
A:SF4500
|
0.0
|
23.8
|
1.0
|
S3
|
A:SF4500
|
2.1
|
15.2
|
1.0
|
S4
|
A:SF4500
|
2.2
|
17.1
|
1.0
|
S2
|
A:SF4500
|
2.2
|
13.4
|
1.0
|
SG
|
A:CYS62
|
2.3
|
12.6
|
1.0
|
FE4
|
A:SF4500
|
2.5
|
28.0
|
1.0
|
FE3
|
A:SF4500
|
2.5
|
28.9
|
1.0
|
FE2
|
A:SF4500
|
2.7
|
25.7
|
1.0
|
CB
|
A:CYS62
|
3.2
|
12.7
|
1.0
|
OG1
|
A:THR114
|
3.8
|
14.9
|
1.0
|
S1
|
A:SF4500
|
3.9
|
15.0
|
1.0
|
N
|
A:SAM501
|
3.9
|
18.7
|
1.0
|
CG
|
A:LYS73
|
4.1
|
12.3
|
0.3
|
CD
|
A:LYS73
|
4.4
|
13.5
|
0.3
|
O
|
A:HOH2066
|
4.4
|
17.8
|
1.0
|
O
|
A:SAM501
|
4.5
|
18.8
|
1.0
|
CG
|
A:LYS73
|
4.6
|
14.0
|
0.7
|
CD
|
A:LYS73
|
4.6
|
16.8
|
0.7
|
CA
|
A:CYS62
|
4.6
|
12.3
|
1.0
|
CB
|
A:LYS73
|
4.6
|
12.9
|
0.3
|
O
|
A:LYS64
|
4.7
|
13.2
|
1.0
|
CB
|
A:LYS73
|
4.7
|
13.4
|
0.7
|
C
|
A:GLY113
|
4.7
|
12.8
|
1.0
|
CA
|
A:GLY113
|
4.7
|
13.2
|
1.0
|
SG
|
A:CYS69
|
4.7
|
15.6
|
1.0
|
SG
|
A:CYS66
|
4.7
|
13.7
|
1.0
|
O
|
A:HOH2132
|
4.8
|
13.4
|
1.0
|
CE
|
A:LYS73
|
4.9
|
17.1
|
0.7
|
O
|
A:GLY113
|
4.9
|
14.0
|
1.0
|
NZ
|
A:LYS73
|
5.0
|
13.1
|
0.3
|
|
Iron binding site 2 out
of 4 in 1olt
Go back to
Iron Binding Sites List in 1olt
Iron binding site 2 out
of 4 in the Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:25.7
occ:1.00
|
FE2
|
A:SF4500
|
0.0
|
25.7
|
1.0
|
S4
|
A:SF4500
|
2.1
|
17.1
|
1.0
|
S3
|
A:SF4500
|
2.2
|
15.2
|
1.0
|
S1
|
A:SF4500
|
2.2
|
15.0
|
1.0
|
SG
|
A:CYS69
|
2.4
|
15.6
|
1.0
|
FE4
|
A:SF4500
|
2.4
|
28.0
|
1.0
|
FE3
|
A:SF4500
|
2.6
|
28.9
|
1.0
|
FE1
|
A:SF4500
|
2.7
|
23.8
|
1.0
|
CB
|
A:CYS69
|
3.1
|
13.8
|
1.0
|
S2
|
A:SF4500
|
3.9
|
13.4
|
1.0
|
NZ
|
A:LYS73
|
4.0
|
13.1
|
0.3
|
CG
|
A:LYS73
|
4.2
|
12.3
|
0.3
|
SG
|
A:CYS71
|
4.2
|
9.6
|
0.5
|
CG
|
A:LYS73
|
4.5
|
14.0
|
0.7
|
O
|
A:SAM501
|
4.5
|
18.8
|
1.0
|
CA
|
A:CYS69
|
4.5
|
12.8
|
1.0
|
SD
|
A:SAM501
|
4.5
|
19.9
|
0.6
|
CB
|
A:CYS66
|
4.6
|
10.4
|
1.0
|
SG
|
A:CYS66
|
4.6
|
13.7
|
1.0
|
CB
|
A:CYS71
|
4.6
|
12.4
|
0.5
|
CB
|
A:CYS71
|
4.6
|
10.9
|
0.5
|
SG
|
A:CYS62
|
4.7
|
12.6
|
1.0
|
CE
|
A:LYS73
|
4.7
|
17.1
|
0.7
|
CD
|
A:LYS73
|
4.7
|
13.5
|
0.3
|
N
|
A:SAM501
|
4.8
|
18.7
|
1.0
|
CD
|
A:LYS73
|
4.9
|
16.8
|
0.7
|
CE1
|
A:PHE68
|
4.9
|
14.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 1olt
Go back to
Iron Binding Sites List in 1olt
Iron binding site 3 out
of 4 in the Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:28.9
occ:1.00
|
FE3
|
A:SF4500
|
0.0
|
28.9
|
1.0
|
S4
|
A:SF4500
|
2.2
|
17.1
|
1.0
|
O
|
A:SAM501
|
2.2
|
18.8
|
1.0
|
S1
|
A:SF4500
|
2.3
|
15.0
|
1.0
|
S2
|
A:SF4500
|
2.3
|
13.4
|
1.0
|
FE4
|
A:SF4500
|
2.4
|
28.0
|
1.0
|
FE1
|
A:SF4500
|
2.5
|
23.8
|
1.0
|
N
|
A:SAM501
|
2.5
|
18.7
|
1.0
|
FE2
|
A:SF4500
|
2.6
|
25.7
|
1.0
|
C
|
A:SAM501
|
3.1
|
19.3
|
1.0
|
CA
|
A:SAM501
|
3.3
|
18.1
|
1.0
|
SD
|
A:SAM501
|
3.5
|
19.9
|
0.6
|
S3
|
A:SF4500
|
3.6
|
15.2
|
1.0
|
CG
|
A:SAM501
|
3.7
|
18.9
|
0.4
|
NH1
|
A:ARG184
|
4.1
|
14.7
|
1.0
|
CB
|
A:SAM501
|
4.1
|
20.0
|
1.0
|
CG
|
A:SAM501
|
4.1
|
20.9
|
0.6
|
CE
|
A:SAM501
|
4.3
|
22.1
|
0.6
|
OXT
|
A:SAM501
|
4.3
|
17.5
|
1.0
|
OG1
|
A:THR114
|
4.3
|
14.9
|
1.0
|
SG
|
A:CYS62
|
4.4
|
12.6
|
1.0
|
O
|
A:GLY113
|
4.6
|
14.0
|
1.0
|
SG
|
A:CYS66
|
4.6
|
13.7
|
1.0
|
SG
|
A:CYS69
|
4.8
|
15.6
|
1.0
|
|
Iron binding site 4 out
of 4 in 1olt
Go back to
Iron Binding Sites List in 1olt
Iron binding site 4 out
of 4 in the Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Coproporphyrinogen III Oxidase (Hemn) From Escherichia Coli Is A Radical Sam Enzyme. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:28.0
occ:1.00
|
FE4
|
A:SF4500
|
0.0
|
28.0
|
1.0
|
S3
|
A:SF4500
|
2.1
|
15.2
|
1.0
|
S2
|
A:SF4500
|
2.2
|
13.4
|
1.0
|
S1
|
A:SF4500
|
2.3
|
15.0
|
1.0
|
FE3
|
A:SF4500
|
2.4
|
28.9
|
1.0
|
FE2
|
A:SF4500
|
2.4
|
25.7
|
1.0
|
FE1
|
A:SF4500
|
2.5
|
23.8
|
1.0
|
SG
|
A:CYS66
|
2.5
|
13.7
|
1.0
|
CB
|
A:CYS66
|
3.3
|
10.4
|
1.0
|
S4
|
A:SF4500
|
3.5
|
17.1
|
1.0
|
O
|
A:SAM501
|
3.7
|
18.8
|
1.0
|
NH1
|
A:ARG184
|
3.8
|
14.7
|
1.0
|
NH2
|
A:ARG149
|
4.3
|
14.6
|
1.0
|
O
|
A:HOH2066
|
4.4
|
17.8
|
1.0
|
N
|
A:CYS66
|
4.4
|
11.1
|
1.0
|
CB
|
A:CYS69
|
4.4
|
13.8
|
1.0
|
CA
|
A:CYS66
|
4.5
|
11.3
|
1.0
|
SG
|
A:CYS69
|
4.5
|
15.6
|
1.0
|
O
|
A:LYS64
|
4.6
|
13.2
|
1.0
|
N
|
A:SAM501
|
4.7
|
18.7
|
1.0
|
CZ
|
A:PHE68
|
4.7
|
14.6
|
1.0
|
SG
|
A:CYS62
|
4.7
|
12.6
|
1.0
|
C
|
A:SAM501
|
4.8
|
19.3
|
1.0
|
|
Reference:
G.Layer,
J.Moser,
D.W.Heinz,
D.Jahn,
W.-D.Schubert.
Crystal Structure of Coproporphyrinogen III Oxidase Reveals Cofactor Geometry of Radical Sam Enzymes Embo J. V. 22 6214 2003.
ISSN: ISSN 0261-4189
PubMed: 14633981
DOI: 10.1093/EMBOJ/CDG598
Page generated: Sat Aug 3 12:31:51 2024
|