Iron in PDB 4zmc: Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
Enzymatic activity of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
All present enzymatic activity of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min):
1.16.3.1;
Protein crystallography data
The structure of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min), PDB code: 4zmc
was solved by
S.Pfaffen,
M.E.P.Murphy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.53 /
1.90
|
Space group
|
P 2 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
174.980,
174.980,
174.980,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.9 /
20.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
(pdb code 4zmc). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the
Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min), PDB code: 4zmc:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
Iron binding site 1 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 1 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:36.5
occ:0.30
|
OE1
|
A:GLU15
|
2.3
|
34.8
|
1.0
|
OE1
|
A:GLU48
|
2.3
|
42.7
|
1.0
|
ND1
|
A:HIS51
|
3.0
|
38.5
|
1.0
|
CD
|
A:GLU15
|
3.1
|
34.1
|
1.0
|
ND2
|
A:ASN97
|
3.2
|
27.9
|
0.5
|
OE2
|
A:GLU15
|
3.3
|
40.1
|
1.0
|
CD
|
A:GLU48
|
3.4
|
36.2
|
1.0
|
O
|
A:HOH325
|
3.4
|
36.6
|
1.0
|
OE2
|
A:GLU48
|
3.7
|
47.4
|
1.0
|
OE1
|
A:GLN127
|
3.8
|
30.9
|
1.0
|
O
|
A:HOH342
|
3.8
|
47.3
|
1.0
|
CG
|
A:HIS51
|
3.9
|
33.0
|
1.0
|
CE1
|
A:HIS51
|
3.9
|
38.9
|
1.0
|
ND2
|
A:ASN97
|
4.0
|
28.2
|
0.5
|
CB
|
A:HIS51
|
4.1
|
24.2
|
1.0
|
CG
|
A:ASN97
|
4.3
|
30.8
|
0.5
|
CG
|
A:GLU15
|
4.6
|
28.2
|
1.0
|
CG
|
A:ASN97
|
4.6
|
30.9
|
0.5
|
CD
|
A:GLN127
|
4.7
|
28.3
|
1.0
|
CG
|
A:GLU48
|
4.7
|
29.9
|
1.0
|
CB
|
A:ASN97
|
4.9
|
29.9
|
0.5
|
CA
|
A:GLU48
|
5.0
|
22.9
|
1.0
|
CB
|
A:ASN97
|
5.0
|
32.3
|
0.5
|
CB
|
A:GLU15
|
5.0
|
25.6
|
1.0
|
|
Iron binding site 2 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 2 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:38.3
occ:0.30
|
OE1
|
D:GLU15
|
2.2
|
28.6
|
1.0
|
OE1
|
D:GLU48
|
2.3
|
44.6
|
1.0
|
ND1
|
D:HIS51
|
3.0
|
35.1
|
1.0
|
ND2
|
D:ASN97
|
3.0
|
26.2
|
0.3
|
CD
|
D:GLU15
|
3.1
|
27.1
|
1.0
|
O
|
D:HOH316
|
3.2
|
48.4
|
1.0
|
OE2
|
D:GLU15
|
3.3
|
34.1
|
1.0
|
CD
|
D:GLU48
|
3.4
|
32.5
|
1.0
|
O
|
D:HOH363
|
3.6
|
36.3
|
1.0
|
OE2
|
D:GLU48
|
3.8
|
47.2
|
1.0
|
CG
|
D:HIS51
|
3.9
|
30.4
|
1.0
|
CE1
|
D:HIS51
|
3.9
|
37.3
|
1.0
|
CB
|
D:HIS51
|
4.0
|
24.9
|
1.0
|
OE1
|
D:GLN127
|
4.0
|
26.0
|
1.0
|
ND2
|
D:ASN97
|
4.1
|
30.0
|
0.7
|
CG
|
D:ASN97
|
4.2
|
26.2
|
0.3
|
CG
|
D:GLU15
|
4.5
|
22.7
|
1.0
|
CG
|
D:ASN97
|
4.5
|
32.3
|
0.7
|
CG
|
D:GLU48
|
4.7
|
28.1
|
1.0
|
CA
|
D:GLU48
|
4.8
|
22.3
|
1.0
|
CB
|
D:GLU15
|
4.9
|
19.8
|
1.0
|
CB
|
D:ASN97
|
4.9
|
30.2
|
0.7
|
CD
|
D:GLN127
|
4.9
|
28.5
|
1.0
|
CB
|
D:GLU48
|
4.9
|
23.0
|
1.0
|
CB
|
D:ASN97
|
4.9
|
26.8
|
0.3
|
OD1
|
D:ASN97
|
5.0
|
26.9
|
0.3
|
|
Iron binding site 3 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 3 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
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 the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:40.3
occ:0.35
|
OE1
|
C:GLU15
|
2.2
|
38.2
|
1.0
|
OE1
|
C:GLU48
|
2.3
|
44.7
|
1.0
|
ND1
|
C:HIS51
|
2.9
|
46.5
|
1.0
|
CD
|
C:GLU15
|
3.1
|
33.2
|
1.0
|
ND2
|
C:ASN97
|
3.2
|
30.2
|
0.4
|
OE2
|
C:GLU15
|
3.3
|
43.5
|
1.0
|
CD
|
C:GLU48
|
3.5
|
35.3
|
1.0
|
O
|
C:HOH360
|
3.7
|
40.8
|
1.0
|
CG
|
C:HIS51
|
3.8
|
35.5
|
1.0
|
CB
|
C:HIS51
|
3.9
|
28.5
|
1.0
|
OE2
|
C:GLU48
|
3.9
|
41.3
|
1.0
|
CE1
|
C:HIS51
|
3.9
|
46.1
|
1.0
|
OE1
|
C:GLN127
|
4.0
|
28.7
|
1.0
|
CG
|
C:ASN97
|
4.3
|
29.1
|
0.4
|
ND2
|
C:ASN97
|
4.3
|
28.4
|
0.6
|
CG
|
C:GLU15
|
4.5
|
27.5
|
1.0
|
CG
|
C:GLU48
|
4.8
|
27.1
|
1.0
|
CG
|
C:ASN97
|
4.8
|
32.5
|
0.6
|
CD
|
C:GLN127
|
4.8
|
27.3
|
1.0
|
CA
|
C:GLU48
|
4.8
|
23.3
|
1.0
|
OD1
|
C:ASN97
|
4.9
|
31.2
|
0.4
|
CB
|
C:GLU48
|
4.9
|
25.3
|
1.0
|
CD2
|
C:HIS51
|
4.9
|
42.9
|
1.0
|
CB
|
C:GLU15
|
5.0
|
23.5
|
1.0
|
NE2
|
C:HIS51
|
5.0
|
48.0
|
1.0
|
|
Iron binding site 4 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 4 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:43.6
occ:0.35
|
OE1
|
E:GLU15
|
2.1
|
39.7
|
1.0
|
OE1
|
E:GLU48
|
2.4
|
43.1
|
1.0
|
CD
|
E:GLU15
|
3.0
|
37.7
|
1.0
|
ND1
|
E:HIS51
|
3.1
|
38.4
|
1.0
|
O
|
E:HOH308
|
3.1
|
44.7
|
1.0
|
OE2
|
E:GLU15
|
3.2
|
43.8
|
1.0
|
CD
|
E:GLU48
|
3.2
|
38.4
|
1.0
|
OE2
|
E:GLU48
|
3.4
|
53.3
|
1.0
|
O
|
E:HOH337
|
3.7
|
32.9
|
1.0
|
CG
|
E:HIS51
|
3.9
|
35.6
|
1.0
|
CB
|
E:HIS51
|
4.0
|
26.5
|
1.0
|
OE1
|
E:GLN127
|
4.0
|
33.1
|
1.0
|
CE1
|
E:HIS51
|
4.0
|
39.7
|
1.0
|
ND2
|
E:ASN97
|
4.1
|
38.3
|
1.0
|
CG
|
E:GLU15
|
4.4
|
29.3
|
1.0
|
CG
|
E:ASN97
|
4.5
|
35.8
|
1.0
|
CG
|
E:GLU48
|
4.6
|
32.0
|
1.0
|
CB
|
E:ASN97
|
4.8
|
29.2
|
1.0
|
CA
|
E:GLU48
|
4.8
|
25.3
|
1.0
|
CD
|
E:GLN127
|
4.9
|
28.2
|
1.0
|
O
|
E:HOH301
|
4.9
|
35.3
|
1.0
|
CB
|
E:GLU48
|
4.9
|
28.9
|
1.0
|
CB
|
E:GLU15
|
4.9
|
23.9
|
1.0
|
|
Iron binding site 5 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 5 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:36.1
occ:0.25
|
O
|
F:HOH1133
|
2.2
|
50.0
|
1.0
|
OE1
|
F:GLU15
|
2.3
|
38.7
|
1.0
|
OE1
|
F:GLU48
|
2.5
|
50.3
|
1.0
|
ND1
|
F:HIS51
|
2.8
|
45.1
|
1.0
|
OD1
|
F:ASN97
|
2.9
|
39.2
|
0.4
|
CD
|
F:GLU15
|
3.1
|
37.0
|
1.0
|
OE2
|
F:GLU15
|
3.1
|
41.2
|
1.0
|
CD
|
F:GLU48
|
3.5
|
38.1
|
1.0
|
CG
|
F:ASN97
|
3.6
|
31.8
|
0.4
|
CE1
|
F:HIS51
|
3.6
|
44.1
|
1.0
|
O
|
F:HOH1145
|
3.7
|
36.7
|
1.0
|
O
|
F:HOH1154
|
3.7
|
37.4
|
1.0
|
CG
|
F:HIS51
|
3.8
|
38.5
|
1.0
|
OE2
|
F:GLU48
|
3.8
|
53.1
|
1.0
|
ND2
|
F:ASN97
|
3.9
|
31.5
|
0.4
|
OE1
|
F:GLN127
|
3.9
|
29.9
|
1.0
|
CB
|
F:HIS51
|
4.1
|
31.5
|
1.0
|
ND2
|
F:ASN97
|
4.2
|
30.7
|
0.6
|
CG
|
F:GLU15
|
4.5
|
27.0
|
1.0
|
CG
|
F:ASN97
|
4.6
|
30.3
|
0.6
|
CB
|
F:ASN97
|
4.7
|
32.6
|
0.4
|
CD
|
F:GLN127
|
4.7
|
31.4
|
1.0
|
NE2
|
F:HIS51
|
4.8
|
46.4
|
1.0
|
CB
|
F:ASN97
|
4.8
|
30.6
|
0.6
|
CG
|
F:GLU48
|
4.8
|
33.8
|
1.0
|
CD2
|
F:HIS51
|
4.9
|
40.7
|
1.0
|
CB
|
F:GLU15
|
4.9
|
25.9
|
1.0
|
CA
|
F:GLU48
|
5.0
|
25.9
|
1.0
|
|
Iron binding site 6 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 6 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:38.8
occ:0.35
|
OE1
|
G:GLU15
|
2.3
|
31.5
|
1.0
|
OE1
|
G:GLU48
|
2.3
|
37.6
|
1.0
|
ND2
|
G:ASN97
|
2.7
|
25.6
|
0.3
|
ND1
|
G:HIS51
|
3.0
|
37.8
|
1.0
|
CD
|
G:GLU15
|
3.2
|
32.1
|
1.0
|
CD
|
G:GLU48
|
3.3
|
30.4
|
1.0
|
OE2
|
G:GLU15
|
3.4
|
33.4
|
1.0
|
O
|
G:HOH350
|
3.6
|
39.1
|
1.0
|
OE2
|
G:GLU48
|
3.6
|
41.9
|
1.0
|
CG
|
G:ASN97
|
3.8
|
25.4
|
0.3
|
CE1
|
G:HIS51
|
3.8
|
36.0
|
1.0
|
OE1
|
G:GLN127
|
3.9
|
25.7
|
1.0
|
CG
|
G:HIS51
|
3.9
|
31.9
|
1.0
|
ND2
|
G:ASN97
|
4.0
|
23.2
|
0.7
|
CB
|
G:HIS51
|
4.2
|
25.7
|
1.0
|
CG
|
G:ASN97
|
4.3
|
26.3
|
0.7
|
OD1
|
G:ASN97
|
4.6
|
28.5
|
0.3
|
CG
|
G:GLU15
|
4.6
|
23.4
|
1.0
|
CB
|
G:ASN97
|
4.6
|
26.1
|
0.7
|
CB
|
G:ASN97
|
4.7
|
25.7
|
0.3
|
CG
|
G:GLU48
|
4.7
|
28.2
|
1.0
|
CD
|
G:GLN127
|
4.7
|
24.9
|
1.0
|
OD1
|
G:ASN97
|
4.9
|
25.8
|
0.7
|
CA
|
G:GLU48
|
4.9
|
22.1
|
1.0
|
CB
|
G:GLU48
|
5.0
|
25.1
|
1.0
|
NE2
|
G:HIS51
|
5.0
|
42.8
|
1.0
|
|
Iron binding site 7 out
of 7 in 4zmc
Go back to
Iron Binding Sites List in 4zmc
Iron binding site 7 out
of 7 in the Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of the Pmftn Variant E130A Soaked in Iron (5 Min) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe201
b:36.9
occ:0.35
|
OE1
|
H:GLU48
|
2.2
|
27.3
|
0.5
|
OE1
|
H:GLU15
|
2.2
|
35.4
|
1.0
|
ND1
|
H:HIS51
|
2.9
|
37.5
|
1.0
|
OE1
|
H:GLU48
|
3.0
|
28.7
|
0.5
|
ND2
|
H:ASN97
|
3.1
|
31.1
|
0.5
|
CD
|
H:GLU15
|
3.1
|
29.4
|
1.0
|
OE2
|
H:GLU15
|
3.3
|
37.1
|
1.0
|
CD
|
H:GLU48
|
3.3
|
26.8
|
0.5
|
OE2
|
H:GLU48
|
3.4
|
30.7
|
0.5
|
O
|
H:HOH353
|
3.5
|
34.8
|
1.0
|
CD
|
H:GLU48
|
3.5
|
30.3
|
0.5
|
OE2
|
H:GLU48
|
3.7
|
25.3
|
0.5
|
CE1
|
H:HIS51
|
3.8
|
34.9
|
1.0
|
CG
|
H:HIS51
|
3.9
|
30.1
|
1.0
|
ND2
|
H:ASN97
|
3.9
|
29.8
|
0.5
|
OE1
|
H:GLN127
|
3.9
|
27.1
|
1.0
|
CB
|
H:HIS51
|
4.1
|
27.7
|
1.0
|
CG
|
H:ASN97
|
4.3
|
31.2
|
0.5
|
CG
|
H:GLU15
|
4.5
|
25.6
|
1.0
|
CG
|
H:ASN97
|
4.6
|
30.0
|
0.5
|
CG
|
H:GLU48
|
4.6
|
26.0
|
0.5
|
CD
|
H:GLN127
|
4.8
|
27.1
|
1.0
|
CB
|
H:GLU48
|
4.8
|
24.6
|
0.5
|
CA
|
H:GLU48
|
4.8
|
23.0
|
0.5
|
CG
|
H:GLU48
|
4.9
|
28.2
|
0.5
|
CA
|
H:GLU48
|
4.9
|
24.3
|
0.5
|
NE2
|
H:HIS51
|
4.9
|
39.2
|
1.0
|
CB
|
H:ASN97
|
5.0
|
26.6
|
0.5
|
CD2
|
H:HIS51
|
5.0
|
32.9
|
1.0
|
|
Reference:
S.Pfaffen,
J.M.Bradley,
R.Abdulqadir,
M.R.Firme,
G.R.Moore,
N.E.Le Brun,
M.E.Murphy.
A Diatom Ferritin Optimized For Iron Oxidation But Not Iron Storage. J.Biol.Chem. V. 290 28416 2015.
ISSN: ESSN 1083-351X
PubMed: 26396187
DOI: 10.1074/JBC.M115.669713
Page generated: Mon Aug 5 18:21:55 2024
|