Iron in PDB 7lkk: Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin
Protein crystallography data
The structure of Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin, PDB code: 7lkk
was solved by
R.K.Harijan,
M.Feng,
J.B.Bonanno,
S.C.Almo,
V.L.Schramm,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.59 /
1.89
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.905,
73.072,
157.44,
90,
98.3,
90
|
R / Rfree (%)
|
23.1 /
26.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin
(pdb code 7lkk). 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 of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin, PDB code: 7lkk:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7lkk
Go back to
Iron Binding Sites List in 7lkk
Iron binding site 1 out
of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin
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 Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:27.3
occ:1.00
|
O8
|
A:MCF506
|
2.0
|
30.8
|
1.0
|
NE2
|
A:HIS67
|
2.0
|
23.0
|
1.0
|
NE2
|
A:HIS65
|
2.1
|
18.4
|
1.0
|
NE2
|
A:HIS207
|
2.4
|
23.8
|
1.0
|
OD1
|
A:ASP314
|
2.7
|
23.1
|
1.0
|
CE1
|
A:HIS67
|
2.9
|
25.0
|
1.0
|
C8
|
A:MCF506
|
2.9
|
28.4
|
1.0
|
CD2
|
A:HIS67
|
3.0
|
26.4
|
1.0
|
CE1
|
A:HIS65
|
3.0
|
20.3
|
1.0
|
CD2
|
A:HIS65
|
3.1
|
19.5
|
1.0
|
CD2
|
A:HIS207
|
3.3
|
23.6
|
1.0
|
C9
|
A:MCF506
|
3.3
|
24.5
|
1.0
|
CE1
|
A:HIS207
|
3.4
|
18.5
|
1.0
|
CG
|
A:ASP314
|
3.6
|
23.7
|
1.0
|
C10
|
A:MCF506
|
3.8
|
25.4
|
1.0
|
OD2
|
A:ASP314
|
3.9
|
19.9
|
1.0
|
N1
|
A:MCF506
|
3.9
|
26.4
|
1.0
|
ND1
|
A:HIS67
|
4.0
|
23.8
|
1.0
|
N4
|
A:MCF506
|
4.1
|
24.7
|
1.0
|
CG
|
A:HIS67
|
4.1
|
22.9
|
1.0
|
ND1
|
A:HIS65
|
4.1
|
14.7
|
1.0
|
CG
|
A:HIS65
|
4.2
|
18.7
|
1.0
|
NE2
|
A:HIS261
|
4.2
|
20.3
|
1.0
|
C7
|
A:MCF506
|
4.3
|
25.6
|
1.0
|
CG
|
A:HIS207
|
4.4
|
19.3
|
1.0
|
C5
|
A:MCF506
|
4.4
|
26.5
|
1.0
|
ND1
|
A:HIS207
|
4.5
|
19.4
|
1.0
|
N6
|
A:MCF506
|
4.6
|
25.3
|
1.0
|
N3
|
A:MCF506
|
4.6
|
23.5
|
1.0
|
C2
|
A:MCF506
|
4.7
|
26.4
|
1.0
|
O
|
A:HOH603
|
4.9
|
28.7
|
1.0
|
CE1
|
A:HIS261
|
4.9
|
20.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 7lkk
Go back to
Iron Binding Sites List in 7lkk
Iron binding site 2 out
of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin
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 Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:26.9
occ:1.00
|
O8
|
B:MCF504
|
1.9
|
33.0
|
1.0
|
NE2
|
B:HIS67
|
2.0
|
24.7
|
1.0
|
NE2
|
B:HIS65
|
2.1
|
20.2
|
1.0
|
NE2
|
B:HIS207
|
2.3
|
24.1
|
1.0
|
OD1
|
B:ASP314
|
2.7
|
22.7
|
1.0
|
C8
|
B:MCF504
|
2.9
|
25.1
|
1.0
|
CE1
|
B:HIS67
|
3.0
|
22.5
|
1.0
|
CD2
|
B:HIS67
|
3.0
|
21.7
|
1.0
|
CE1
|
B:HIS65
|
3.0
|
17.1
|
1.0
|
CD2
|
B:HIS65
|
3.1
|
22.4
|
1.0
|
CD2
|
B:HIS207
|
3.1
|
26.1
|
1.0
|
CE1
|
B:HIS207
|
3.3
|
22.1
|
1.0
|
C9
|
B:MCF504
|
3.3
|
23.4
|
1.0
|
CG
|
B:ASP314
|
3.6
|
23.3
|
1.0
|
OD2
|
B:ASP314
|
3.9
|
29.2
|
1.0
|
C10
|
B:MCF504
|
3.9
|
23.6
|
1.0
|
N1
|
B:MCF504
|
4.0
|
24.2
|
1.0
|
ND1
|
B:HIS67
|
4.1
|
20.4
|
1.0
|
CG
|
B:HIS67
|
4.1
|
25.0
|
1.0
|
N4
|
B:MCF504
|
4.1
|
23.7
|
1.0
|
ND1
|
B:HIS65
|
4.1
|
14.8
|
1.0
|
NE2
|
B:HIS261
|
4.2
|
18.9
|
1.0
|
CG
|
B:HIS65
|
4.2
|
14.2
|
1.0
|
C7
|
B:MCF504
|
4.3
|
26.4
|
1.0
|
CG
|
B:HIS207
|
4.3
|
23.2
|
1.0
|
ND1
|
B:HIS207
|
4.4
|
23.5
|
1.0
|
C5
|
B:MCF504
|
4.4
|
23.9
|
1.0
|
N6
|
B:MCF504
|
4.5
|
26.1
|
1.0
|
N3
|
B:MCF504
|
4.7
|
23.5
|
1.0
|
C2
|
B:MCF504
|
4.7
|
26.0
|
1.0
|
CE1
|
B:HIS261
|
4.9
|
20.8
|
1.0
|
O
|
B:HOH624
|
4.9
|
22.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 7lkk
Go back to
Iron Binding Sites List in 7lkk
Iron binding site 3 out
of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin
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 Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:28.9
occ:1.00
|
O8
|
C:MCF504
|
2.0
|
37.5
|
1.0
|
NE2
|
C:HIS67
|
2.1
|
23.7
|
1.0
|
NE2
|
C:HIS65
|
2.1
|
23.9
|
1.0
|
NE2
|
C:HIS207
|
2.4
|
24.9
|
1.0
|
OD1
|
C:ASP314
|
2.6
|
25.3
|
1.0
|
C8
|
C:MCF504
|
2.9
|
29.5
|
1.0
|
CE1
|
C:HIS67
|
3.0
|
25.4
|
1.0
|
CD2
|
C:HIS65
|
3.0
|
22.9
|
1.0
|
CD2
|
C:HIS67
|
3.1
|
26.5
|
1.0
|
CE1
|
C:HIS65
|
3.1
|
21.7
|
1.0
|
CD2
|
C:HIS207
|
3.2
|
25.5
|
1.0
|
C9
|
C:MCF504
|
3.3
|
27.2
|
1.0
|
CE1
|
C:HIS207
|
3.5
|
22.5
|
1.0
|
CG
|
C:ASP314
|
3.6
|
26.4
|
1.0
|
OD2
|
C:ASP314
|
3.8
|
24.7
|
1.0
|
C10
|
C:MCF504
|
3.9
|
26.8
|
1.0
|
N1
|
C:MCF504
|
3.9
|
27.6
|
1.0
|
NE2
|
C:HIS261
|
4.1
|
25.1
|
1.0
|
ND1
|
C:HIS67
|
4.1
|
25.2
|
1.0
|
CG
|
C:HIS67
|
4.2
|
27.1
|
1.0
|
N4
|
C:MCF504
|
4.2
|
25.1
|
1.0
|
ND1
|
C:HIS65
|
4.2
|
23.1
|
1.0
|
CG
|
C:HIS65
|
4.2
|
22.5
|
1.0
|
C7
|
C:MCF504
|
4.3
|
28.2
|
1.0
|
CG
|
C:HIS207
|
4.4
|
22.6
|
1.0
|
ND1
|
C:HIS207
|
4.5
|
23.3
|
1.0
|
C5
|
C:MCF504
|
4.5
|
26.3
|
1.0
|
N6
|
C:MCF504
|
4.6
|
28.5
|
1.0
|
N3
|
C:MCF504
|
4.7
|
26.3
|
1.0
|
C2
|
C:MCF504
|
4.7
|
24.2
|
1.0
|
CE1
|
C:HIS261
|
4.8
|
24.6
|
1.0
|
CG1
|
C:VAL260
|
4.9
|
20.2
|
1.0
|
O
|
C:HOH616
|
4.9
|
27.0
|
1.0
|
CB
|
C:ASP314
|
4.9
|
19.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 7lkk
Go back to
Iron Binding Sites List in 7lkk
Iron binding site 4 out
of 4 in the Crystal Structure of Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin
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 Helicobacter Pylori Aminofutalosine Deaminase (Aflda) in Complex with Methylthio-Coformycin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:32.6
occ:1.00
|
NE2
|
D:HIS67
|
2.0
|
27.5
|
1.0
|
O8
|
D:MCF507
|
2.0
|
37.2
|
1.0
|
NE2
|
D:HIS65
|
2.0
|
24.3
|
1.0
|
NE2
|
D:HIS207
|
2.4
|
27.7
|
1.0
|
OD1
|
D:ASP314
|
2.7
|
30.2
|
1.0
|
CE1
|
D:HIS65
|
3.0
|
23.6
|
1.0
|
CD2
|
D:HIS67
|
3.0
|
29.1
|
1.0
|
C8
|
D:MCF507
|
3.0
|
31.3
|
1.0
|
CE1
|
D:HIS67
|
3.0
|
27.0
|
1.0
|
CD2
|
D:HIS65
|
3.1
|
22.9
|
1.0
|
CD2
|
D:HIS207
|
3.3
|
29.1
|
1.0
|
C9
|
D:MCF507
|
3.3
|
28.1
|
1.0
|
CE1
|
D:HIS207
|
3.5
|
25.1
|
1.0
|
CG
|
D:ASP314
|
3.6
|
28.0
|
1.0
|
N1
|
D:MCF507
|
3.9
|
29.4
|
1.0
|
C10
|
D:MCF507
|
3.9
|
30.7
|
1.0
|
OD2
|
D:ASP314
|
3.9
|
27.1
|
1.0
|
ND1
|
D:HIS65
|
4.1
|
19.6
|
1.0
|
ND1
|
D:HIS67
|
4.1
|
25.0
|
1.0
|
CG
|
D:HIS67
|
4.1
|
28.9
|
1.0
|
CG
|
D:HIS65
|
4.2
|
23.5
|
1.0
|
N4
|
D:MCF507
|
4.2
|
27.2
|
1.0
|
NE2
|
D:HIS261
|
4.2
|
24.1
|
1.0
|
C7
|
D:MCF507
|
4.4
|
27.1
|
1.0
|
CG
|
D:HIS207
|
4.5
|
22.2
|
1.0
|
ND1
|
D:HIS207
|
4.5
|
24.4
|
1.0
|
C5
|
D:MCF507
|
4.6
|
26.4
|
1.0
|
N3
|
D:MCF507
|
4.6
|
31.6
|
1.0
|
C2
|
D:MCF507
|
4.6
|
30.3
|
1.0
|
N6
|
D:MCF507
|
4.7
|
26.9
|
1.0
|
CE1
|
D:HIS261
|
4.9
|
25.3
|
1.0
|
CG1
|
D:VAL260
|
4.9
|
21.5
|
1.0
|
CB
|
D:ASP314
|
5.0
|
25.8
|
1.0
|
|
Reference:
M.Feng,
R.K.Harijan,
L.D.Harris,
P.C.Tyler,
R.F.G.Frohlich,
M.Brown,
V.L.Schramm.
Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter Pylori Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 34077175
DOI: 10.1021/ACS.BIOCHEM.1C00215
Page generated: Thu Aug 8 07:04:59 2024
|