Iron in PDB 7vm1: Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin
Protein crystallography data
The structure of Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin, PDB code: 7vm1
was solved by
Y.Shisaka,
G.Ueda,
E.Sakakibara,
H.Sugimoto,
O.Shoji,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.37 /
2.00
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
31.318,
43.981,
130.116,
99.17,
93.9,
92.87
|
R / Rfree (%)
|
22.9 /
26
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin
(pdb code 7vm1). 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 Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin, PDB code: 7vm1:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7vm1
Go back to
Iron Binding Sites List in 7vm1
Iron binding site 1 out
of 4 in the Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin
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 Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:13.8
occ:1.00
|
FE
|
A:7OH201
|
0.0
|
13.8
|
1.0
|
NAS
|
A:7OH201
|
2.0
|
13.7
|
1.0
|
NAX
|
A:7OH201
|
2.0
|
13.5
|
1.0
|
NAN
|
A:7OH201
|
2.0
|
13.8
|
1.0
|
NAI
|
A:7OH201
|
2.1
|
13.4
|
1.0
|
OH
|
A:TYR75
|
2.1
|
14.9
|
1.0
|
NE2
|
A:HIS32
|
2.2
|
14.9
|
1.0
|
CAR
|
A:7OH201
|
3.0
|
13.3
|
1.0
|
CAO
|
A:7OH201
|
3.0
|
14.9
|
1.0
|
CZ
|
A:TYR75
|
3.0
|
14.1
|
1.0
|
CAT
|
A:7OH201
|
3.0
|
14.3
|
1.0
|
CAW
|
A:7OH201
|
3.0
|
13.5
|
1.0
|
CAM
|
A:7OH201
|
3.0
|
14.8
|
1.0
|
CAJ
|
A:7OH201
|
3.0
|
14.0
|
1.0
|
CAE
|
A:7OH201
|
3.1
|
14.3
|
1.0
|
CAH
|
A:7OH201
|
3.1
|
14.1
|
1.0
|
CD2
|
A:HIS32
|
3.1
|
15.1
|
1.0
|
CE1
|
A:HIS32
|
3.3
|
15.8
|
1.0
|
CAC
|
A:7OH201
|
3.4
|
13.9
|
1.0
|
CAB
|
A:7OH201
|
3.4
|
14.9
|
1.0
|
CAD
|
A:7OH201
|
3.4
|
14.4
|
1.0
|
CAA
|
A:7OH201
|
3.4
|
13.9
|
1.0
|
CE1
|
A:TYR75
|
3.7
|
13.3
|
1.0
|
CE2
|
A:TYR75
|
3.8
|
13.0
|
1.0
|
CAQ
|
A:7OH201
|
4.0
|
14.3
|
1.0
|
CAP
|
A:7OH201
|
4.0
|
14.8
|
1.0
|
ND1
|
A:HIS83
|
4.1
|
14.0
|
1.0
|
CAV
|
A:7OH201
|
4.1
|
14.2
|
1.0
|
CAU
|
A:7OH201
|
4.1
|
14.2
|
1.0
|
CAL
|
A:7OH201
|
4.1
|
14.9
|
1.0
|
CAK
|
A:7OH201
|
4.2
|
14.8
|
1.0
|
CAF
|
A:7OH201
|
4.2
|
13.5
|
1.0
|
CAG
|
A:7OH201
|
4.2
|
13.8
|
1.0
|
CG
|
A:HIS32
|
4.3
|
15.3
|
1.0
|
ND1
|
A:HIS32
|
4.3
|
15.3
|
1.0
|
CBK
|
A:7OH201
|
4.8
|
13.0
|
1.0
|
CB
|
A:HIS83
|
4.8
|
14.4
|
1.0
|
CBE
|
A:7OH201
|
4.8
|
14.8
|
1.0
|
CBQ
|
A:7OH201
|
4.8
|
15.6
|
1.0
|
CD1
|
A:TYR75
|
4.8
|
14.1
|
1.0
|
CG
|
A:HIS83
|
4.8
|
14.3
|
1.0
|
CAY
|
A:7OH201
|
4.9
|
14.4
|
1.0
|
CD2
|
A:TYR75
|
4.9
|
13.6
|
1.0
|
CE1
|
A:HIS83
|
5.0
|
15.0
|
1.0
|
|
Iron binding site 2 out
of 4 in 7vm1
Go back to
Iron Binding Sites List in 7vm1
Iron binding site 2 out
of 4 in the Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin
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 Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:12.9
occ:1.00
|
FE
|
B:7OH201
|
0.0
|
12.9
|
1.0
|
NAI
|
B:7OH201
|
2.0
|
13.0
|
1.0
|
NAX
|
B:7OH201
|
2.0
|
12.4
|
1.0
|
NAS
|
B:7OH201
|
2.0
|
14.1
|
1.0
|
NAN
|
B:7OH201
|
2.1
|
13.6
|
1.0
|
NE2
|
B:HIS32
|
2.1
|
15.3
|
1.0
|
OH
|
B:TYR75
|
2.2
|
14.6
|
1.0
|
CE1
|
B:HIS32
|
3.0
|
16.1
|
1.0
|
CAH
|
B:7OH201
|
3.0
|
13.9
|
1.0
|
CAE
|
B:7OH201
|
3.0
|
14.7
|
1.0
|
CAW
|
B:7OH201
|
3.0
|
13.0
|
1.0
|
CAJ
|
B:7OH201
|
3.0
|
13.5
|
1.0
|
CZ
|
B:TYR75
|
3.0
|
15.4
|
1.0
|
CAR
|
B:7OH201
|
3.0
|
14.3
|
1.0
|
CAT
|
B:7OH201
|
3.0
|
13.1
|
1.0
|
CAO
|
B:7OH201
|
3.0
|
13.7
|
1.0
|
CAM
|
B:7OH201
|
3.1
|
13.4
|
1.0
|
CD2
|
B:HIS32
|
3.2
|
15.9
|
1.0
|
CAA
|
B:7OH201
|
3.3
|
14.0
|
1.0
|
CAD
|
B:7OH201
|
3.4
|
13.9
|
1.0
|
CAC
|
B:7OH201
|
3.4
|
13.7
|
1.0
|
CAB
|
B:7OH201
|
3.4
|
13.5
|
1.0
|
CE2
|
B:TYR75
|
3.7
|
14.6
|
1.0
|
CE1
|
B:TYR75
|
3.8
|
14.1
|
1.0
|
CAG
|
B:7OH201
|
4.1
|
15.1
|
1.0
|
ND1
|
B:HIS32
|
4.1
|
15.5
|
1.0
|
CAF
|
B:7OH201
|
4.1
|
14.8
|
1.0
|
CAP
|
B:7OH201
|
4.1
|
14.3
|
1.0
|
CAU
|
B:7OH201
|
4.1
|
13.9
|
1.0
|
CAQ
|
B:7OH201
|
4.1
|
14.6
|
1.0
|
CAV
|
B:7OH201
|
4.1
|
13.5
|
1.0
|
CAK
|
B:7OH201
|
4.1
|
14.2
|
1.0
|
CAL
|
B:7OH201
|
4.2
|
13.0
|
1.0
|
ND1
|
B:HIS83
|
4.2
|
15.1
|
1.0
|
CG
|
B:HIS32
|
4.3
|
15.9
|
1.0
|
CAY
|
B:7OH201
|
4.7
|
14.7
|
1.0
|
CBQ
|
B:7OH201
|
4.8
|
14.5
|
1.0
|
CBK
|
B:7OH201
|
4.8
|
13.5
|
1.0
|
CD2
|
B:TYR75
|
4.9
|
14.1
|
1.0
|
CBE
|
B:7OH201
|
4.9
|
13.7
|
1.0
|
CB
|
B:HIS83
|
4.9
|
14.2
|
1.0
|
CG
|
B:HIS83
|
4.9
|
14.4
|
1.0
|
CD1
|
B:TYR75
|
4.9
|
13.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 7vm1
Go back to
Iron Binding Sites List in 7vm1
Iron binding site 3 out
of 4 in the Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin
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 Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:12.1
occ:1.00
|
FE
|
C:7OH201
|
0.0
|
12.1
|
1.0
|
NAS
|
C:7OH201
|
2.0
|
11.5
|
1.0
|
NAN
|
C:7OH201
|
2.0
|
12.0
|
1.0
|
NAX
|
C:7OH201
|
2.0
|
11.3
|
1.0
|
NAI
|
C:7OH201
|
2.0
|
12.7
|
1.0
|
OH
|
C:TYR75
|
2.1
|
10.9
|
1.0
|
NE2
|
C:HIS32
|
2.2
|
12.5
|
1.0
|
CZ
|
C:TYR75
|
3.0
|
10.7
|
1.0
|
CAR
|
C:7OH201
|
3.0
|
12.0
|
1.0
|
CAM
|
C:7OH201
|
3.0
|
12.4
|
1.0
|
CAJ
|
C:7OH201
|
3.0
|
13.4
|
1.0
|
CAO
|
C:7OH201
|
3.0
|
12.4
|
1.0
|
CAW
|
C:7OH201
|
3.0
|
11.9
|
1.0
|
CAE
|
C:7OH201
|
3.0
|
12.5
|
1.0
|
CAH
|
C:7OH201
|
3.0
|
13.8
|
1.0
|
CAT
|
C:7OH201
|
3.0
|
11.4
|
1.0
|
CE1
|
C:HIS32
|
3.2
|
12.6
|
1.0
|
CD2
|
C:HIS32
|
3.2
|
12.3
|
1.0
|
CAD
|
C:7OH201
|
3.4
|
12.5
|
1.0
|
CAA
|
C:7OH201
|
3.4
|
13.5
|
1.0
|
CAC
|
C:7OH201
|
3.4
|
11.4
|
1.0
|
CAB
|
C:7OH201
|
3.4
|
12.5
|
1.0
|
CE1
|
C:TYR75
|
3.7
|
10.5
|
1.0
|
CE2
|
C:TYR75
|
3.8
|
10.1
|
1.0
|
ND1
|
C:HIS83
|
4.1
|
12.6
|
1.0
|
CAL
|
C:7OH201
|
4.1
|
13.0
|
1.0
|
CAQ
|
C:7OH201
|
4.1
|
12.1
|
1.0
|
CAK
|
C:7OH201
|
4.1
|
12.8
|
1.0
|
CAP
|
C:7OH201
|
4.1
|
13.1
|
1.0
|
CAV
|
C:7OH201
|
4.1
|
12.0
|
1.0
|
CAU
|
C:7OH201
|
4.1
|
11.3
|
1.0
|
CAF
|
C:7OH201
|
4.1
|
13.5
|
1.0
|
CAG
|
C:7OH201
|
4.1
|
13.2
|
1.0
|
ND1
|
C:HIS32
|
4.3
|
14.0
|
1.0
|
CG
|
C:HIS32
|
4.3
|
12.6
|
1.0
|
CB
|
C:HIS83
|
4.7
|
12.8
|
1.0
|
CG
|
C:HIS83
|
4.7
|
12.7
|
1.0
|
CAY
|
C:7OH201
|
4.8
|
15.0
|
1.0
|
CD1
|
C:TYR75
|
4.8
|
10.8
|
1.0
|
CBQ
|
C:7OH201
|
4.8
|
12.6
|
1.0
|
CBK
|
C:7OH201
|
4.8
|
11.3
|
1.0
|
CBE
|
C:7OH201
|
4.8
|
13.0
|
1.0
|
CD2
|
C:TYR75
|
4.9
|
11.0
|
1.0
|
CE1
|
C:HIS83
|
5.0
|
15.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 7vm1
Go back to
Iron Binding Sites List in 7vm1
Iron binding site 4 out
of 4 in the Crystal Structure of Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin
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 Hasap Capturing Iron Tetra(4-Pyridyl)Porphyrin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:12.8
occ:1.00
|
FE
|
D:7OH201
|
0.0
|
12.8
|
1.0
|
NAX
|
D:7OH201
|
2.0
|
13.1
|
1.0
|
NAN
|
D:7OH201
|
2.0
|
12.2
|
1.0
|
NAS
|
D:7OH201
|
2.1
|
12.4
|
1.0
|
NAI
|
D:7OH201
|
2.1
|
14.0
|
1.0
|
OH
|
D:TYR75
|
2.2
|
12.1
|
1.0
|
NE2
|
D:HIS32
|
2.2
|
14.2
|
1.0
|
CAW
|
D:7OH201
|
3.0
|
13.3
|
1.0
|
CAT
|
D:7OH201
|
3.0
|
12.7
|
1.0
|
CAM
|
D:7OH201
|
3.0
|
12.8
|
1.0
|
CAJ
|
D:7OH201
|
3.0
|
13.4
|
1.0
|
CZ
|
D:TYR75
|
3.0
|
12.4
|
1.0
|
CAO
|
D:7OH201
|
3.1
|
13.1
|
1.0
|
CAR
|
D:7OH201
|
3.1
|
12.5
|
1.0
|
CAE
|
D:7OH201
|
3.1
|
13.1
|
1.0
|
CAH
|
D:7OH201
|
3.1
|
13.9
|
1.0
|
CD2
|
D:HIS32
|
3.2
|
14.3
|
1.0
|
CE1
|
D:HIS32
|
3.2
|
13.5
|
1.0
|
CAC
|
D:7OH201
|
3.4
|
12.6
|
1.0
|
CAD
|
D:7OH201
|
3.4
|
13.3
|
1.0
|
CAB
|
D:7OH201
|
3.4
|
13.2
|
1.0
|
CAA
|
D:7OH201
|
3.4
|
13.8
|
1.0
|
CE1
|
D:TYR75
|
3.7
|
12.4
|
1.0
|
CE2
|
D:TYR75
|
3.8
|
12.7
|
1.0
|
CAU
|
D:7OH201
|
4.1
|
13.2
|
1.0
|
CAV
|
D:7OH201
|
4.1
|
13.5
|
1.0
|
ND1
|
D:HIS83
|
4.1
|
14.9
|
1.0
|
CAL
|
D:7OH201
|
4.1
|
12.5
|
1.0
|
CAK
|
D:7OH201
|
4.1
|
12.9
|
1.0
|
CAQ
|
D:7OH201
|
4.2
|
13.1
|
1.0
|
CAP
|
D:7OH201
|
4.2
|
13.6
|
1.0
|
CAF
|
D:7OH201
|
4.2
|
13.4
|
1.0
|
CAG
|
D:7OH201
|
4.2
|
13.3
|
1.0
|
ND1
|
D:HIS32
|
4.3
|
14.7
|
1.0
|
CG
|
D:HIS32
|
4.3
|
14.0
|
1.0
|
CBK
|
D:7OH201
|
4.8
|
12.3
|
1.0
|
CB
|
D:HIS83
|
4.8
|
14.5
|
1.0
|
CBQ
|
D:7OH201
|
4.8
|
12.8
|
1.0
|
CG
|
D:HIS83
|
4.8
|
14.8
|
1.0
|
CAY
|
D:7OH201
|
4.8
|
15.2
|
1.0
|
CBE
|
D:7OH201
|
4.8
|
14.8
|
1.0
|
CD1
|
D:TYR75
|
4.9
|
12.9
|
1.0
|
CE1
|
D:HIS83
|
5.0
|
15.7
|
1.0
|
CD2
|
D:TYR75
|
5.0
|
13.4
|
1.0
|
|
Reference:
Y.Shisaka,
E.Sakakibara,
K.Suzuki,
J.K.Stanfield,
H.Onoda,
G.Ueda,
M.Hatano,
H.Sugimoto,
O.Shoji.
Tetraphenylporphyrin Enters the Ring: First Example of A Complex Between Highly Bulky Porphyrins and A Protein. Chembiochem V. 23 00095 2022.
ISSN: ESSN 1439-7633
PubMed: 35352458
DOI: 10.1002/CBIC.202200095
Page generated: Fri Aug 9 05:34:22 2024
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