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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

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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

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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

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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

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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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