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Iron in PDB 3e74: Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center

Enzymatic activity of Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center

All present enzymatic activity of Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center:
3.5.2.5;

Protein crystallography data

The structure of Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center, PDB code: 3e74 was solved by K.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.681, 92.450, 168.430, 90.00, 93.30, 90.00
R / Rfree (%) 19.9 / 24

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center (pdb code 3e74). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center, PDB code: 3e74:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3e74

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Iron binding site 1 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe454

b:35.1
occ:1.00
OQ1 A:KCX146 2.1 32.8 1.0
NE2 A:HIS61 2.2 27.4 1.0
OD1 A:ASP315 2.3 26.6 1.0
NE2 A:HIS59 2.3 26.7 1.0
CX A:KCX146 3.1 32.5 1.0
CE1 A:HIS59 3.1 26.1 1.0
CE1 A:HIS61 3.2 29.0 1.0
O A:HOH456 3.2 21.8 1.0
CD2 A:HIS61 3.2 26.8 1.0
CG A:ASP315 3.3 26.5 1.0
CD2 A:HIS59 3.4 24.2 1.0
FE A:FE455 3.4 34.6 1.0
OQ2 A:KCX146 3.5 26.3 1.0
O A:HOH643 3.6 51.3 1.0
OD2 A:ASP315 3.7 27.2 1.0
NZ A:KCX146 4.1 30.6 1.0
ND1 A:HIS59 4.3 26.1 1.0
ND1 A:HIS61 4.3 29.0 1.0
CG A:HIS61 4.4 27.9 1.0
CG A:HIS59 4.4 24.6 1.0
CD2 A:HIS242 4.5 20.6 1.0
CB A:ASP315 4.5 25.8 1.0
O A:HOH605 4.6 48.1 1.0
NE2 A:HIS242 4.8 17.2 1.0
CA A:ASP315 4.8 24.3 1.0
CG A:MSE91 4.9 38.3 1.0

Iron binding site 2 out of 8 in 3e74

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Iron binding site 2 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe455

b:34.6
occ:1.00
OQ2 A:KCX146 2.1 26.3 1.0
ND1 A:HIS186 2.2 24.6 1.0
NE2 A:HIS242 2.4 17.2 1.0
CE1 A:HIS186 2.8 24.5 1.0
CX A:KCX146 3.0 32.5 1.0
O A:HOH456 3.1 21.8 1.0
OQ1 A:KCX146 3.1 32.8 1.0
CD2 A:HIS242 3.2 20.6 1.0
FE A:FE454 3.4 35.1 1.0
CG A:HIS186 3.4 23.9 1.0
CE1 A:HIS242 3.5 19.3 1.0
CB A:HIS186 4.0 24.2 1.0
NE2 A:HIS186 4.1 25.9 1.0
CE2 A:PHE148 4.1 32.3 1.0
NZ A:KCX146 4.2 30.6 1.0
CD2 A:HIS186 4.4 24.6 1.0
CG A:HIS242 4.5 21.6 1.0
CE1 A:HIS59 4.5 26.1 1.0
OD2 A:ASP315 4.5 27.2 1.0
ND1 A:HIS242 4.6 21.8 1.0
O A:HOH643 4.7 51.3 1.0
NE2 A:HIS59 4.7 26.7 1.0
OD1 A:ASP315 4.7 26.6 1.0
CZ A:PHE148 4.7 32.6 1.0
CE A:KCX146 4.9 31.7 1.0
CA A:HIS186 4.9 24.1 1.0
CG A:ASP315 5.0 26.5 1.0
CB A:SER288 5.0 41.1 1.0

Iron binding site 3 out of 8 in 3e74

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Iron binding site 3 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe454

b:37.1
occ:1.00
OQ1 B:KCX146 2.0 38.7 1.0
ND1 B:HIS186 2.4 25.8 1.0
NE2 B:HIS242 2.4 21.3 1.0
CX B:KCX146 2.7 39.0 1.0
O B:HOH684 2.9 29.8 1.0
OQ2 B:KCX146 2.9 36.1 1.0
CE1 B:HIS186 3.1 26.4 1.0
CD2 B:HIS242 3.3 21.9 1.0
FE B:FE455 3.4 36.0 1.0
CE1 B:HIS242 3.4 24.4 1.0
CG B:HIS186 3.5 24.9 1.0
NZ B:KCX146 3.9 37.7 1.0
CB B:HIS186 4.0 23.8 1.0
CE2 B:PHE148 4.1 22.4 1.0
NE2 B:HIS186 4.3 27.7 1.0
CG B:HIS242 4.5 21.7 1.0
OD2 B:ASP315 4.5 27.9 1.0
ND1 B:HIS242 4.5 22.4 1.0
CD2 B:HIS186 4.5 24.8 1.0
CE1 B:HIS59 4.6 18.8 1.0
NE2 B:HIS59 4.6 17.8 1.0
CZ B:PHE148 4.8 21.9 1.0
OD1 B:ASP315 4.8 27.9 1.0
CB B:SER288 4.9 41.5 1.0
O B:HOH924 4.9 42.8 1.0
CA B:HIS186 4.9 22.4 1.0
CD2 B:PHE148 5.0 25.0 1.0
CG B:ASP315 5.0 26.4 1.0

Iron binding site 4 out of 8 in 3e74

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Iron binding site 4 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe455

b:36.0
occ:1.00
OD1 B:ASP315 2.3 27.9 1.0
NE2 B:HIS59 2.4 17.8 1.0
OQ2 B:KCX146 2.4 36.1 1.0
NE2 B:HIS61 2.4 25.9 1.0
CD2 B:HIS61 3.2 24.8 1.0
O B:HOH684 3.3 29.8 1.0
CE1 B:HIS59 3.3 18.8 1.0
CX B:KCX146 3.3 39.0 1.0
CG B:ASP315 3.3 26.4 1.0
CD2 B:HIS59 3.3 18.3 1.0
FE B:FE454 3.4 37.1 1.0
CE1 B:HIS61 3.4 23.9 1.0
OQ1 B:KCX146 3.6 38.7 1.0
OD2 B:ASP315 3.7 27.9 1.0
O B:HOH924 4.0 42.8 1.0
ND1 B:HIS59 4.4 20.9 1.0
CG B:HIS61 4.4 25.8 1.0
NZ B:KCX146 4.4 37.7 1.0
CG B:HIS59 4.4 20.5 1.0
CD2 B:HIS242 4.5 21.9 1.0
ND1 B:HIS61 4.5 24.6 1.0
CB B:ASP315 4.5 23.7 1.0
NE2 B:HIS242 4.6 21.3 1.0
OG B:SER317 4.7 34.8 1.0
CA B:ASP315 4.8 22.5 1.0
CG B:MSE91 4.9 33.8 1.0
CE B:KCX146 4.9 35.1 1.0

Iron binding site 5 out of 8 in 3e74

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Iron binding site 5 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe454

b:32.3
occ:1.00
OQ2 C:KCX146 2.2 28.9 1.0
NE2 C:HIS242 2.3 16.9 1.0
ND1 C:HIS186 2.3 24.2 1.0
O C:HOH722 2.6 46.8 1.0
CE1 C:HIS186 3.0 26.7 1.0
CX C:KCX146 3.1 29.3 1.0
O C:HOH531 3.1 22.5 1.0
CE1 C:HIS242 3.2 19.4 1.0
OQ1 C:KCX146 3.2 29.8 1.0
CD2 C:HIS242 3.3 20.6 1.0
FE C:FE455 3.4 36.2 1.0
CG C:HIS186 3.4 25.0 1.0
O C:HOH570 3.6 38.5 1.0
CB C:HIS186 3.9 23.5 1.0
CE2 C:PHE148 4.1 32.0 1.0
NE2 C:HIS186 4.2 27.4 1.0
NZ C:KCX146 4.3 24.6 1.0
ND1 C:HIS242 4.3 19.9 1.0
CG C:HIS242 4.4 20.8 1.0
CE1 C:HIS59 4.4 25.5 1.0
NE2 C:HIS59 4.5 25.2 1.0
CD2 C:HIS186 4.5 26.7 1.0
OD2 C:ASP315 4.6 27.7 1.0
CZ C:PHE148 4.7 33.7 1.0
O C:HOH663 4.8 32.0 1.0
CA C:HIS186 4.8 23.5 1.0
OD1 C:ASP315 4.8 22.2 1.0
CE C:KCX146 4.9 23.7 1.0

Iron binding site 6 out of 8 in 3e74

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Iron binding site 6 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe455

b:36.2
occ:1.00
OQ1 C:KCX146 2.1 29.8 1.0
NE2 C:HIS59 2.3 25.2 1.0
NE2 C:HIS61 2.3 30.2 1.0
OD1 C:ASP315 2.4 22.2 1.0
CX C:KCX146 3.1 29.3 1.0
O C:HOH531 3.2 22.5 1.0
CD2 C:HIS61 3.2 28.4 1.0
CD2 C:HIS59 3.2 23.6 1.0
CE1 C:HIS59 3.3 25.5 1.0
CG C:ASP315 3.4 22.9 1.0
CE1 C:HIS61 3.4 28.2 1.0
FE C:FE454 3.4 32.3 1.0
OQ2 C:KCX146 3.5 28.9 1.0
O C:HOH663 3.7 32.0 1.0
OD2 C:ASP315 3.8 27.7 1.0
O C:HOH722 4.1 46.8 1.0
NZ C:KCX146 4.2 24.6 1.0
CG C:HIS59 4.4 23.7 1.0
ND1 C:HIS59 4.4 24.7 1.0
CG C:HIS61 4.4 28.1 1.0
ND1 C:HIS61 4.4 28.9 1.0
CD2 C:HIS242 4.5 20.6 1.0
NE2 C:HIS242 4.5 16.9 1.0
CB C:ASP315 4.5 22.2 1.0
OG C:SER317 4.6 29.9 1.0
CA C:ASP315 4.8 21.8 1.0
O C:HOH570 4.8 38.5 1.0
CG C:MSE91 5.0 31.0 1.0
O C:ASP315 5.0 21.4 1.0

Iron binding site 7 out of 8 in 3e74

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Iron binding site 7 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


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 E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe454

b:43.2
occ:1.00
ND1 D:HIS186 2.2 26.7 1.0
OQ1 D:KCX146 2.3 41.2 1.0
NE2 D:HIS242 2.3 26.1 1.0
CE1 D:HIS186 2.9 28.9 1.0
O D:HOH482 3.1 27.1 1.0
CD2 D:HIS242 3.3 24.7 1.0
CE1 D:HIS242 3.3 25.4 1.0
CX D:KCX146 3.3 41.9 1.0
CG D:HIS186 3.4 25.9 1.0
FE D:FE455 3.4 44.3 1.0
NZ D:KCX146 3.8 41.8 1.0
CB D:HIS186 3.9 24.8 1.0
CE2 D:PHE148 4.0 28.1 1.0
NE2 D:HIS186 4.1 28.3 1.0
OQ2 D:KCX146 4.3 46.1 1.0
ND1 D:HIS242 4.4 24.7 1.0
CD2 D:HIS186 4.4 27.1 1.0
CG D:HIS242 4.4 24.2 1.0
OD2 D:ASP315 4.6 25.3 1.0
NE2 D:HIS59 4.6 26.6 1.0
CZ D:PHE148 4.6 29.6 1.0
CB D:SER288 4.7 44.4 1.0
OG D:SER288 4.7 45.1 1.0
CE1 D:HIS59 4.7 25.8 1.0
CA D:HIS186 4.8 22.5 1.0
CD D:PRO289 4.8 38.4 1.0
OD1 D:ASP315 4.9 29.9 1.0
CD2 D:PHE148 5.0 30.0 1.0

Iron binding site 8 out of 8 in 3e74

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Iron binding site 8 out of 8 in the Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of E. Coli Allantoinase with Iron Ions at the Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe455

b:44.3
occ:1.00
NE2 D:HIS61 2.4 37.1 1.0
OD1 D:ASP315 2.5 29.9 1.0
NE2 D:HIS59 2.6 26.6 1.0
OQ1 D:KCX146 2.6 41.2 1.0
CD2 D:HIS61 3.1 34.8 1.0
O D:HOH482 3.2 27.1 1.0
OQ2 D:KCX146 3.2 46.1 1.0
CX D:KCX146 3.3 41.9 1.0
CD2 D:HIS59 3.4 27.2 1.0
FE D:FE454 3.4 43.2 1.0
CG D:ASP315 3.4 27.8 1.0
CE1 D:HIS61 3.5 36.9 1.0
CE1 D:HIS59 3.6 25.8 1.0
OD2 D:ASP315 3.8 25.3 1.0
O D:HOH572 4.1 38.6 1.0
CG D:HIS61 4.4 35.1 1.0
ND1 D:HIS61 4.5 36.2 1.0
CD2 D:HIS242 4.5 24.7 1.0
OG D:SER317 4.5 44.3 1.0
NZ D:KCX146 4.6 41.8 1.0
NE2 D:HIS242 4.6 26.1 1.0
CG D:HIS59 4.6 26.7 1.0
CB D:ASP315 4.7 26.4 1.0
ND1 D:HIS59 4.7 27.8 1.0
CG D:MSE91 4.9 37.4 1.0
CA D:ASP315 5.0 26.3 1.0

Reference:

K.Kim, M.I.Kim, J.Chung, J.H.Ahn, S.Rhee. Crystal Structure of Metal-Dependent Allantoinase From Escherichia Coli J.Mol.Biol. V. 387 1067 2009.
ISSN: ISSN 0022-2836
PubMed: 19248789
DOI: 10.1016/J.JMB.2009.02.041
Page generated: Sun Dec 13 15:04:36 2020

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