Iron in PDB 7lvz: Crystal Structure of Ado

Enzymatic activity of Crystal Structure of Ado

All present enzymatic activity of Crystal Structure of Ado:
1.13.11.19;

Protein crystallography data

The structure of Crystal Structure of Ado, PDB code: 7lvz was solved by C.A.Bingman, R.L.Fernandez, R.W.Smith, B.G.Fox, T.C.Brunold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.17 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.296, 139.525, 142.007, 90, 90, 90
R / Rfree (%) 19.1 / 22.8

Other elements in 7lvz:

The structure of Crystal Structure of Ado also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ado (pdb code 7lvz). 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 Ado, PDB code: 7lvz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7lvz

Go back to Iron Binding Sites List in 7lvz
Iron binding site 1 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.4
occ:1.00
O A:HOH518 2.2 30.8 1.0
O A:HOH465 2.2 28.6 1.0
NE2 A:HIS102 2.3 24.8 1.0
NE2 A:HIS100 2.3 29.4 1.0
O A:HOH454 2.3 33.5 1.0
NE2 A:HIS179 2.4 27.8 1.0
CE1 A:HIS100 3.2 30.4 1.0
CD2 A:HIS102 3.2 30.1 1.0
CE1 A:HIS102 3.2 26.6 1.0
CD2 A:HIS100 3.3 25.5 1.0
CE1 A:HIS179 3.3 29.9 1.0
CD2 A:HIS179 3.3 28.7 1.0
HE1 A:HIS100 3.3 36.5 1.0
HD2 A:HIS102 3.4 36.2 1.0
HE1 A:HIS102 3.4 31.9 1.0
HD2 A:HIS100 3.4 30.6 1.0
HD2 A:HIS179 3.5 34.5 1.0
HE1 A:HIS179 3.5 35.9 1.0
O A:HOH431 4.0 34.7 1.0
HD11 A:ILE181 4.1 37.5 1.0
HD22 A:LEU194 4.2 43.5 1.0
OH A:TYR198 4.3 32.2 1.0
ND1 A:HIS100 4.3 29.3 1.0
ND1 A:HIS102 4.4 30.2 1.0
CG A:HIS100 4.4 27.8 1.0
CG A:HIS102 4.4 29.5 1.0
O A:HOH506 4.4 35.5 1.0
ND1 A:HIS179 4.4 31.7 1.0
HD21 A:LEU171 4.4 39.8 1.0
CG A:HIS179 4.5 29.3 1.0
OD2 A:ASP192 4.5 40.4 1.0
HH A:TYR198 4.6 38.8 1.0
HD13 A:LEU194 4.7 43.0 1.0
HG23 A:ILE97 4.8 37.0 1.0
HD12 A:ILE181 4.8 37.5 1.0
CD1 A:ILE181 4.9 31.2 1.0

Iron binding site 2 out of 4 in 7lvz

Go back to Iron Binding Sites List in 7lvz
Iron binding site 2 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:26.1
occ:1.00
O B:HOH498 2.2 22.2 1.0
O B:HOH441 2.2 22.7 1.0
NE2 B:HIS102 2.3 21.4 1.0
NE2 B:HIS100 2.3 22.3 1.0
O B:HOH557 2.3 35.1 1.0
NE2 B:HIS179 2.5 25.6 1.0
CD2 B:HIS100 3.2 29.2 1.0
CE1 B:HIS102 3.2 24.2 1.0
CD2 B:HIS102 3.3 22.6 1.0
HD2 B:HIS100 3.3 35.1 1.0
CE1 B:HIS100 3.3 23.0 1.0
CE1 B:HIS179 3.3 25.2 1.0
HE1 B:HIS102 3.4 29.1 1.0
CD2 B:HIS179 3.4 27.8 1.0
HD2 B:HIS102 3.4 27.2 1.0
HE1 B:HIS179 3.5 30.3 1.0
HE1 B:HIS100 3.5 27.7 1.0
HD2 B:HIS179 3.6 33.4 1.0
O B:HOH434 3.9 32.7 1.0
HD12 B:ILE181 4.1 41.1 1.0
OH B:TYR198 4.3 29.2 1.0
HD23 B:LEU194 4.3 37.7 1.0
ND1 B:HIS102 4.4 26.4 1.0
CG B:HIS100 4.4 23.9 1.0
ND1 B:HIS100 4.4 25.6 1.0
ND1 B:HIS179 4.4 29.6 1.0
CG B:HIS102 4.4 26.5 1.0
OD2 B:ASP192 4.4 39.8 1.0
CG B:HIS179 4.5 24.6 1.0
O B:HOH506 4.5 33.2 1.0
HH B:TYR198 4.6 35.1 1.0
HD11 B:LEU194 4.6 44.0 1.0
HD22 B:LEU171 4.6 37.1 1.0
HD13 B:ILE181 4.7 41.1 1.0
HG21 B:ILE97 4.8 38.0 1.0
CD1 B:ILE181 4.9 34.2 1.0

Iron binding site 3 out of 4 in 7lvz

Go back to Iron Binding Sites List in 7lvz
Iron binding site 3 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:31.3
occ:1.00
O B:HOH529 2.1 32.9 1.0
O C:HOH460 2.2 31.1 1.0
NE2 C:HIS102 2.2 27.0 1.0
NE2 C:HIS100 2.3 29.5 1.0
NE2 C:HIS179 2.3 25.0 1.0
O C:HOH485 2.4 35.4 1.0
CE1 C:HIS102 3.1 32.3 1.0
CD2 C:HIS102 3.2 30.4 1.0
CD2 C:HIS100 3.2 28.1 1.0
CE1 C:HIS179 3.3 30.8 1.0
CE1 C:HIS100 3.3 27.9 1.0
HE1 C:HIS102 3.3 38.9 1.0
HE2 B:HIS130 3.3 44.6 1.0
HD2 C:HIS100 3.3 33.8 1.0
CD2 C:HIS179 3.3 27.7 1.0
HD2 C:HIS102 3.3 36.5 1.0
HE1 C:HIS179 3.4 37.0 1.0
HE1 C:HIS100 3.5 33.6 1.0
HD2 C:HIS179 3.5 33.3 1.0
O C:HOH427 4.1 34.2 1.0
NE2 B:HIS130 4.1 37.5 1.0
HD22 C:LEU194 4.2 45.3 1.0
ND1 C:HIS102 4.3 28.7 1.0
OH C:TYR198 4.3 30.3 1.0
CG C:HIS102 4.3 33.2 1.0
HD11 C:ILE181 4.3 39.1 1.0
HD22 C:LEU171 4.4 38.8 1.0
ND1 C:HIS179 4.4 32.8 1.0
CG C:HIS100 4.4 26.2 1.0
ND1 C:HIS100 4.4 29.2 1.0
CG C:HIS179 4.4 27.1 1.0
HH C:TYR198 4.5 36.4 1.0
HD13 C:LEU194 4.5 50.7 1.0
O C:HOH462 4.5 33.4 1.0
OD2 C:ASP192 4.5 38.2 1.0
HE1 B:HIS130 4.6 45.1 1.0
CE1 B:HIS130 4.8 37.9 1.0
HG21 C:ILE97 4.9 43.9 1.0

Iron binding site 4 out of 4 in 7lvz

Go back to Iron Binding Sites List in 7lvz
Iron binding site 4 out of 4 in the Crystal Structure of Ado


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 Ado within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:42.6
occ:1.00
NE2 D:HIS100 2.3 35.0 1.0
NE2 D:HIS102 2.3 33.7 1.0
O D:HOH449 2.4 44.5 1.0
NE2 D:HIS179 2.4 29.9 1.0
O D:HOH414 2.5 35.2 1.0
O D:HOH491 2.6 46.7 1.0
CD2 D:HIS100 3.2 31.9 1.0
CE1 D:HIS102 3.2 31.7 1.0
CE1 D:HIS100 3.3 35.9 1.0
CE1 D:HIS179 3.3 34.9 1.0
CD2 D:HIS102 3.3 33.6 1.0
HD2 D:HIS100 3.3 38.4 1.0
HE1 D:HIS102 3.4 38.1 1.0
CD2 D:HIS179 3.4 33.5 1.0
HE2 A:HIS130 3.4 53.5 1.0
HE1 D:HIS179 3.5 42.0 1.0
HE1 D:HIS100 3.5 43.2 1.0
HD2 D:HIS179 3.5 40.3 1.0
HD2 D:HIS102 3.5 40.4 1.0
O D:HOH410 4.0 37.8 1.0
HD11 D:ILE181 4.2 58.3 1.0
HD23 D:LEU194 4.2 51.7 1.0
NE2 A:HIS130 4.2 44.8 1.0
OH D:TYR198 4.3 34.0 1.0
OD2 D:ASP192 4.4 52.2 1.0
ND1 D:HIS102 4.4 32.8 1.0
CG D:HIS100 4.4 36.6 1.0
ND1 D:HIS100 4.4 39.8 1.0
ND1 D:HIS179 4.4 35.3 1.0
HD11 D:LEU194 4.4 48.2 1.0
CG D:HIS102 4.5 32.8 1.0
HD23 D:LEU171 4.5 41.5 1.0
CG D:HIS179 4.5 35.3 1.0
O D:HOH422 4.6 39.8 1.0
HH D:TYR198 4.6 40.5 1.0
HD12 D:ILE181 4.7 58.3 1.0
HE1 A:HIS130 4.7 54.3 1.0
HG22 D:ILE97 4.8 53.5 1.0
CE1 A:HIS130 4.9 45.5 1.0
CD1 D:ILE181 4.9 48.5 1.0
HE2 D:TYR198 4.9 41.8 1.0

Reference:

R.L.Fernandez, L.D.Elmendorf, R.W.Smith, C.A.Bingman, B.G.Fox, T.C.Brunold. The Crystal Structure of Cysteamine Dioxygenase Reveals the Origin of the Large Substrate Scope of This Vital Mammalian Enzyme. Biochemistry V. 60 3728 2021.
ISSN: ISSN 0006-2960
PubMed: 34762398
DOI: 10.1021/ACS.BIOCHEM.1C00463
Page generated: Thu Mar 31 03:19:55 2022

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