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Iron in PDB 4yip: X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans

Enzymatic activity of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans

All present enzymatic activity of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans:
1.15.1.1;

Protein crystallography data

The structure of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans, PDB code: 4yip was solved by I.Russo Krauss, A.Merlino, A.Pica, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.39 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.964, 82.879, 72.779, 90.00, 94.25, 90.00
R / Rfree (%) 19.3 / 25.9

Iron Binding Sites:

The binding sites of Iron atom in the X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans (pdb code 4yip). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans, PDB code: 4yip:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4yip

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Iron binding site 1 out of 4 in the X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:34.9
occ:1.00
 OD2 A:ASP162 1.9 23.9 1.0
O A:HOH412 2.1 21.9 1.0
NE2 A:HIS26 2.1 28.5 1.0
NE2 A:HIS80 2.2 27.5 1.0
NE2 A:HIS166 2.3 25.1 1.0
CG A:ASP162 3.0 28.6 1.0
CE1 A:HIS80 3.0 28.7 1.0
O A:HOH470 3.1 30.4 0.4
CE1 A:HIS26 3.1 22.6 1.0
CD2 A:HIS26 3.1 21.8 1.0
CE1 A:HIS166 3.2 25.1 1.0
CD2 A:HIS80 3.3 27.4 1.0
CD2 A:HIS166 3.3 25.4 1.0
OD1 A:ASP162 3.4 31.9 1.0
ND1 A:HIS26 4.2 23.8 1.0
ND1 A:HIS80 4.2 29.9 1.0
CG A:HIS26 4.3 24.7 1.0
CB A:ASP162 4.3 24.1 1.0
ND1 A:HIS166 4.4 24.9 1.0
CG A:HIS80 4.4 28.3 1.0
CG A:HIS166 4.4 24.1 1.0
CB A:TRP164 4.5 22.6 1.0
CZ2 A:TRP128 4.5 20.1 1.0
CG A:TRP164 4.6 22.3 1.0
NE2 A:GLN147 4.6 22.6 1.0
CD1 A:TRP164 4.8 22.0 1.0
CB A:ALA167 5.0 20.8 1.0

Iron binding site 2 out of 4 in 4yip

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Iron binding site 2 out of 4 in the X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:35.6
occ:1.00
 OD2 B:ASP162 2.0 22.3 1.0
NE2 B:HIS26 2.2 24.9 1.0
O B:HOH415 2.2 19.2 1.0
NE2 B:HIS80 2.3 33.0 1.0
NE2 B:HIS166 2.4 25.0 1.0
CG B:ASP162 3.1 21.8 1.0
CE1 B:HIS80 3.1 31.7 1.0
CD2 B:HIS26 3.2 23.2 1.0
CE1 B:HIS26 3.2 20.6 1.0
CD2 B:HIS166 3.3 23.9 1.0
CE1 B:HIS166 3.4 23.3 1.0
CD2 B:HIS80 3.4 29.2 1.0
OD1 B:ASP162 3.4 24.9 1.0
ND1 B:HIS80 4.2 30.1 1.0
ND1 B:HIS26 4.3 25.3 1.0
CB B:ASP162 4.3 22.5 1.0
CG B:HIS26 4.3 27.1 1.0
CG B:HIS80 4.4 31.4 1.0
CG B:HIS166 4.5 20.9 1.0
ND1 B:HIS166 4.5 19.8 1.0
CZ2 B:TRP128 4.5 20.8 1.0
NE2 B:GLN147 4.5 21.3 1.0
CB B:TRP164 4.6 20.6 1.0
CG B:TRP164 4.7 21.8 1.0
CD1 B:TRP164 4.9 23.0 1.0

Iron binding site 3 out of 4 in 4yip

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Iron binding site 3 out of 4 in the X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:33.7
occ:1.00
 NE2 C:HIS26 2.1 21.4 1.0
OD2 C:ASP162 2.1 34.5 1.0
O C:HOH410 2.3 23.8 1.0
NE2 C:HIS80 2.3 21.6 1.0
NE2 C:HIS166 2.3 27.8 1.0
CE1 C:HIS26 3.0 22.4 1.0
CD2 C:HIS26 3.0 23.2 1.0
CD2 C:HIS166 3.1 23.0 1.0
CG C:ASP162 3.2 34.0 1.0
CD2 C:HIS80 3.2 22.4 1.0
CE1 C:HIS80 3.3 24.4 1.0
CE1 C:HIS166 3.5 26.5 1.0
OD1 C:ASP162 3.7 33.2 1.0
ND1 C:HIS26 4.1 22.9 1.0
CG C:HIS26 4.2 24.0 1.0
CG C:HIS166 4.3 23.8 1.0
CG C:HIS80 4.4 23.1 1.0
ND1 C:HIS80 4.4 25.1 1.0
CB C:ASP162 4.4 33.4 1.0
ND1 C:HIS166 4.5 23.0 1.0
NE2 C:GLN147 4.7 20.9 1.0
CB C:TRP164 4.7 20.9 1.0
CZ2 C:TRP128 4.7 25.9 1.0
CG C:TRP164 4.8 19.9 1.0
CB C:ALA167 5.0 23.7 1.0

Iron binding site 4 out of 4 in 4yip

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Iron binding site 4 out of 4 in the X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Iron/Manganese Cambialistic Superoxide Dismutase From Streptococcus Mutans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe301

b:32.3
occ:1.00
 OD2 D:ASP162 2.0 27.4 1.0
O D:HOH418 2.0 22.7 1.0
NE2 D:HIS26 2.2 20.8 1.0
NE2 D:HIS166 2.2 22.4 1.0
NE2 D:HIS80 2.3 24.0 1.0
CG D:ASP162 3.1 26.4 1.0
CD2 D:HIS26 3.1 22.6 1.0
CE1 D:HIS26 3.1 24.7 1.0
CD2 D:HIS166 3.2 20.6 1.0
CD2 D:HIS80 3.2 23.1 1.0
CE1 D:HIS166 3.2 21.7 1.0
CE1 D:HIS80 3.2 22.5 1.0
OD1 D:ASP162 3.5 25.6 1.0
ND1 D:HIS26 4.3 23.9 1.0
CG D:HIS26 4.3 25.2 1.0
ND1 D:HIS166 4.3 21.6 1.0
CB D:ASP162 4.3 24.6 1.0
CG D:HIS166 4.3 23.1 1.0
ND1 D:HIS80 4.4 22.7 1.0
CG D:HIS80 4.4 24.6 1.0
CB D:TRP164 4.5 22.7 1.0
NE2 D:GLN147 4.6 20.1 1.0
CG D:TRP164 4.6 22.6 1.0
CZ2 D:TRP128 4.6 22.4 1.0
CD1 D:TRP164 4.9 23.9 1.0
CE2 D:TYR34 4.9 22.6 1.0

Reference:

I.Russo Krauss, A.Merlino, A.Pica, R.Rullo, A.Bertoni, A.Capasso, M.Amato, F.Riccitiello, E.De Vendittis, F.Sica. Fine Tuning of Metal-Specific Activity in the Mn-Like Group of Cambialistic Superoxide Dismutases Rsc Adv V. 5 87876 2015.
ISSN: ESSN 2046-2069
DOI: 10.1039/C5RA13559A
Page generated: Mon Aug 5 16:11:42 2024

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