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Manganese in PDB 4e4e: Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase

Enzymatic activity of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase

All present enzymatic activity of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase, PDB code: 4e4e was solved by Y.Sheng, D.Cascio, J.S.Valentine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.18 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.139, 63.022, 63.943, 112.19, 106.78, 103.88
R / Rfree (%) 19 / 23.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase (pdb code 4e4e). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase, PDB code: 4e4e:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4e4e

Go back to Manganese Binding Sites List in 4e4e
Manganese binding site 1 out of 4 in the Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:17.2
occ:1.00
 OD2 A:ASP168 2.1 17.2 1.0
O A:HOH403 2.3 18.7 1.0
NE2 A:HIS172 2.3 21.4 1.0
NE2 A:HIS81 2.3 19.6 1.0
NE2 A:HIS26 2.4 19.6 1.0
CG A:ASP168 3.2 20.5 1.0
CD2 A:HIS172 3.2 17.7 1.0
CE1 A:HIS81 3.2 24.6 1.0
CD2 A:HIS81 3.3 24.9 1.0
CD2 A:HIS26 3.3 19.9 1.0
CE1 A:HIS172 3.3 22.6 1.0
CE1 A:HIS26 3.4 21.6 1.0
OD1 A:ASP168 3.6 19.7 1.0
CZ2 A:TRP133 4.3 20.7 1.0
ND1 A:HIS81 4.3 20.9 1.0
O A:HOH436 4.4 32.0 1.0
CG A:HIS172 4.4 19.1 1.0
ND1 A:HIS172 4.4 20.1 1.0
CB A:TRP170 4.4 18.0 1.0
CG A:HIS81 4.4 22.0 1.0
CB A:ASP168 4.4 15.3 1.0
ND1 A:HIS26 4.5 20.8 1.0
CG A:HIS26 4.5 22.6 1.0
CG A:TRP170 4.7 20.6 1.0
CH2 A:TRP133 4.7 18.1 1.0
NE2 A:GLN154 4.8 19.7 1.0
CD1 A:TRP170 5.0 19.1 1.0

Manganese binding site 2 out of 4 in 4e4e

Go back to Manganese Binding Sites List in 4e4e
Manganese binding site 2 out of 4 in the Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:18.2
occ:1.00
 OD2 B:ASP168 2.1 19.7 1.0
O B:HOH401 2.3 18.0 1.0
NE2 B:HIS81 2.3 22.9 1.0
NE2 B:HIS26 2.3 15.9 1.0
NE2 B:HIS172 2.4 18.6 1.0
CG B:ASP168 3.1 19.4 1.0
CD2 B:HIS172 3.2 16.4 1.0
CE1 B:HIS81 3.2 20.2 1.0
CD2 B:HIS81 3.3 20.5 1.0
CD2 B:HIS26 3.3 18.8 1.0
CE1 B:HIS26 3.3 19.2 1.0
CE1 B:HIS172 3.4 21.5 1.0
OD1 B:ASP168 3.5 19.7 1.0
CZ2 B:TRP133 4.2 20.4 1.0
ND1 B:HIS81 4.3 21.6 1.0
ND1 B:HIS26 4.4 15.5 1.0
CG B:HIS81 4.4 21.3 1.0
CB B:ASP168 4.4 18.9 1.0
CG B:HIS172 4.4 20.6 1.0
CG B:HIS26 4.4 19.5 1.0
ND1 B:HIS172 4.5 18.6 1.0
CB B:TRP170 4.5 19.7 1.0
CH2 B:TRP133 4.6 20.4 1.0
O B:HOH459 4.6 28.7 1.0
NE2 B:GLN154 4.7 20.0 1.0
CG B:TRP170 4.8 20.5 1.0
CB B:ALA173 4.9 18.4 1.0

Manganese binding site 3 out of 4 in 4e4e

Go back to Manganese Binding Sites List in 4e4e
Manganese binding site 3 out of 4 in the Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:19.0
occ:1.00
 OD2 C:ASP168 2.1 18.0 1.0
O C:HOH401 2.2 17.9 1.0
NE2 C:HIS81 2.3 19.7 1.0
NE2 C:HIS26 2.3 18.4 1.0
NE2 C:HIS172 2.4 22.2 1.0
CE1 C:HIS81 3.1 17.8 1.0
CG C:ASP168 3.2 21.2 1.0
CD2 C:HIS26 3.2 20.5 1.0
CD2 C:HIS172 3.2 20.9 1.0
CD2 C:HIS81 3.2 21.9 1.0
CE1 C:HIS26 3.3 22.6 1.0
CE1 C:HIS172 3.5 22.9 1.0
OD1 C:ASP168 3.6 19.1 1.0
ND1 C:HIS81 4.3 19.8 1.0
CZ2 C:TRP133 4.3 20.4 1.0
CG C:HIS81 4.3 20.8 1.0
CB C:ASP168 4.4 16.4 1.0
ND1 C:HIS26 4.4 21.6 1.0
CG C:HIS26 4.4 21.1 1.0
CG C:HIS172 4.4 22.9 1.0
CB C:TRP170 4.5 16.1 1.0
ND1 C:HIS172 4.5 19.3 1.0
O C:HOH457 4.6 31.3 1.0
CH2 C:TRP133 4.7 20.4 1.0
CG C:TRP170 4.7 19.8 1.0
NE2 C:GLN154 4.7 21.1 1.0
CB C:ALA173 4.9 18.2 1.0
CD1 C:TRP170 5.0 21.9 1.0

Manganese binding site 4 out of 4 in 4e4e

Go back to Manganese Binding Sites List in 4e4e
Manganese binding site 4 out of 4 in the Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Y34F Mutant of Saccharomyces Cerevisiae Manganese Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:19.2
occ:1.00
 OD2 D:ASP168 2.2 19.6 1.0
O D:HOH401 2.2 17.1 1.0
NE2 D:HIS26 2.3 18.9 1.0
NE2 D:HIS81 2.3 21.0 1.0
NE2 D:HIS172 2.4 18.5 1.0
CD2 D:HIS172 3.2 21.6 1.0
CG D:ASP168 3.2 21.4 1.0
CE1 D:HIS26 3.2 22.3 1.0
CD2 D:HIS26 3.2 20.3 1.0
CE1 D:HIS81 3.3 23.5 1.0
CD2 D:HIS81 3.3 21.8 1.0
CE1 D:HIS172 3.4 23.1 1.0
OD1 D:ASP168 3.6 20.1 1.0
ND1 D:HIS26 4.3 22.4 1.0
ND1 D:HIS81 4.3 18.6 1.0
CZ2 D:TRP133 4.4 21.2 1.0
CG D:HIS81 4.4 18.1 1.0
CG D:HIS172 4.4 19.8 1.0
CG D:HIS26 4.4 22.9 1.0
CB D:ASP168 4.4 19.9 1.0
ND1 D:HIS172 4.5 19.6 1.0
CB D:TRP170 4.5 22.3 1.0
O D:HOH456 4.6 28.1 1.0
CH2 D:TRP133 4.7 22.6 1.0
CG D:TRP170 4.7 21.2 1.0
NE2 D:GLN154 4.8 20.1 1.0
CB D:ALA173 5.0 19.1 1.0

Reference:

Y.Sheng, E.Butler Gralla, M.Schumacher, D.Cascio, D.E.Cabelli, J.Selverstone Valentine. Six-Coordinate Manganese(3+) in Catalysis By Yeast Manganese Superoxide Dismutase. Proc.Natl.Acad.Sci.Usa V. 109 14314 2012.
ISSN: ISSN 0027-8424
PubMed: 22908245
DOI: 10.1073/PNAS.1212367109
Page generated: Sat Oct 5 19:08:00 2024

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