Manganese in PDB 7svs: Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei

Enzymatic activity of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei

All present enzymatic activity of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei, PDB code: 7svs was solved by E.Mendoza Rengifo, J.R.Ferreira Jr., C.R.Garratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.14 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.17, 110.62, 180.93, 90, 90, 90
R / Rfree (%) 19 / 25.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei (pdb code 7svs). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei, PDB code: 7svs:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7svs

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Manganese binding site 1 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:26.4
occ:1.00
 O A:HOH401 1.7 26.1 1.0
OD2 A:ASP163 1.9 26.7 1.0
NE2 A:HIS167 2.1 26.7 1.0
NE2 A:HIS30 2.1 26.9 1.0
NE2 A:HIS78 2.2 26.0 1.0
CE1 A:HIS167 3.0 26.4 1.0
CE1 A:HIS30 3.0 27.3 1.0
CD2 A:HIS78 3.1 26.2 1.0
CG A:ASP163 3.1 26.8 1.0
CD2 A:HIS30 3.2 27.0 1.0
CE1 A:HIS78 3.2 25.6 1.0
CD2 A:HIS167 3.2 27.1 1.0
OD1 A:ASP163 3.6 26.7 1.0
ND1 A:HIS30 4.2 27.6 1.0
ND1 A:HIS167 4.2 26.7 1.0
CG A:HIS78 4.2 25.9 1.0
ND1 A:HIS78 4.2 25.6 1.0
CG A:HIS30 4.2 27.4 1.0
CG A:HIS167 4.3 27.1 1.0
CB A:ASP163 4.3 27.0 1.0
CZ2 A:TRP131 4.3 25.9 1.0
CB A:TRP165 4.5 26.7 1.0
CG A:TRP165 4.6 26.2 1.0
NE2 A:GLN149 4.7 25.2 1.0
CH2 A:TRP131 4.8 26.2 1.0
CB A:ALA168 4.9 27.9 1.0
CD1 A:TRP165 4.9 26.1 1.0

Manganese binding site 2 out of 8 in 7svs

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Manganese binding site 2 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:23.1
occ:1.00
 OD2 B:ASP163 1.9 25.1 1.0
NE2 B:HIS30 2.1 24.2 1.0
O B:HOH401 2.1 22.8 1.0
NE2 B:HIS167 2.1 23.2 1.0
NE2 B:HIS78 2.3 23.0 1.0
CG B:ASP163 3.0 23.2 1.0
CD2 B:HIS30 3.1 24.6 1.0
CD2 B:HIS167 3.1 23.4 1.0
CE1 B:HIS30 3.1 23.8 1.0
CE1 B:HIS167 3.1 23.0 1.0
CD2 B:HIS78 3.2 23.2 1.0
CE1 B:HIS78 3.3 22.8 1.0
OD1 B:ASP163 3.5 23.8 1.0
ND1 B:HIS30 4.2 24.0 1.0
CB B:ASP163 4.2 23.4 1.0
CG B:HIS30 4.2 24.4 1.0
ND1 B:HIS167 4.2 23.2 1.0
CG B:HIS167 4.2 23.6 1.0
CG B:HIS78 4.4 23.0 1.0
ND1 B:HIS78 4.4 22.8 1.0
CZ2 B:TRP131 4.4 22.9 1.0
CB B:TRP165 4.5 23.0 1.0
CG B:TRP165 4.7 22.7 1.0
NE2 B:GLN149 4.7 22.3 1.0
CH2 B:TRP131 4.9 23.1 1.0
CD1 B:TRP165 4.9 22.6 1.0

Manganese binding site 3 out of 8 in 7svs

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Manganese binding site 3 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:24.2
occ:1.00
 OD2 C:ASP163 1.9 24.3 1.0
NE2 C:HIS78 2.1 24.0 1.0
NE2 C:HIS30 2.2 26.5 1.0
NE2 C:HIS167 2.2 24.3 1.0
O C:HOH404 2.5 23.6 1.0
CE1 C:HIS78 3.0 23.7 1.0
CG C:ASP163 3.0 24.3 1.0
CD2 C:HIS78 3.1 24.2 1.0
CE1 C:HIS30 3.1 28.4 1.0
CE1 C:HIS167 3.2 24.1 1.0
CD2 C:HIS30 3.2 26.4 1.0
CD2 C:HIS167 3.3 26.6 1.0
OD1 C:ASP163 3.6 24.1 1.0
ND1 C:HIS78 4.1 23.7 1.0
CG C:HIS78 4.2 24.0 1.0
CZ2 C:TRP131 4.2 23.8 1.0
CB C:ASP163 4.2 24.5 1.0
ND1 C:HIS30 4.2 25.6 1.0
ND1 C:HIS167 4.3 24.4 1.0
CG C:HIS30 4.3 25.4 1.0
CG C:HIS167 4.4 28.1 1.0
CB C:TRP165 4.6 23.9 1.0
OE1 C:GLN149 4.7 27.5 1.0
CH2 C:TRP131 4.7 24.1 1.0
CG C:TRP165 4.8 23.6 1.0
CB C:ALA168 5.0 28.1 1.0

Manganese binding site 4 out of 8 in 7svs

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Manganese binding site 4 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:27.0
occ:1.00
 OD2 D:ASP163 2.0 27.4 1.0
NE2 D:HIS78 2.1 30.5 1.0
NE2 D:HIS30 2.2 27.6 1.0
NE2 D:HIS167 2.2 27.3 1.0
O D:HOH402 2.3 26.5 1.0
CE1 D:HIS78 2.9 28.9 1.0
CE1 D:HIS30 3.0 28.0 1.0
CE1 D:HIS167 3.1 27.0 1.0
CG D:ASP163 3.2 27.4 1.0
CD2 D:HIS167 3.2 27.7 1.0
CD2 D:HIS78 3.2 31.1 1.0
CD2 D:HIS30 3.2 27.7 1.0
OD1 D:ASP163 3.7 27.2 1.0
ND1 D:HIS78 4.0 31.5 1.0
ND1 D:HIS30 4.2 28.3 1.0
CG D:HIS78 4.2 32.3 1.0
ND1 D:HIS167 4.2 27.3 1.0
CZ2 D:TRP131 4.3 28.2 1.0
CG D:HIS167 4.3 27.8 1.0
CG D:HIS30 4.3 28.2 1.0
CB D:ASP163 4.3 27.7 1.0
CB D:TRP165 4.5 27.2 1.0
CG D:TRP165 4.7 26.7 1.0
NE2 D:GLN149 4.7 34.9 1.0
CH2 D:TRP131 4.8 26.8 1.0

Manganese binding site 5 out of 8 in 7svs

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Manganese binding site 5 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:24.2
occ:1.00
 OD2 E:ASP163 2.0 24.0 1.0
O E:HOH408 2.1 23.7 1.0
NE2 E:HIS30 2.2 27.4 1.0
NE2 E:HIS78 2.3 24.3 1.0
NE2 E:HIS167 2.4 24.1 1.0
CD2 E:HIS78 3.1 24.6 1.0
CG E:ASP163 3.1 24.2 1.0
CD2 E:HIS30 3.1 25.7 1.0
CE1 E:HIS30 3.2 27.2 1.0
CD2 E:HIS167 3.3 24.3 1.0
CE1 E:HIS167 3.4 24.0 1.0
CE1 E:HIS78 3.4 24.3 1.0
OD1 E:ASP163 3.7 23.5 1.0
ND1 E:HIS30 4.3 25.8 1.0
CG E:HIS30 4.3 25.2 1.0
CB E:ASP163 4.3 23.9 1.0
CG E:HIS78 4.3 24.7 1.0
ND1 E:HIS78 4.4 24.5 1.0
CG E:HIS167 4.5 24.3 1.0
ND1 E:HIS167 4.5 24.0 1.0
CZ2 E:TRP131 4.5 23.9 1.0
NE2 E:GLN149 4.6 23.5 1.0
CB E:TRP165 4.7 23.3 1.0
CG E:TRP165 4.8 23.2 1.0

Manganese binding site 6 out of 8 in 7svs

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Manganese binding site 6 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn301

b:29.0
occ:1.00
 NE2 F:HIS30 2.0 29.6 1.0
NE2 F:HIS78 2.0 29.3 1.0
OD2 F:ASP163 2.1 30.7 1.0
NE2 F:HIS167 2.2 28.9 1.0
O F:HOH403 2.5 29.3 1.0
CE1 F:HIS30 2.8 29.6 1.0
CE1 F:HIS78 2.9 29.8 1.0
CE1 F:HIS167 3.0 28.7 1.0
CD2 F:HIS78 3.2 29.9 1.0
CD2 F:HIS30 3.2 30.1 1.0
CG F:ASP163 3.2 33.4 1.0
CD2 F:HIS167 3.3 29.1 1.0
OD1 F:ASP163 3.7 35.7 1.0
ND1 F:HIS30 4.0 30.0 1.0
ND1 F:HIS78 4.0 31.3 1.0
ND1 F:HIS167 4.2 28.7 1.0
CG F:HIS30 4.2 30.4 1.0
CG F:HIS78 4.2 34.0 1.0
CG F:HIS167 4.4 29.0 1.0
CZ2 F:TRP131 4.4 31.6 1.0
CB F:ASP163 4.5 32.1 1.0
NE2 F:GLN149 4.6 31.5 1.0
CB F:TRP165 4.8 27.6 1.0
CG F:TRP165 4.8 27.4 1.0
OH F:TYR38 4.8 39.1 1.0
CH2 F:TRP131 4.9 34.0 1.0
CD1 F:TRP165 4.9 30.5 1.0

Manganese binding site 7 out of 8 in 7svs

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Manganese binding site 7 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn301

b:24.9
occ:1.00
 O G:HOH405 2.0 24.4 1.0
OD2 G:ASP163 2.0 27.2 1.0
NE2 G:HIS30 2.1 28.6 1.0
NE2 G:HIS167 2.1 25.0 1.0
NE2 G:HIS78 2.1 26.2 1.0
CE1 G:HIS167 2.9 24.9 1.0
CE1 G:HIS30 3.0 26.8 1.0
CD2 G:HIS78 3.1 26.0 1.0
CE1 G:HIS78 3.1 24.9 1.0
CD2 G:HIS30 3.1 28.3 1.0
CG G:ASP163 3.1 27.3 1.0
CD2 G:HIS167 3.2 25.3 1.0
OD1 G:ASP163 3.6 26.7 1.0
ND1 G:HIS167 4.1 25.0 1.0
ND1 G:HIS30 4.1 27.3 1.0
ND1 G:HIS78 4.2 26.6 1.0
CG G:HIS78 4.2 26.2 1.0
CG G:HIS30 4.2 26.4 1.0
CZ2 G:TRP131 4.2 25.4 1.0
CG G:HIS167 4.2 25.2 1.0
CB G:ASP163 4.4 25.3 1.0
NE2 G:GLN149 4.5 24.0 1.0
CB G:TRP165 4.6 25.4 1.0
CG G:TRP165 4.7 23.9 1.0
CH2 G:TRP131 4.9 24.7 1.0
CB G:ALA168 4.9 28.2 1.0

Manganese binding site 8 out of 8 in 7svs

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Manganese binding site 8 out of 8 in the Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure Analysis of the G73A Mutant of Superoxide Dismutase From Trichoderma Reesei within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn301

b:31.0
occ:1.00
 NE2 H:HIS78 2.1 33.1 1.0
O H:HOH403 2.1 28.7 1.0
OD2 H:ASP163 2.1 34.2 1.0
NE2 H:HIS30 2.2 32.7 1.0
NE2 H:HIS167 2.3 32.4 1.0
CE1 H:HIS78 2.9 30.1 1.0
CD2 H:HIS30 3.1 36.4 1.0
CE1 H:HIS30 3.2 35.1 1.0
CD2 H:HIS78 3.2 35.1 1.0
CD2 H:HIS167 3.2 32.9 1.0
CG H:ASP163 3.2 32.9 1.0
CE1 H:HIS167 3.3 30.6 1.0
OD1 H:ASP163 3.6 32.0 1.0
ND1 H:HIS78 4.1 31.0 1.0
CG H:HIS78 4.2 33.3 1.0
ND1 H:HIS30 4.3 37.5 1.0
CG H:HIS30 4.3 38.1 1.0
CG H:HIS167 4.4 32.5 1.0
CZ2 H:TRP131 4.4 34.6 1.0
ND1 H:HIS167 4.4 29.8 1.0
CB H:TRP165 4.4 29.2 1.0
CB H:ASP163 4.5 29.1 1.0
CG H:TRP165 4.6 27.9 1.0
NE2 H:GLN149 4.7 31.2 1.0
CH2 H:TRP131 4.8 32.9 1.0
CD1 H:TRP165 4.9 28.2 1.0

Reference:

E.Mendoza Rengifo, L.Stelmastchuk Benassi Fontolan, J.Ribamar Ferreira-Junior, L.Bleicher, J.Penner-Hahn, R.Charles Garratt. Unexpected Plasticity of the Quaternary Structure of Iron-Manganese Superoxide Dismutases. J.Struct.Biol. V. 214 07855 2022.
ISSN: ESSN 1095-8657
PubMed: 35390463
DOI: 10.1016/J.JSB.2022.107855
Page generated: Fri Apr 7 12:29:09 2023

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