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Zinc in PDB 7xx3: Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)

Enzymatic activity of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)

All present enzymatic activity of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb):
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb), PDB code: 7xx3 was solved by B.Padmanabhan, S.Unni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.69 / 1.90
Space group P 63 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 242.445, 242.445, 144.491, 90, 90, 120
R / Rfree (%) 19.9 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) (pdb code 7xx3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb), PDB code: 7xx3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7xx3

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Zinc binding site 1 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:54.6
occ:1.00
 OD1 A:ASP83 2.0 22.7 1.0
ND1 A:HIS63 2.1 32.4 1.0
ND1 A:HIS80 2.1 29.7 1.0
ND1 A:HIS71 2.2 30.0 1.0
CG A:ASP83 2.8 25.4 1.0
CE1 A:HIS80 2.9 25.0 1.0
OD2 A:ASP83 3.0 25.2 1.0
CE1 A:HIS63 3.0 26.8 1.0
CG A:HIS80 3.1 24.7 1.0
CG A:HIS63 3.1 23.6 1.0
CE1 A:HIS71 3.1 31.4 1.0
CG A:HIS71 3.2 34.7 1.0
CB A:HIS63 3.5 24.8 1.0
CB A:HIS71 3.5 31.0 1.0
CB A:HIS80 3.5 23.2 1.0
O A:LYS136 3.7 38.8 1.0
CA A:HIS71 4.0 30.9 1.0
NE2 A:HIS80 4.0 24.7 1.0
CD2 A:HIS80 4.1 28.3 1.0
NE2 A:HIS63 4.2 28.7 1.0
CD2 A:HIS63 4.2 24.8 1.0
CB A:ASP83 4.3 28.0 1.0
NE2 A:HIS71 4.3 29.8 1.0
CD2 A:HIS71 4.3 29.2 1.0
C A:LYS136 4.7 36.2 1.0
CA A:ASP83 4.7 24.2 1.0
N A:HIS80 4.8 24.2 1.0
CA A:HIS80 4.8 28.5 1.0
O A:HOH367 4.8 26.8 1.0
N A:GLY72 4.9 30.1 1.0
N A:ASP83 5.0 23.2 1.0
N A:HIS71 5.0 30.1 1.0
CA A:HIS63 5.0 24.1 1.0
C A:HIS71 5.0 34.8 1.0

Zinc binding site 2 out of 9 in 7xx3

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Zinc binding site 2 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:26.9
occ:1.00
 OD1 B:ASP83 2.0 20.2 1.0
ND1 B:HIS63 2.1 21.1 1.0
ND1 B:HIS80 2.1 17.7 1.0
ND1 B:HIS71 2.2 22.4 1.0
CG B:ASP83 2.8 17.9 1.0
CE1 B:HIS80 2.9 21.6 1.0
OD2 B:ASP83 2.9 22.1 1.0
CE1 B:HIS63 3.0 22.4 1.0
CG B:HIS80 3.0 19.4 1.0
CE1 B:HIS71 3.1 17.6 1.0
CG B:HIS63 3.1 22.8 1.0
CG B:HIS71 3.2 22.1 1.0
O B:HOH308 3.3 46.2 1.0
CB B:HIS63 3.4 22.0 1.0
CB B:HIS80 3.5 17.0 1.0
CB B:HIS71 3.6 20.7 1.0
O B:LYS136 3.8 24.2 1.0
NE2 B:HIS80 3.9 20.8 1.0
CA B:HIS71 4.0 19.7 1.0
CD2 B:HIS80 4.0 21.9 1.0
NE2 B:HIS63 4.2 23.4 1.0
CB B:ASP83 4.2 18.5 1.0
CD2 B:HIS63 4.2 22.6 1.0
NE2 B:HIS71 4.2 21.3 1.0
CD2 B:HIS71 4.3 16.1 1.0
CA B:ASP83 4.7 15.9 1.0
N B:HIS80 4.7 16.4 1.0
CA B:HIS80 4.7 17.6 1.0
C B:LYS136 4.8 23.4 1.0
N B:GLY72 4.8 17.4 1.0
N B:ASP83 4.9 18.1 1.0
O B:HOH357 4.9 25.4 1.0
CA B:HIS63 4.9 19.2 1.0
C B:HIS71 5.0 23.9 1.0

Zinc binding site 3 out of 9 in 7xx3

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Zinc binding site 3 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:45.5
occ:1.00
 OD1 D:ASP83 2.0 32.5 1.0
ND1 D:HIS80 2.1 52.1 1.0
ND1 D:HIS71 2.1 47.0 1.0
ND1 D:HIS63 2.1 48.5 1.0
CG D:ASP83 2.8 35.4 1.0
OD2 D:ASP83 2.9 41.5 1.0
CE1 D:HIS80 3.0 43.2 1.0
CE1 D:HIS71 3.0 45.1 1.0
CG D:HIS80 3.0 41.4 1.0
CE1 D:HIS63 3.1 45.3 1.0
CG D:HIS63 3.1 42.5 1.0
CG D:HIS71 3.2 47.2 1.0
CB D:HIS63 3.4 35.7 1.0
CB D:HIS80 3.5 39.0 1.0
CB D:HIS71 3.5 44.1 1.0
O D:LYS136 3.8 50.5 1.0
CA D:HIS71 3.9 38.6 1.0
NE2 D:HIS80 4.0 43.8 1.0
CD2 D:HIS80 4.1 47.7 1.0
NE2 D:HIS71 4.2 49.5 1.0
CB D:ASP83 4.2 34.8 1.0
NE2 D:HIS63 4.2 35.1 1.0
CD2 D:HIS71 4.2 44.0 1.0
CD2 D:HIS63 4.3 37.7 1.0
N D:HIS80 4.6 39.8 1.0
CA D:HIS80 4.7 33.4 1.0
CA D:ASP83 4.7 29.1 1.0
C D:LYS136 4.8 52.6 1.0
N D:GLY72 4.8 36.8 1.0
N D:HIS71 4.9 48.1 1.0
C D:HIS71 4.9 41.0 1.0
N D:ASP83 5.0 39.4 1.0
CA D:HIS63 5.0 27.1 1.0
O D:HOH365 5.0 42.1 1.0

Zinc binding site 4 out of 9 in 7xx3

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Zinc binding site 4 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:48.8
occ:1.00
 OD1 C:ASP83 2.0 27.0 1.0
ND1 C:HIS63 2.1 24.5 1.0
ND1 C:HIS80 2.2 25.4 1.0
ND1 C:HIS71 2.2 24.0 1.0
CG C:ASP83 2.8 15.9 1.0
OD2 C:ASP83 2.9 14.6 1.0
CE1 C:HIS80 3.0 20.0 1.0
CE1 C:HIS63 3.0 20.2 1.0
CE1 C:HIS71 3.1 17.5 1.0
CG C:HIS63 3.1 18.9 1.0
CG C:HIS80 3.1 20.7 1.0
CG C:HIS71 3.3 20.2 1.0
CB C:HIS63 3.4 21.4 1.0
CB C:HIS80 3.6 20.1 1.0
CB C:HIS71 3.6 19.7 1.0
O C:LYS136 3.7 24.7 1.0
CA C:HIS71 4.0 23.6 1.0
NE2 C:HIS80 4.1 19.7 1.0
NE2 C:HIS63 4.2 23.7 1.0
CD2 C:HIS80 4.2 23.3 1.0
CD2 C:HIS63 4.2 21.5 1.0
NE2 C:HIS71 4.2 19.9 1.0
CB C:ASP83 4.2 18.0 1.0
CD2 C:HIS71 4.3 19.2 1.0
CA C:ASP83 4.7 17.0 1.0
C C:LYS136 4.8 19.0 1.0
N C:HIS80 4.8 15.8 1.0
CA C:HIS80 4.8 13.4 1.0
N C:GLY72 4.8 17.0 1.0
O C:HOH371 4.9 25.3 1.0
CA C:HIS63 5.0 20.3 1.0
N C:ASP83 5.0 16.5 1.0
CD2 C:HIS46 5.0 17.6 1.0
C C:HIS71 5.0 21.3 1.0
N C:HIS71 5.0 22.0 1.0

Zinc binding site 5 out of 9 in 7xx3

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Zinc binding site 5 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:49.2
occ:1.00
 OD1 H:ASP83 2.0 52.4 1.0
ND1 H:HIS71 2.1 59.2 1.0
ND1 H:HIS80 2.1 59.0 1.0
OD2 H:ASP83 2.1 58.7 1.0
ND1 H:HIS63 2.1 53.7 1.0
CG H:ASP83 2.3 53.2 1.0
CE1 H:HIS71 2.9 53.5 1.0
CE1 H:HIS80 3.0 46.7 1.0
CE1 H:HIS63 3.0 39.8 1.0
CG H:HIS63 3.1 38.6 1.0
CG H:HIS80 3.1 49.6 1.0
CG H:HIS71 3.2 56.5 1.0
CB H:HIS63 3.4 35.9 1.0
CB H:HIS80 3.5 39.7 1.0
CB H:HIS71 3.6 54.5 1.0
CB H:ASP83 3.9 43.3 1.0
CA H:HIS71 3.9 53.8 1.0
NE2 H:HIS71 4.1 52.8 1.0
NE2 H:HIS80 4.1 48.0 1.0
NE2 H:HIS63 4.2 42.6 1.0
O H:LYS136 4.2 58.2 1.0
CD2 H:HIS63 4.2 43.3 1.0
CD2 H:HIS80 4.2 48.7 1.0
CD2 H:HIS71 4.2 49.5 1.0
N H:HIS80 4.6 48.7 1.0
N H:GLY72 4.6 55.3 1.0
CA H:ASP83 4.6 34.4 1.0
CA H:HIS80 4.7 42.3 1.0
C H:HIS71 4.8 53.9 1.0
CD2 H:HIS46 4.8 44.7 1.0
O H:GLY72 4.9 52.5 1.0
N H:ASP83 4.9 38.0 1.0
CA H:HIS63 5.0 29.1 1.0
N H:HIS71 5.0 54.1 1.0

Zinc binding site 6 out of 9 in 7xx3

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Zinc binding site 6 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:38.0
occ:1.00
 OD1 E:ASP83 1.9 17.3 1.0
ND1 E:HIS80 2.1 22.4 1.0
ND1 E:HIS63 2.1 22.2 1.0
ND1 E:HIS71 2.1 22.9 1.0
OD2 E:ASP83 2.6 21.6 1.0
CG E:ASP83 2.6 20.5 1.0
CE1 E:HIS80 2.9 21.2 1.0
CE1 E:HIS71 3.0 22.8 1.0
CE1 E:HIS63 3.0 22.0 1.0
CG E:HIS80 3.0 21.8 1.0
CG E:HIS63 3.1 17.7 1.0
CG E:HIS71 3.2 23.6 1.0
CB E:HIS80 3.4 19.1 1.0
CB E:HIS63 3.5 20.0 1.0
CB E:HIS71 3.6 19.3 1.0
O E:LYS136 3.8 22.5 1.0
CA E:HIS71 4.0 20.6 1.0
NE2 E:HIS80 4.0 20.8 1.0
CD2 E:HIS80 4.0 19.2 1.0
CB E:ASP83 4.1 19.7 1.0
NE2 E:HIS63 4.1 22.9 1.0
NE2 E:HIS71 4.2 18.9 1.0
CD2 E:HIS63 4.2 22.6 1.0
CD2 E:HIS71 4.3 18.0 1.0
CA E:ASP83 4.6 19.8 1.0
N E:HIS80 4.7 21.7 1.0
CA E:HIS80 4.7 19.7 1.0
N E:GLY72 4.8 16.9 1.0
C E:LYS136 4.8 23.1 1.0
N E:ASP83 4.9 20.8 1.0
C E:HIS71 4.9 20.9 1.0
N E:HIS71 5.0 22.7 1.0

Zinc binding site 7 out of 9 in 7xx3

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Zinc binding site 7 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:53.7
occ:1.00
 OD1 F:ASP83 2.0 53.6 1.0
ND1 F:HIS63 2.0 49.6 1.0
ND1 F:HIS80 2.0 55.4 1.0
ND1 F:HIS71 2.1 57.0 1.0
CE1 F:HIS80 2.9 44.9 1.0
CE1 F:HIS63 2.9 43.0 1.0
CG F:ASP83 2.9 47.3 1.0
CE1 F:HIS71 3.0 47.8 1.0
CG F:HIS80 3.1 45.0 1.0
CG F:HIS63 3.1 42.5 1.0
CG F:HIS71 3.1 50.6 1.0
OD2 F:ASP83 3.2 42.4 1.0
CB F:HIS71 3.4 47.5 1.0
CB F:HIS63 3.5 39.0 1.0
CB F:HIS80 3.5 43.3 1.0
O F:LYS136 3.7 51.6 1.0
CA F:HIS71 3.9 50.6 1.0
NE2 F:HIS80 4.0 46.9 1.0
NE2 F:HIS63 4.0 41.9 1.0
CD2 F:HIS80 4.1 43.8 1.0
CD2 F:HIS63 4.1 42.2 1.0
NE2 F:HIS71 4.2 51.8 1.0
CD2 F:HIS71 4.2 51.4 1.0
CB F:ASP83 4.3 38.5 1.0
N F:HIS80 4.6 49.8 1.0
CA F:ASP83 4.7 39.3 1.0
CA F:HIS80 4.7 46.3 1.0
O F:HOH350 4.7 51.4 1.0
CD2 F:HIS46 4.8 37.4 1.0
N F:GLY72 4.8 47.9 1.0
C F:LYS136 4.9 46.2 1.0
C F:HIS71 4.9 50.2 1.0
N F:HIS71 4.9 49.0 1.0
N F:ASP83 5.0 40.2 1.0

Zinc binding site 8 out of 9 in 7xx3

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Zinc binding site 8 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:48.8
occ:1.00
 OD1 G:ASP83 2.0 34.9 1.0
ND1 G:HIS80 2.1 32.8 1.0
ND1 G:HIS71 2.1 36.5 1.0
ND1 G:HIS63 2.1 33.8 1.0
OD2 G:ASP83 2.4 30.6 1.0
CG G:ASP83 2.5 29.3 1.0
CE1 G:HIS80 3.0 27.5 1.0
CE1 G:HIS71 3.0 26.8 1.0
CG G:HIS80 3.1 28.7 1.0
CE1 G:HIS63 3.1 30.8 1.0
CG G:HIS63 3.1 29.9 1.0
CG G:HIS71 3.2 30.9 1.0
CB G:HIS63 3.5 33.7 1.0
CB G:HIS80 3.5 31.4 1.0
CB G:HIS71 3.5 29.8 1.0
CA G:HIS71 3.9 31.1 1.0
O G:LYS136 3.9 38.4 1.0
CB G:ASP83 4.0 29.0 1.0
NE2 G:HIS80 4.1 36.3 1.0
CD2 G:HIS80 4.1 31.1 1.0
NE2 G:HIS71 4.2 29.8 1.0
NE2 G:HIS63 4.2 38.7 1.0
CD2 G:HIS71 4.2 29.6 1.0
CD2 G:HIS63 4.3 33.3 1.0
N G:HIS80 4.6 31.0 1.0
CA G:ASP83 4.6 33.9 1.0
CA G:HIS80 4.7 32.4 1.0
N G:GLY72 4.7 36.5 1.0
O G:HOH344 4.8 42.1 1.0
C G:HIS71 4.9 34.7 1.0
N G:ASP83 4.9 32.6 1.0
CD2 G:HIS46 4.9 31.4 1.0
N G:HIS71 4.9 31.9 1.0
C G:LYS136 4.9 33.6 1.0
CA G:HIS63 5.0 33.4 1.0

Zinc binding site 9 out of 9 in 7xx3

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Zinc binding site 9 out of 9 in the Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Human Superoxide Dismutase (SOD1) in Complex with A Fungal Metabolite Molecule, Phialomustin B (Pb) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:52.0
occ:1.00
 OD1 I:ASP83 2.0 30.7 1.0
ND1 I:HIS71 2.1 34.7 1.0
ND1 I:HIS63 2.1 31.1 1.0
ND1 I:HIS80 2.1 28.3 1.0
CG I:ASP83 2.8 29.0 1.0
CE1 I:HIS80 2.9 26.6 1.0
OD2 I:ASP83 2.9 24.4 1.0
CE1 I:HIS71 3.0 26.2 1.0
CE1 I:HIS63 3.0 26.7 1.0
CG I:HIS63 3.1 26.4 1.0
CG I:HIS80 3.1 25.9 1.0
CG I:HIS71 3.1 28.6 1.0
CB I:HIS63 3.4 23.1 1.0
CB I:HIS71 3.5 26.9 1.0
CB I:HIS80 3.6 31.3 1.0
O I:LYS136 3.7 27.8 1.0
CA I:HIS71 3.9 28.1 1.0
NE2 I:HIS80 4.0 31.6 1.0
NE2 I:HIS71 4.1 29.9 1.0
CD2 I:HIS80 4.1 31.4 1.0
NE2 I:HIS63 4.2 27.8 1.0
CD2 I:HIS63 4.2 24.6 1.0
CD2 I:HIS71 4.2 27.4 1.0
CB I:ASP83 4.2 24.6 1.0
CA I:ASP83 4.7 26.5 1.0
C I:LYS136 4.7 28.2 1.0
N I:HIS80 4.7 29.9 1.0
CA I:HIS80 4.8 24.5 1.0
N I:GLY72 4.8 25.8 1.0
C I:HIS71 4.9 30.8 1.0
CA I:HIS63 4.9 24.9 1.0
N I:HIS71 4.9 32.6 1.0
O I:HOH362 5.0 28.4 1.0

Reference:

S.Unni, B.Padmanabhan. Phialomustin-B A Fungal Metabolite Isolated From Phialophora Mustea Modulates Superoxide Dismutase 1 (SOD1) Aggregation: Therapeutic Potential in Amyotrophic Lateral Sclerosis (Als) To Be Published.
Page generated: Wed Oct 30 15:21:35 2024

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