Zinc in PDB 5yto: Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.

Enzymatic activity of Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.

All present enzymatic activity of Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound., PDB code: 5yto was solved by B.Padmanabhan, R.Manjula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 63 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 243.941, 243.941, 144.775, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. (pdb code 5yto). 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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound., PDB code: 5yto:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5yto

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Zinc binding site 1 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:34.3
occ:1.00
 OD1 A:ASP83 2.0 20.1 1.0
ND1 A:HIS63 2.0 22.7 1.0
ND1 A:HIS80 2.1 22.9 1.0
ND1 A:HIS71 2.3 25.2 1.0
CG A:ASP83 2.9 21.1 1.0
CE1 A:HIS80 2.9 23.7 1.0
CG A:HIS63 3.0 20.6 1.0
CE1 A:HIS63 3.0 21.9 1.0
OD2 A:ASP83 3.0 24.9 1.0
CG A:HIS80 3.1 24.4 1.0
CE1 A:HIS71 3.2 28.5 1.0
CB A:HIS63 3.3 22.1 1.0
CG A:HIS71 3.3 28.7 1.0
CB A:HIS80 3.6 23.8 1.0
CB A:HIS71 3.7 27.5 1.0
O A:LYS136 3.8 32.4 1.0
NE2 A:HIS80 4.0 24.7 1.0
CA A:HIS71 4.0 28.6 1.0
CD2 A:HIS80 4.1 24.9 1.0
NE2 A:HIS63 4.1 21.6 1.0
CD2 A:HIS63 4.1 20.5 1.0
CB A:ASP83 4.3 21.0 1.0
NE2 A:HIS71 4.3 29.0 1.0
CD2 A:HIS71 4.4 24.2 1.0
CA A:ASP83 4.7 21.8 1.0
O A:HOH402 4.7 26.2 1.0
N A:HIS80 4.7 24.5 1.0
CA A:HIS80 4.8 25.8 1.0
C A:LYS136 4.8 33.5 1.0
N A:ASP83 4.9 20.8 1.0
CA A:HIS63 4.9 19.7 1.0
N A:GLY72 4.9 26.2 1.0

Zinc binding site 2 out of 9 in 5yto

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Zinc binding site 2 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:24.1
occ:1.00
 OD1 B:ASP83 1.9 16.9 1.0
ND1 B:HIS63 2.0 17.9 1.0
ND1 B:HIS80 2.0 16.0 1.0
ND1 B:HIS71 2.2 18.7 1.0
CG B:ASP83 2.8 16.0 1.0
CE1 B:HIS80 2.9 18.3 1.0
OD2 B:ASP83 2.9 16.2 1.0
CE1 B:HIS63 3.0 18.7 1.0
CE1 B:HIS71 3.0 15.7 1.0
CG B:HIS63 3.0 19.0 1.0
CG B:HIS80 3.1 16.2 1.0
CG B:HIS71 3.3 18.3 1.0
CB B:HIS63 3.4 18.3 1.0
CB B:HIS80 3.6 14.3 1.0
CB B:HIS71 3.7 19.4 1.0
O B:LYS136 3.9 23.1 1.0
CA B:HIS71 4.0 20.1 1.0
NE2 B:HIS80 4.0 16.7 1.0
CD2 B:HIS80 4.1 17.5 1.0
NE2 B:HIS63 4.1 20.1 1.0
CD2 B:HIS63 4.2 19.8 1.0
CB B:ASP83 4.2 15.5 1.0
NE2 B:HIS71 4.2 16.8 1.0
CD2 B:HIS71 4.3 16.4 1.0
CA B:ASP83 4.7 14.1 1.0
N B:HIS80 4.7 14.6 1.0
CA B:HIS80 4.8 15.3 1.0
N B:GLY72 4.8 16.8 1.0
O B:HOH405 4.8 23.3 1.0
C B:LYS136 4.9 20.9 1.0
N B:ASP83 4.9 15.3 1.0
CA B:HIS63 4.9 18.4 1.0
C B:HIS71 4.9 20.4 1.0
N B:HIS71 5.0 18.2 1.0

Zinc binding site 3 out of 9 in 5yto

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Zinc binding site 3 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:23.5
occ:1.00
 OD1 C:ASP83 2.0 16.6 1.0
ND1 C:HIS63 2.0 19.0 1.0
ND1 C:HIS80 2.1 16.1 1.0
ND1 C:HIS71 2.2 16.6 1.0
CG C:ASP83 2.8 15.7 1.0
CE1 C:HIS80 2.9 17.5 1.0
CE1 C:HIS63 2.9 18.0 1.0
OD2 C:ASP83 2.9 16.0 1.0
CE1 C:HIS71 3.0 17.5 1.0
CG C:HIS63 3.0 18.9 1.0
CG C:HIS80 3.1 16.9 1.0
CG C:HIS71 3.2 17.6 1.0
CB C:HIS63 3.4 19.2 1.0
CB C:HIS80 3.6 15.7 1.0
CB C:HIS71 3.6 18.0 1.0
O C:LYS136 3.8 21.0 1.0
CA C:HIS71 4.0 19.8 1.0
NE2 C:HIS80 4.0 16.9 1.0
NE2 C:HIS63 4.0 20.0 1.0
CD2 C:HIS63 4.1 20.1 1.0
CD2 C:HIS80 4.1 16.3 1.0
CB C:ASP83 4.2 15.3 1.0
NE2 C:HIS71 4.2 16.8 1.0
CD2 C:HIS71 4.3 17.9 1.0
CA C:ASP83 4.7 15.7 1.0
N C:HIS80 4.8 16.9 1.0
CA C:HIS80 4.8 16.7 1.0
C C:LYS136 4.9 18.3 1.0
O C:HOH396 4.9 26.1 1.0
N C:GLY72 4.9 17.0 1.0
N C:ASP83 4.9 14.3 1.0
CA C:HIS63 4.9 18.2 1.0
C C:HIS71 5.0 19.8 1.0
N C:HIS71 5.0 19.6 1.0

Zinc binding site 4 out of 9 in 5yto

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Zinc binding site 4 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:34.7
occ:1.00
 OD1 D:ASP83 1.8 30.4 1.0
ND1 D:HIS80 2.0 36.3 1.0
ND1 D:HIS71 2.2 33.6 1.0
ND1 D:HIS63 2.3 28.6 1.0
CG D:ASP83 2.7 29.9 1.0
OD2 D:ASP83 2.8 31.3 1.0
CE1 D:HIS80 2.9 35.0 1.0
CE1 D:HIS71 3.0 34.3 1.0
CG D:HIS80 3.1 31.6 1.0
CG D:HIS63 3.2 30.6 1.0
CG D:HIS71 3.3 36.9 1.0
CE1 D:HIS63 3.3 31.4 1.0
CB D:HIS63 3.4 27.9 1.0
CB D:HIS80 3.5 30.8 1.0
CB D:HIS71 3.7 37.0 1.0
NE2 D:HIS80 4.0 33.0 1.0
CA D:HIS71 4.0 33.4 1.0
O D:LYS136 4.1 38.2 1.0
CD2 D:HIS80 4.1 35.1 1.0
CB D:ASP83 4.1 30.5 1.0
NE2 D:HIS71 4.2 35.8 1.0
CD2 D:HIS71 4.4 36.1 1.0
CD2 D:HIS63 4.4 27.7 1.0
NE2 D:HIS63 4.4 30.8 1.0
N D:HIS80 4.6 31.6 1.0
CA D:HIS80 4.7 28.3 1.0
CA D:ASP83 4.7 26.7 1.0
N D:GLY72 4.8 31.7 1.0
N D:ASP83 4.9 29.1 1.0
CA D:HIS63 4.9 26.7 1.0
O D:HOH375 5.0 32.6 1.0
C D:HIS71 5.0 35.4 1.0
N D:HIS71 5.0 38.1 1.0

Zinc binding site 5 out of 9 in 5yto

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Zinc binding site 5 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:24.1
occ:1.00
 OD1 E:ASP83 1.9 15.4 1.0
ND1 E:HIS80 2.0 16.1 1.0
ND1 E:HIS63 2.0 19.4 1.0
ND1 E:HIS71 2.2 19.7 1.0
CG E:ASP83 2.8 16.5 1.0
CE1 E:HIS80 2.8 17.7 1.0
OD2 E:ASP83 2.9 16.6 1.0
CE1 E:HIS63 3.0 17.5 1.0
CE1 E:HIS71 3.0 18.6 1.0
CG E:HIS63 3.0 18.4 1.0
CG E:HIS80 3.1 16.6 1.0
CG E:HIS71 3.3 19.1 1.0
CB E:HIS63 3.4 17.9 1.0
CB E:HIS80 3.5 15.8 1.0
CB E:HIS71 3.7 17.8 1.0
O E:LYS136 3.8 21.7 1.0
NE2 E:HIS80 3.9 18.2 1.0
CA E:HIS71 4.0 20.5 1.0
CD2 E:HIS80 4.1 16.7 1.0
NE2 E:HIS63 4.1 19.7 1.0
CD2 E:HIS63 4.2 20.2 1.0
CB E:ASP83 4.2 16.1 1.0
NE2 E:HIS71 4.2 19.1 1.0
CD2 E:HIS71 4.3 18.0 1.0
CA E:ASP83 4.6 16.0 1.0
N E:HIS80 4.7 18.5 1.0
CA E:HIS80 4.8 17.3 1.0
N E:GLY72 4.8 16.0 1.0
C E:LYS136 4.8 20.6 1.0
O E:HOH358 4.9 23.5 1.0
N E:ASP83 4.9 17.0 1.0
C E:HIS71 4.9 19.6 1.0
CA E:HIS63 5.0 17.5 1.0
N E:HIS71 5.0 20.6 1.0

Zinc binding site 6 out of 9 in 5yto

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Zinc binding site 6 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:40.0
occ:1.00
 ND1 F:HIS80 1.9 32.9 1.0
OD1 F:ASP83 1.9 33.0 1.0
ND1 F:HIS63 2.2 34.0 1.0
ND1 F:HIS71 2.3 39.2 1.0
CG F:ASP83 2.7 34.8 1.0
CE1 F:HIS80 2.8 36.3 1.0
OD2 F:ASP83 2.9 39.3 1.0
CG F:HIS80 2.9 37.8 1.0
CG F:HIS63 3.1 33.7 1.0
CE1 F:HIS63 3.2 36.2 1.0
CE1 F:HIS71 3.2 43.5 1.0
CG F:HIS71 3.3 43.4 1.0
CB F:HIS63 3.3 30.9 1.0
CB F:HIS80 3.4 31.7 1.0
CB F:HIS71 3.5 44.2 1.0
CA F:HIS71 3.9 44.0 1.0
NE2 F:HIS80 3.9 32.9 1.0
O F:LYS136 3.9 45.8 1.0
CD2 F:HIS80 4.0 38.0 1.0
CB F:ASP83 4.1 33.2 1.0
CD2 F:HIS63 4.2 37.9 1.0
NE2 F:HIS63 4.3 35.2 1.0
NE2 F:HIS71 4.4 45.5 1.0
CD2 F:HIS71 4.4 43.1 1.0
N F:HIS80 4.5 35.1 1.0
CA F:ASP83 4.6 32.0 1.0
CA F:HIS80 4.6 33.4 1.0
N F:GLY72 4.7 41.3 1.0
CD2 F:HIS46 4.8 37.5 1.0
C F:HIS71 4.8 44.5 1.0
CA F:HIS63 4.8 29.4 1.0
N F:ASP83 4.9 32.7 1.0
C F:LYS136 4.9 48.7 1.0
N F:HIS71 4.9 42.5 1.0
O F:HOH374 5.0 35.1 1.0

Zinc binding site 7 out of 9 in 5yto

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Zinc binding site 7 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:27.9
occ:1.00
 OD1 G:ASP83 2.0 26.4 1.0
ND1 G:HIS80 2.0 23.1 1.0
ND1 G:HIS63 2.1 25.4 1.0
ND1 G:HIS71 2.2 25.4 1.0
CG G:ASP83 2.7 25.6 1.0
OD2 G:ASP83 2.8 26.3 1.0
CE1 G:HIS80 2.9 24.5 1.0
CG G:HIS63 3.0 25.3 1.0
CE1 G:HIS71 3.1 24.9 1.0
CG G:HIS80 3.1 23.3 1.0
CE1 G:HIS63 3.2 24.7 1.0
CG G:HIS71 3.2 26.4 1.0
CB G:HIS63 3.3 27.2 1.0
CB G:HIS80 3.5 24.6 1.0
CB G:HIS71 3.6 25.6 1.0
O G:LYS136 3.9 31.8 1.0
CA G:HIS71 4.0 27.6 1.0
NE2 G:HIS80 4.0 24.6 1.0
CD2 G:HIS80 4.1 24.7 1.0
CB G:ASP83 4.2 24.4 1.0
CD2 G:HIS63 4.2 27.3 1.0
NE2 G:HIS71 4.2 26.3 1.0
NE2 G:HIS63 4.2 28.6 1.0
CD2 G:HIS71 4.3 25.6 1.0
N G:HIS80 4.6 28.1 1.0
CA G:ASP83 4.7 27.8 1.0
CA G:HIS80 4.7 26.6 1.0
O G:HOH356 4.8 32.9 1.0
N G:GLY72 4.8 27.7 1.0
CA G:HIS63 4.9 26.8 1.0
C G:LYS136 4.9 28.5 1.0
N G:ASP83 4.9 26.9 1.0
C G:HIS71 4.9 29.1 1.0
CD2 G:HIS46 4.9 25.8 1.0
N G:HIS71 5.0 27.9 1.0

Zinc binding site 8 out of 9 in 5yto

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Zinc binding site 8 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:35.1
occ:1.00
 ND1 H:HIS63 1.9 30.6 1.0
OD1 H:ASP83 2.0 34.5 1.0
ND1 H:HIS80 2.1 32.9 1.0
ND1 H:HIS71 2.2 33.5 1.0
CG H:ASP83 2.9 33.5 1.0
CE1 H:HIS80 2.9 31.3 1.0
CG H:HIS63 2.9 32.6 1.0
CE1 H:HIS63 2.9 31.1 1.0
OD2 H:ASP83 3.0 31.6 1.0
CE1 H:HIS71 3.1 32.9 1.0
CG H:HIS80 3.1 34.9 1.0
CB H:HIS63 3.2 33.5 1.0
CG H:HIS71 3.3 36.7 1.0
CB H:HIS80 3.6 31.2 1.0
CB H:HIS71 3.6 35.9 1.0
O H:LYS136 3.9 38.0 1.0
CA H:HIS71 4.0 38.1 1.0
NE2 H:HIS80 4.0 29.4 1.0
CD2 H:HIS63 4.0 30.1 1.0
NE2 H:HIS63 4.0 32.3 1.0
CD2 H:HIS80 4.1 32.4 1.0
CB H:ASP83 4.2 29.5 1.0
NE2 H:HIS71 4.3 34.7 1.0
CD2 H:HIS71 4.4 35.7 1.0
N H:HIS80 4.6 34.5 1.0
CA H:ASP83 4.7 27.6 1.0
O H:HOH388 4.7 39.5 1.0
CA H:HIS80 4.7 35.6 1.0
CD2 H:HIS46 4.8 30.2 1.0
N H:GLY72 4.8 36.8 1.0
CA H:HIS63 4.8 36.4 1.0
C H:HIS71 4.9 38.7 1.0
C H:LYS136 5.0 36.5 1.0
N H:ASP83 5.0 28.0 1.0
N H:HIS71 5.0 35.2 1.0

Zinc binding site 9 out of 9 in 5yto

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Zinc binding site 9 out of 9 in the Crystal Structure of Human Superoxide Dismutase I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound.


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 I (HSOD1) in Complex with A Napthalene-Catechol Linked Compound. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:29.4
occ:1.00
 OD1 I:ASP83 2.0 23.9 1.0
ND1 I:HIS80 2.1 24.0 1.0
ND1 I:HIS63 2.1 26.6 1.0
ND1 I:HIS71 2.1 26.1 1.0
CG I:ASP83 2.8 26.1 1.0
OD2 I:ASP83 2.9 24.2 1.0
CE1 I:HIS80 3.0 25.1 1.0
CE1 I:HIS71 3.0 25.8 1.0
CE1 I:HIS63 3.1 25.5 1.0
CG I:HIS80 3.1 23.6 1.0
CG I:HIS63 3.1 25.3 1.0
CG I:HIS71 3.2 26.0 1.0
CB I:HIS63 3.4 24.7 1.0
CB I:HIS80 3.5 25.4 1.0
CB I:HIS71 3.6 25.3 1.0
O I:LYS136 3.8 30.2 1.0
CA I:HIS71 3.9 26.4 1.0
NE2 I:HIS80 4.1 24.7 1.0
CD2 I:HIS80 4.1 23.7 1.0
CB I:ASP83 4.2 25.0 1.0
NE2 I:HIS71 4.2 24.3 1.0
NE2 I:HIS63 4.2 26.8 1.0
CD2 I:HIS63 4.2 23.9 1.0
CD2 I:HIS71 4.3 23.9 1.0
N I:HIS80 4.7 25.7 1.0
CA I:ASP83 4.7 24.7 1.0
CA I:HIS80 4.7 25.7 1.0
N I:GLY72 4.8 25.6 1.0
C I:LYS136 4.8 27.9 1.0
O I:HOH371 4.9 28.3 1.0
C I:HIS71 4.9 29.3 1.0
CA I:HIS63 4.9 24.8 1.0
N I:HIS71 4.9 30.8 1.0
N I:ASP83 4.9 25.4 1.0

Reference:

R.Manjula, G.S.A.Wright, R.W.Strange, B.Padmanabhan. Assessment of Ligand Binding at A Site Relevant to SOD1 Oxidation and Aggregation Febs Lett. V. 592 1725 2018.
ISSN: ISSN 1873-3468
PubMed: 29679384
DOI: 10.1002/1873-3468.13055
Page generated: Wed Dec 16 11:24:30 2020

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