Atomistry » Zinc » PDB 5ynq-5yxc » 5yto
Atomistry »
  Zinc »
    PDB 5ynq-5yxc »
      5yto »

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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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

Go back to Zinc Binding Sites List in 5yto
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: Mon Oct 28 16:18:26 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy