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Zinc in PDB 3t5w: 2ME Modified Human SOD1

Enzymatic activity of 2ME Modified Human SOD1

All present enzymatic activity of 2ME Modified Human SOD1:
1.15.1.1;

Protein crystallography data

The structure of 2ME Modified Human SOD1, PDB code: 3t5w was solved by K.Ihara, Y.Yamaguchi, H.Torigoe, S.Wakatsuki, N.Taniguchi, K.Suzuki, N.Fujiwara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.04 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.086, 163.277, 173.628, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.1

Other elements in 3t5w:

The structure of 2ME Modified Human SOD1 also contains other interesting chemical elements:

Copper (Cu) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the 2ME Modified Human SOD1 (pdb code 3t5w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the 2ME Modified Human SOD1, PDB code: 3t5w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 3t5w

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Zinc binding site 1 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:5.4
occ:1.00
OD1 A:ASP83 1.9 3.5 1.0
ND1 A:HIS63 2.1 5.3 1.0
ND1 A:HIS71 2.1 6.8 1.0
ND1 A:HIS80 2.1 3.5 1.0
CG A:ASP83 2.8 4.9 1.0
OD2 A:ASP83 2.9 2.4 1.0
CE1 A:HIS80 3.0 5.8 1.0
CE1 A:HIS71 3.0 6.9 1.0
CE1 A:HIS63 3.0 4.3 1.0
CG A:HIS63 3.1 5.0 1.0
CG A:HIS80 3.1 6.3 1.0
CG A:HIS71 3.2 6.0 1.0
CB A:HIS63 3.4 3.6 1.0
CB A:HIS80 3.6 4.3 1.0
CB A:HIS71 3.6 6.2 1.0
O A:LYS136 3.8 7.9 1.0
CA A:HIS71 3.9 6.7 1.0
NE2 A:HIS80 4.1 5.5 1.0
NE2 A:HIS63 4.1 3.2 1.0
NE2 A:HIS71 4.1 6.5 1.0
CB A:ASP83 4.2 5.5 1.0
CD2 A:HIS80 4.2 3.3 1.0
CD2 A:HIS63 4.2 2.0 1.0
CD2 A:HIS71 4.3 5.7 1.0
N A:HIS80 4.7 6.3 1.0
CA A:ASP83 4.7 5.1 1.0
C A:LYS136 4.7 8.8 1.0
N A:GLY72 4.7 6.8 1.0
CA A:HIS80 4.7 4.9 1.0
O A:HOH167 4.8 5.4 1.0
CD2 A:HIS46 4.9 2.0 1.0
C A:HIS71 4.9 6.8 1.0
N A:HIS71 4.9 7.4 1.0
CA A:HIS63 4.9 3.7 1.0
N A:ASP83 4.9 4.8 1.0

Zinc binding site 2 out of 12 in 3t5w

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Zinc binding site 2 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:4.2
occ:1.00
OD1 B:ASP83 2.0 4.2 1.0
ND1 B:HIS63 2.1 2.9 1.0
ND1 B:HIS80 2.1 4.8 1.0
ND1 B:HIS71 2.1 3.7 1.0
CG B:ASP83 2.8 3.1 1.0
OD2 B:ASP83 2.9 2.0 1.0
CE1 B:HIS71 3.0 3.4 1.0
CE1 B:HIS80 3.0 5.0 1.0
CE1 B:HIS63 3.0 3.6 1.0
CG B:HIS63 3.1 3.3 1.0
CG B:HIS80 3.2 3.1 1.0
CG B:HIS71 3.2 4.2 1.0
CB B:HIS63 3.4 2.8 1.0
CB B:HIS80 3.5 2.7 1.0
CB B:HIS71 3.7 3.4 1.0
O B:LYS136 3.8 4.5 1.0
CA B:HIS71 4.0 4.0 1.0
NE2 B:HIS80 4.1 4.4 1.0
NE2 B:HIS71 4.1 4.3 1.0
NE2 B:HIS63 4.2 4.7 1.0
CB B:ASP83 4.2 3.6 1.0
CD2 B:HIS63 4.2 2.0 1.0
CD2 B:HIS80 4.2 2.0 1.0
CD2 B:HIS71 4.3 4.2 1.0
CA B:ASP83 4.7 3.6 1.0
N B:HIS80 4.7 3.9 1.0
N B:GLY72 4.7 4.7 1.0
CA B:HIS80 4.8 2.9 1.0
C B:LYS136 4.8 5.3 1.0
C B:HIS71 4.9 4.3 1.0
CA B:HIS63 4.9 3.3 1.0
O B:HOH160 4.9 4.9 1.0
CD2 B:HIS46 4.9 5.4 1.0
N B:ASP83 5.0 3.8 1.0
N B:HIS71 5.0 4.4 1.0

Zinc binding site 3 out of 12 in 3t5w

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Zinc binding site 3 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:5.5
occ:1.00
OD1 D:ASP83 2.0 5.3 1.0
ND1 D:HIS63 2.1 2.0 1.0
ND1 D:HIS80 2.1 3.7 1.0
ND1 D:HIS71 2.1 5.9 1.0
CG D:ASP83 2.8 5.7 1.0
OD2 D:ASP83 2.9 2.0 1.0
CE1 D:HIS71 2.9 4.3 1.0
CE1 D:HIS80 3.0 6.5 1.0
CE1 D:HIS63 3.0 4.0 1.0
CG D:HIS63 3.1 4.0 1.0
CG D:HIS80 3.2 4.2 1.0
CG D:HIS71 3.3 6.8 1.0
CB D:HIS63 3.4 2.8 1.0
CB D:HIS80 3.6 5.8 1.0
CB D:HIS71 3.7 5.3 1.0
O D:LYS136 3.7 4.8 1.0
CA D:HIS71 4.0 6.4 1.0
NE2 D:HIS71 4.1 3.3 1.0
NE2 D:HIS80 4.1 6.2 1.0
NE2 D:HIS63 4.2 4.2 1.0
CB D:ASP83 4.2 5.7 1.0
CD2 D:HIS63 4.2 2.0 1.0
CD2 D:HIS80 4.2 5.1 1.0
CD2 D:HIS71 4.3 5.2 1.0
N D:GLY72 4.7 6.0 1.0
CA D:ASP83 4.7 5.1 1.0
C D:LYS136 4.7 6.3 1.0
N D:HIS80 4.7 5.0 1.0
CA D:HIS80 4.8 5.3 1.0
C D:HIS71 4.9 6.5 1.0
CD2 D:HIS46 4.9 4.4 1.0
N D:ASP83 4.9 5.2 1.0
CA D:HIS63 4.9 3.2 1.0
O D:HOH307 5.0 6.0 1.0
N D:HIS71 5.0 5.8 1.0

Zinc binding site 4 out of 12 in 3t5w

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Zinc binding site 4 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:5.3
occ:1.00
OD1 E:ASP83 2.0 4.8 1.0
ND1 E:HIS63 2.1 3.7 1.0
ND1 E:HIS80 2.1 4.9 1.0
ND1 E:HIS71 2.1 3.7 1.0
CG E:ASP83 2.8 6.2 1.0
OD2 E:ASP83 2.9 4.0 1.0
CE1 E:HIS71 2.9 2.6 1.0
CE1 E:HIS80 3.0 4.6 1.0
CE1 E:HIS63 3.0 4.9 1.0
CG E:HIS63 3.1 3.7 1.0
CG E:HIS80 3.1 2.9 1.0
CG E:HIS71 3.2 5.2 1.0
CB E:HIS63 3.4 3.6 1.0
CB E:HIS80 3.5 3.5 1.0
CB E:HIS71 3.6 5.4 1.0
O E:LYS136 3.7 7.9 1.0
CA E:HIS71 4.0 5.7 1.0
NE2 E:HIS80 4.1 6.1 1.0
NE2 E:HIS71 4.1 4.5 1.0
NE2 E:HIS63 4.1 3.7 1.0
CD2 E:HIS80 4.2 4.5 1.0
CD2 E:HIS63 4.2 4.2 1.0
CB E:ASP83 4.2 5.6 1.0
CD2 E:HIS71 4.3 2.0 1.0
CA E:ASP83 4.7 5.5 1.0
C E:LYS136 4.7 8.6 1.0
N E:GLY72 4.8 5.7 1.0
N E:HIS80 4.8 3.8 1.0
CA E:HIS80 4.8 3.1 1.0
N E:ASP83 4.9 5.1 1.0
C E:HIS71 4.9 6.1 1.0
CD2 E:HIS46 4.9 3.1 1.0
CA E:HIS63 5.0 4.0 1.0
N E:HIS71 5.0 6.6 1.0

Zinc binding site 5 out of 12 in 3t5w

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Zinc binding site 5 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn300

b:11.5
occ:1.00
OD1 F:ASP83 2.0 9.5 1.0
ND1 F:HIS80 2.1 13.6 1.0
ND1 F:HIS63 2.1 9.0 1.0
ND1 F:HIS71 2.1 10.9 1.0
CE1 F:HIS80 2.6 12.5 1.0
CG F:ASP83 2.8 8.7 1.0
OD2 F:ASP83 2.9 7.7 1.0
CE1 F:HIS71 3.0 10.5 1.0
CE1 F:HIS63 3.1 10.6 1.0
CG F:HIS63 3.1 10.1 1.0
CG F:HIS71 3.2 12.7 1.0
CG F:HIS80 3.3 12.2 1.0
CB F:HIS63 3.4 10.2 1.0
CB F:HIS71 3.7 12.5 1.0
O F:LYS136 3.8 14.6 1.0
NE2 F:HIS80 3.8 12.3 1.0
CA F:HIS71 3.9 11.7 1.0
CB F:HIS80 4.0 11.1 1.0
NE2 F:HIS71 4.1 12.8 1.0
CD2 F:HIS80 4.2 10.8 1.0
NE2 F:HIS63 4.2 8.8 1.0
CD2 F:HIS63 4.2 9.6 1.0
CB F:ASP83 4.2 8.6 1.0
CD2 F:HIS71 4.3 11.5 1.0
N F:GLY72 4.7 10.7 1.0
CA F:ASP83 4.8 8.9 1.0
C F:LYS136 4.8 14.3 1.0
N F:HIS80 4.9 10.5 1.0
C F:HIS71 4.9 11.8 1.0
CD2 F:HIS46 4.9 9.9 1.0
CA F:HIS63 4.9 11.0 1.0
O F:HOH607 4.9 13.5 1.0
N F:HIS71 5.0 12.5 1.0
N F:ASP83 5.0 8.7 1.0

Zinc binding site 6 out of 12 in 3t5w

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Zinc binding site 6 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn300

b:16.6
occ:1.00
OD1 G:ASP83 2.0 14.1 1.0
ND1 G:HIS63 2.1 17.2 1.0
ND1 G:HIS80 2.1 19.0 1.0
ND1 G:HIS71 2.2 18.6 1.0
CG G:ASP83 2.8 16.1 1.0
OD2 G:ASP83 2.9 14.1 1.0
CE1 G:HIS71 3.0 19.0 1.0
CE1 G:HIS80 3.0 19.2 1.0
CG G:HIS63 3.0 17.3 1.0
CE1 G:HIS63 3.1 17.1 1.0
CG G:HIS80 3.2 17.9 1.0
CB G:HIS63 3.3 16.8 1.0
CG G:HIS71 3.3 19.5 1.0
CB G:HIS80 3.6 18.6 1.0
CB G:HIS71 3.8 19.9 1.0
O G:LYS136 3.9 18.6 1.0
CA G:HIS71 4.1 20.1 1.0
NE2 G:HIS71 4.2 19.4 1.0
NE2 G:HIS80 4.2 17.3 1.0
CB G:ASP83 4.2 16.5 1.0
CD2 G:HIS63 4.2 17.4 1.0
NE2 G:HIS63 4.2 19.7 1.0
CD2 G:HIS80 4.3 16.9 1.0
CD2 G:HIS71 4.3 20.3 1.0
CA G:ASP83 4.7 17.1 1.0
CA G:HIS80 4.8 18.5 1.0
N G:HIS80 4.8 19.7 1.0
C G:LYS136 4.8 17.8 1.0
CA G:HIS63 4.8 16.8 1.0
CD2 G:HIS46 4.8 19.0 1.0
N G:ASP83 4.9 16.9 1.0
N G:GLY72 4.9 20.1 1.0

Zinc binding site 7 out of 12 in 3t5w

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Zinc binding site 7 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn300

b:11.8
occ:1.00
OD1 H:ASP83 2.0 10.6 1.0
ND1 H:HIS80 2.1 7.9 1.0
ND1 H:HIS63 2.1 11.5 1.0
ND1 H:HIS71 2.1 10.1 1.0
CG H:ASP83 2.7 9.4 1.0
OD2 H:ASP83 2.8 5.7 1.0
CE1 H:HIS80 2.9 7.1 1.0
CE1 H:HIS71 2.9 10.3 1.0
CE1 H:HIS63 3.1 11.0 1.0
CG H:HIS63 3.1 12.8 1.0
CG H:HIS80 3.2 9.2 1.0
CG H:HIS71 3.2 8.4 1.0
CB H:HIS63 3.4 13.8 1.0
CB H:HIS80 3.6 8.8 1.0
CB H:HIS71 3.7 9.4 1.0
O H:LYS136 3.9 15.4 1.0
CA H:HIS71 3.9 9.9 1.0
NE2 H:HIS80 4.1 8.5 1.0
NE2 H:HIS71 4.1 6.5 1.0
CB H:ASP83 4.1 9.4 1.0
NE2 H:HIS63 4.2 10.3 1.0
CD2 H:HIS80 4.2 9.2 1.0
CD2 H:HIS63 4.2 12.0 1.0
CD2 H:HIS71 4.3 9.3 1.0
CA H:ASP83 4.7 9.6 1.0
N H:GLY72 4.7 9.7 1.0
N H:HIS80 4.7 9.8 1.0
CA H:HIS80 4.8 9.3 1.0
C H:LYS136 4.8 14.7 1.0
C H:HIS71 4.9 9.7 1.0
O H:HOH163 4.9 17.2 1.0
CD2 H:HIS46 4.9 11.9 1.0
N H:HIS71 5.0 9.7 1.0
CA H:HIS63 5.0 13.8 1.0
N H:ASP83 5.0 9.7 1.0

Zinc binding site 8 out of 12 in 3t5w

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Zinc binding site 8 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn300

b:27.3
occ:1.00
OD1 I:ASP83 2.0 29.9 1.0
ND1 I:HIS71 2.2 32.8 1.0
ND1 I:HIS80 2.2 30.6 1.0
ND1 I:HIS63 2.2 32.8 1.0
CG I:ASP83 2.7 31.3 1.0
OD2 I:ASP83 2.7 30.9 1.0
CG I:HIS63 3.0 30.6 1.0
CE1 I:HIS80 3.1 31.4 1.0
CE1 I:HIS71 3.1 34.1 1.0
CE1 I:HIS63 3.1 32.8 1.0
CG I:HIS80 3.2 31.4 1.0
CG I:HIS71 3.2 33.4 1.0
CB I:HIS63 3.3 28.4 1.0
CB I:HIS71 3.6 33.2 1.0
CB I:HIS80 3.6 31.2 1.0
O I:LYS136 3.7 38.5 1.0
CA I:HIS71 3.9 33.3 1.0
CD2 I:HIS63 4.0 32.6 1.0
NE2 I:HIS63 4.1 32.8 1.0
CB I:ASP83 4.1 30.6 1.0
NE2 I:HIS80 4.2 30.8 1.0
NE2 I:HIS71 4.2 33.0 1.0
CD2 I:HIS80 4.3 31.4 1.0
CD2 I:HIS71 4.3 33.1 1.0
N I:HIS80 4.7 32.3 1.0
CA I:ASP83 4.7 30.6 1.0
N I:GLY72 4.7 33.4 1.0
CA I:HIS80 4.7 31.2 1.0
C I:LYS136 4.8 38.1 1.0
CA I:HIS63 4.8 28.1 1.0
C I:HIS71 4.9 33.5 1.0
N I:HIS71 4.9 33.5 1.0
N I:ASP83 4.9 30.0 1.0
O I:HOH858 4.9 29.3 1.0

Zinc binding site 9 out of 12 in 3t5w

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Zinc binding site 9 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn300

b:9.3
occ:1.00
OD1 J:ASP83 1.9 4.5 1.0
ND1 J:HIS63 2.1 8.6 1.0
ND1 J:HIS71 2.1 8.8 1.0
ND1 J:HIS80 2.1 7.1 1.0
CG J:ASP83 2.7 6.6 1.0
OD2 J:ASP83 2.9 6.0 1.0
CE1 J:HIS71 3.0 8.9 1.0
CE1 J:HIS80 3.1 8.8 1.0
CG J:HIS63 3.1 8.4 1.0
CE1 J:HIS63 3.1 8.7 1.0
CG J:HIS80 3.1 6.6 1.0
CG J:HIS71 3.2 10.0 1.0
CB J:HIS63 3.4 7.7 1.0
CB J:HIS80 3.5 5.9 1.0
CB J:HIS71 3.6 9.2 1.0
O J:LYS136 3.7 11.7 1.0
CA J:HIS71 4.0 9.8 1.0
CB J:ASP83 4.1 7.7 1.0
NE2 J:HIS71 4.2 9.9 1.0
NE2 J:HIS80 4.2 8.0 1.0
NE2 J:HIS63 4.2 9.6 1.0
CD2 J:HIS63 4.2 7.8 1.0
CD2 J:HIS80 4.2 8.2 1.0
CD2 J:HIS71 4.3 7.9 1.0
CA J:ASP83 4.7 8.2 1.0
N J:HIS80 4.7 7.6 1.0
C J:LYS136 4.7 11.7 1.0
CA J:HIS80 4.7 7.6 1.0
N J:GLY72 4.8 9.0 1.0
CA J:HIS63 4.9 8.1 1.0
O J:HOH347 4.9 10.3 1.0
C J:HIS71 4.9 9.2 1.0
N J:ASP83 4.9 7.5 1.0
CD2 J:HIS46 5.0 9.4 1.0
N J:HIS71 5.0 10.8 1.0

Zinc binding site 10 out of 12 in 3t5w

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Zinc binding site 10 out of 12 in the 2ME Modified Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of 2ME Modified Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn300

b:31.4
occ:1.00
OD1 K:ASP83 2.0 26.3 1.0
ND1 K:HIS80 2.1 29.6 1.0
ND1 K:HIS71 2.2 34.1 1.0
ND1 K:HIS63 2.2 31.4 1.0
CG K:ASP83 2.9 26.6 1.0
CE1 K:HIS80 2.9 29.6 1.0
CE1 K:HIS71 3.0 34.0 1.0
CG K:HIS63 3.1 30.4 1.0
OD2 K:ASP83 3.1 28.0 1.0
CE1 K:HIS63 3.1 31.2 1.0
CG K:HIS80 3.2 30.4 1.0
CG K:HIS71 3.3 35.0 1.0
CB K:HIS63 3.4 30.5 1.0
CB K:HIS80 3.6 31.0 1.0
CB K:HIS71 3.7 34.9 1.0
O K:LYS136 3.9 41.0 1.0
CA K:HIS71 4.0 35.1 1.0
NE2 K:HIS80 4.1 28.9 1.0
NE2 K:HIS71 4.1 33.7 1.0
NE2 K:HIS63 4.2 31.9 1.0
CD2 K:HIS63 4.2 30.9 1.0
CD2 K:HIS80 4.2 29.9 1.0
CD2 K:HIS71 4.3 34.5 1.0
CB K:ASP83 4.3 26.0 1.0
CA K:ASP83 4.8 26.0 1.0
N K:GLY72 4.8 34.8 1.0
N K:HIS80 4.8 31.6 1.0
CA K:HIS80 4.8 30.9 1.0
O K:HOH1290 4.9 28.8 1.0
CA K:HIS63 4.9 30.3 1.0
C K:HIS71 4.9 35.1 1.0
N K:HIS71 4.9 35.3 1.0
CD2 K:HIS46 4.9 31.4 1.0
N K:ASP83 5.0 26.6 1.0

Reference:

K.Ihara, N.Fujiwara, Y.Yamaguchi, H.Torigoe, S.Wakatsuki, N.Taniguchi, K.Suzuki. Structural Switching of Cu,Zn-Superoxide Dismutases at Loop VI: Insights From the Crystal Structure of 2-Mercaptoethanol-Modified Enzyme Biosci.Rep. V. 32 539 2012.
ISSN: ISSN 0144-8463
PubMed: 22804629
DOI: 10.1042/BSR20120029
Page generated: Wed Dec 16 04:51:30 2020

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