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Zinc in PDB 8yat: SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex

Enzymatic activity of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex

All present enzymatic activity of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex:
1.15.1.1;

Protein crystallography data

The structure of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex, PDB code: 8yat was solved by S.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 80.82 / 3.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 377.129, 46.672, 156.949, 90, 90, 90
R / Rfree (%) 30.3 / 36.8

Zinc Binding Sites:

The binding sites of Zinc atom in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex (pdb code 8yat). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex, PDB code: 8yat:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8yat

Go back to Zinc Binding Sites List in 8yat
Zinc binding site 1 out of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:44.0
occ:1.00
 OD1 A:ASP83 2.1 50.7 1.0
ND1 A:HIS71 2.3 58.3 1.0
ND1 A:HIS80 2.3 59.5 1.0
ND1 A:HIS63 2.3 51.3 1.0
OD2 A:ASP83 2.6 55.8 1.0
CG A:ASP83 2.7 53.8 1.0
CG A:HIS80 2.9 64.8 1.0
CE1 A:HIS71 2.9 57.7 1.0
CE1 A:HIS80 3.1 58.4 1.0
CG A:HIS63 3.2 52.0 1.0
CB A:HIS80 3.3 63.7 1.0
CE1 A:HIS63 3.3 44.9 1.0
CB A:HIS63 3.4 54.3 1.0
CG A:HIS71 3.5 54.5 1.0
O A:LYS136 3.7 60.4 1.0
CD2 A:HIS80 3.8 68.0 1.0
NE2 A:HIS80 3.9 60.8 1.0
CB A:ASP83 4.1 54.5 1.0
CB A:HIS71 4.1 53.7 1.0
NE2 A:HIS71 4.2 54.9 1.0
CD2 A:HIS63 4.4 51.4 1.0
NE2 A:HIS63 4.4 44.8 1.0
N A:HIS80 4.4 66.2 1.0
CA A:HIS71 4.5 56.5 1.0
CA A:HIS80 4.5 64.1 1.0
CD2 A:HIS71 4.5 52.4 1.0
CD2 A:HIS46 4.6 50.9 1.0
CA A:ASP83 4.7 55.9 1.0
O A:THR137 4.9 53.0 1.0
C A:LYS136 4.9 60.3 1.0
N A:ASP83 4.9 60.7 1.0
CA A:HIS63 5.0 53.9 1.0

Zinc binding site 2 out of 4 in 8yat

Go back to Zinc Binding Sites List in 8yat
Zinc binding site 2 out of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:65.2
occ:1.00
 ND1 E:HIS80 2.3 54.8 1.0
ND1 E:HIS71 2.3 53.1 1.0
ND1 E:HIS63 2.3 50.5 1.0
OD1 E:ASP83 2.4 51.0 1.0
CE1 E:HIS80 2.9 56.0 1.0
CG E:ASP83 3.1 52.0 1.0
CG E:HIS80 3.1 51.1 1.0
OD2 E:ASP83 3.2 56.9 1.0
CE1 E:HIS71 3.2 49.2 1.0
CE1 E:HIS63 3.2 51.5 1.0
CG E:HIS63 3.3 47.5 1.0
CG E:HIS71 3.4 56.8 1.0
O E:LYS136 3.5 61.7 1.0
CB E:HIS63 3.6 45.7 1.0
CB E:HIS80 3.7 51.0 1.0
CB E:HIS71 3.7 59.7 1.0
NE2 E:HIS80 3.9 59.5 1.0
CD2 E:HIS80 4.0 56.8 1.0
CA E:HIS71 4.1 61.1 1.0
NE2 E:HIS71 4.3 53.6 1.0
NE2 E:HIS63 4.3 48.7 1.0
CD2 E:HIS63 4.4 48.2 1.0
CD2 E:HIS71 4.5 55.4 1.0
CB E:ASP83 4.6 47.2 1.0
N E:HIS80 4.7 58.3 1.0
C E:LYS136 4.8 58.5 1.0
CA E:HIS80 4.8 55.3 1.0

Zinc binding site 3 out of 4 in 8yat

Go back to Zinc Binding Sites List in 8yat
Zinc binding site 3 out of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:77.9
occ:1.00
 CG I:HIS80 2.0 96.0 1.0
CD2 I:HIS80 2.2 93.2 1.0
ND1 I:HIS71 2.3 71.9 1.0
ND1 I:HIS63 2.4 64.5 1.0
ND1 I:HIS80 2.4 98.2 1.0
NE2 I:HIS80 2.6 96.2 1.0
CE1 I:HIS80 2.7 95.4 1.0
CB I:HIS80 2.8 87.6 1.0
CE1 I:HIS71 2.8 73.8 1.0
OD1 I:ASP83 2.9 73.0 1.0
OD2 I:ASP83 3.1 74.5 1.0
CG I:HIS63 3.2 77.1 1.0
CG I:ASP83 3.2 74.2 1.0
CB I:HIS63 3.3 81.0 1.0
CE1 I:HIS63 3.4 61.8 1.0
CG I:HIS71 3.6 72.6 1.0
O I:LYS136 3.8 82.0 1.0
NE2 I:HIS71 4.1 74.3 1.0
CA I:HIS80 4.2 85.6 1.0
CB I:HIS71 4.2 76.2 1.0
CD2 I:HIS63 4.4 77.6 1.0
CD2 I:HIS71 4.5 74.2 1.0
NE2 I:HIS63 4.5 61.2 1.0
N I:HIS80 4.5 85.4 1.0
CB I:ASP83 4.5 78.4 1.0
CA I:HIS71 4.6 78.3 1.0
CA I:HIS63 4.8 71.3 1.0
CD2 I:HIS46 5.0 74.1 1.0
C I:LYS136 5.0 73.8 1.0

Zinc binding site 4 out of 4 in 8yat

Go back to Zinc Binding Sites List in 8yat
Zinc binding site 4 out of 4 in the SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SOD1, NANOBODY1, NANOBODY2 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn201

b:88.9
occ:1.00
 OD1 M:ASP83 2.3 73.0 1.0
ND1 M:HIS71 2.3 73.0 1.0
ND1 M:HIS63 2.3 75.5 1.0
ND1 M:HIS80 2.3 75.7 1.0
OD2 M:ASP83 2.8 77.8 1.0
CE1 M:HIS71 2.8 71.7 1.0
CG M:ASP83 2.9 73.2 1.0
CG M:HIS80 3.0 72.5 1.0
CE1 M:HIS80 3.1 74.7 1.0
CG M:HIS63 3.2 70.5 1.0
CE1 M:HIS63 3.3 73.3 1.0
CB M:HIS80 3.4 69.5 1.0
CB M:HIS63 3.5 68.2 1.0
CG M:HIS71 3.6 79.9 1.0
O M:LYS136 3.8 78.3 1.0
CD2 M:HIS80 3.9 73.4 1.0
NE2 M:HIS80 3.9 74.2 1.0
NE2 M:HIS71 4.1 79.6 1.0
CB M:HIS71 4.2 81.6 1.0
NE2 M:HIS63 4.3 69.9 1.0
CD2 M:HIS63 4.3 71.6 1.0
CB M:ASP83 4.4 67.3 1.0
CD2 M:HIS71 4.5 81.4 1.0
CA M:HIS71 4.5 78.4 1.0
CA M:HIS80 4.6 69.8 1.0
N M:HIS80 4.6 80.1 1.0
CD2 M:HIS46 4.6 75.6 1.0
CA M:ASP83 4.9 63.0 1.0
C M:LYS136 5.0 82.7 1.0

Reference:

S.Cheng, S.Cheng. N/A N/A.
Page generated: Fri Aug 22 15:49:29 2025

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