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Copper in PDB 8k3l: SOD1 and NANOBODY3 Complex

Enzymatic activity of SOD1 and NANOBODY3 Complex

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

Protein crystallography data

The structure of SOD1 and NANOBODY3 Complex, PDB code: 8k3l was solved by S.Cheng, R.Liu, Y.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.07 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.214, 62.442, 314.928, 90, 90, 90
R / Rfree (%) 19.5 / 23.5

Other elements in 8k3l:

The structure of SOD1 and NANOBODY3 Complex also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the SOD1 and NANOBODY3 Complex (pdb code 8k3l). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the SOD1 and NANOBODY3 Complex, PDB code: 8k3l:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 8k3l

Go back to Copper Binding Sites List in 8k3l
Copper binding site 1 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of SOD1 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:41.3
occ:1.00
O A:HOH305 1.8 30.9 1.0
ND1 A:HIS46 2.1 35.4 1.0
NE2 A:HIS120 2.2 31.8 1.0
NE2 A:HIS48 2.2 36.3 1.0
CD2 A:HIS120 2.9 32.2 1.0
CG A:HIS46 3.1 32.9 1.0
CD2 A:HIS48 3.1 30.5 1.0
NE2 A:HIS63 3.1 36.7 1.0
CE1 A:HIS48 3.2 32.2 1.0
CE1 A:HIS46 3.2 31.7 1.0
CB A:HIS46 3.3 32.0 1.0
CE1 A:HIS120 3.3 34.4 1.0
CD2 A:HIS63 3.5 35.0 1.0
CG1 A:VAL118 4.0 32.5 1.0
O A:HOH352 4.0 27.1 1.0
CG A:HIS120 4.1 33.3 1.0
CE1 A:HIS63 4.2 34.8 1.0
CB A:VAL118 4.2 30.0 1.0
CD2 A:HIS46 4.2 33.0 1.0
NE2 A:HIS46 4.3 35.9 1.0
ND1 A:HIS48 4.3 38.1 1.0
CG A:HIS48 4.3 35.3 1.0
ND1 A:HIS120 4.3 34.2 1.0
CA A:HIS46 4.3 29.9 1.0
N A:HIS46 4.4 30.5 1.0
O A:VAL118 4.5 32.3 1.0
O A:HIS46 4.6 32.0 1.0
CG A:HIS63 4.7 36.2 1.0
C A:HIS46 4.7 31.8 1.0
ND1 A:HIS63 4.9 31.2 1.0

Copper binding site 2 out of 4 in 8k3l

Go back to Copper Binding Sites List in 8k3l
Copper binding site 2 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of SOD1 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:41.7
occ:1.00
NE2 C:HIS120 2.0 36.0 1.0
NE2 C:HIS48 2.1 40.9 1.0
ND1 C:HIS46 2.2 40.9 1.0
CE1 C:HIS120 2.9 38.1 1.0
CD2 C:HIS120 3.0 35.7 1.0
CE1 C:HIS48 3.0 39.2 1.0
CE1 C:HIS46 3.1 37.0 1.0
NE2 C:HIS63 3.2 48.1 1.0
CG C:HIS46 3.2 38.6 1.0
CD2 C:HIS48 3.2 38.8 1.0
CB C:HIS46 3.5 33.9 1.0
CD2 C:HIS63 3.6 42.8 1.0
O C:HOH345 3.8 33.6 1.0
ND1 C:HIS120 4.0 41.1 1.0
CG C:HIS120 4.1 42.2 1.0
CE1 C:HIS63 4.1 43.8 1.0
ND1 C:HIS48 4.2 44.2 1.0
CG1 C:VAL118 4.2 35.2 1.0
NE2 C:HIS46 4.2 38.4 1.0
CG C:HIS48 4.3 39.2 1.0
CD2 C:HIS46 4.3 37.0 1.0
CB C:VAL118 4.4 36.3 1.0
CG C:HIS63 4.6 41.6 1.0
CA C:HIS46 4.7 32.5 1.0
N C:HIS46 4.8 32.2 1.0
ND1 C:HIS63 4.9 37.8 1.0
O C:VAL118 4.9 37.9 1.0

Copper binding site 3 out of 4 in 8k3l

Go back to Copper Binding Sites List in 8k3l
Copper binding site 3 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of SOD1 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu201

b:47.9
occ:1.00
O E:HOH302 1.9 36.9 1.0
ND1 E:HIS46 2.2 49.6 1.0
NE2 E:HIS120 2.2 41.0 1.0
CE1 E:HIS48 2.3 42.9 1.0
NE2 E:HIS63 2.6 47.2 1.0
NE2 E:HIS48 2.7 39.8 1.0
CE1 E:HIS46 2.9 43.9 1.0
CE1 E:HIS120 2.9 42.5 1.0
CG E:HIS46 3.0 46.3 1.0
CD2 E:HIS120 3.1 47.6 1.0
CD2 E:HIS63 3.2 48.1 1.0
ND1 E:HIS48 3.4 43.5 1.0
CB E:HIS46 3.5 38.8 1.0
CE1 E:HIS63 3.7 48.4 1.0
NE2 E:HIS46 3.9 47.3 1.0
CD2 E:HIS46 4.0 45.0 1.0
CD2 E:HIS48 4.0 41.7 1.0
ND1 E:HIS120 4.0 48.7 1.0
CG E:HIS120 4.1 48.6 1.0
CG E:HIS48 4.3 41.9 1.0
CG E:HIS63 4.4 39.9 1.0
CG1 E:VAL118 4.5 42.2 1.0
ND1 E:HIS63 4.6 47.1 1.0
CB E:VAL118 4.6 37.7 1.0
CA E:HIS46 4.7 38.5 1.0
N E:HIS46 4.9 38.3 1.0

Copper binding site 4 out of 4 in 8k3l

Go back to Copper Binding Sites List in 8k3l
Copper binding site 4 out of 4 in the SOD1 and NANOBODY3 Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of SOD1 and NANOBODY3 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu201

b:47.1
occ:1.00
NE2 G:HIS120 1.9 40.6 1.0
NE2 G:HIS48 2.0 44.5 1.0
ND1 G:HIS46 2.1 48.2 1.0
CE1 G:HIS48 2.7 42.0 1.0
CE1 G:HIS120 2.7 41.8 1.0
NE2 G:HIS63 3.0 46.5 1.0
CD2 G:HIS120 3.0 37.3 1.0
CE1 G:HIS46 3.0 41.4 1.0
CG G:HIS46 3.1 46.4 1.0
CD2 G:HIS48 3.2 37.1 1.0
CD2 G:HIS63 3.2 46.1 1.0
CB G:HIS46 3.4 37.5 1.0
ND1 G:HIS120 3.9 42.0 1.0
ND1 G:HIS48 3.9 45.1 1.0
CG G:HIS120 4.0 43.0 1.0
NE2 G:HIS46 4.1 45.0 1.0
CG G:HIS48 4.2 40.7 1.0
CD2 G:HIS46 4.2 41.1 1.0
CG1 G:VAL118 4.2 41.3 1.0
CE1 G:HIS63 4.2 46.1 1.0
CB G:VAL118 4.3 40.7 1.0
CA G:HIS46 4.5 38.7 1.0
CG G:HIS63 4.6 42.3 1.0
N G:HIS46 4.6 41.4 1.0
O G:VAL118 5.0 43.2 1.0

Reference:

C.Shihao, S.Cheng, R.Liu, Y.Ding. N/A N/A.
Page generated: Mon Jul 14 09:02:35 2025

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