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Copper in PDB 7yrk: Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex

Enzymatic activity of Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex

All present enzymatic activity of Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex, PDB code: 7yrk was solved by M.Unno, T.Furuya, K.Kitanishi, T.Akitsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.18 / 0.92
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.671, 78.671, 37.203, 90, 90, 90
R / Rfree (%) 11.3 / 12.8

Other elements in 7yrk:

The structure of Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex also contains other interesting chemical elements:

Sodium (Na) 3 atoms
Chlorine (Cl) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex (pdb code 7yrk). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex, PDB code: 7yrk:

Copper binding site 1 out of 1 in 7yrk

Go back to Copper Binding Sites List in 7yrk
Copper binding site 1 out of 1 in the Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu203

b:8.1
occ:0.72
 CU A:JI6203 0.0 8.1 0.7
N1 A:JI6203 2.0 8.2 0.7
NE2 A:HIS15 2.0 10.4 1.0
O3 A:JI6203 2.0 11.1 0.7
O2 A:JI6203 2.0 9.6 0.7
OG1 A:THR89 2.5 9.3 1.0
HG1 A:THR89 2.6 11.2 1.0
C1 A:JI6203 2.9 8.6 0.7
C8 A:JI6203 2.9 8.8 0.7
CE1 A:HIS15 2.9 10.1 1.0
C9 A:JI6203 3.0 8.2 0.7
C2 A:JI6203 3.0 10.0 0.7
CD2 A:HIS15 3.0 10.4 1.0
HE1 A:HIS15 3.1 12.2 1.0
HD2 A:HIS15 3.2 12.5 1.0
HH22 A:ARG14 3.3 19.2 0.4
C7 A:JI6203 3.3 9.6 0.7
HH12 A:ARG14 3.4 17.8 0.4
HH12 A:ARG14 3.4 24.3 0.6
NH2 A:ARG14 3.5 16.0 0.4
O4 A:JI6203 3.6 9.7 0.7
NH1 A:ARG14 3.7 14.8 0.4
CZ A:ARG14 3.8 14.3 0.4
OD1 A:ASP87 3.9 11.4 1.0
CB A:THR89 3.9 8.4 1.0
NH1 A:ARG14 3.9 20.2 0.6
C10 A:JI6203 3.9 9.1 0.7
HH11 A:ARG14 3.9 24.3 0.6
HH21 A:ARG14 4.0 19.2 0.4
O1 A:JI6203 4.1 9.8 0.7
O A:HOH315 4.1 30.8 1.0
ND1 A:HIS15 4.1 9.6 1.0
CG A:HIS15 4.1 10.3 1.0
HG23 A:THR89 4.1 12.5 1.0
HG21 A:THR89 4.1 12.5 1.0
HH11 A:ARG14 4.2 17.8 0.4
C3 A:JI6203 4.2 11.3 0.7
CG2 A:THR89 4.3 10.4 1.0
H A:THR89 4.3 8.6 1.0
HA A:THR89 4.4 8.6 1.0
HB A:THR89 4.4 10.1 1.0
CA A:THR89 4.6 7.2 1.0
NE A:ARG14 4.6 12.4 0.4
C6 A:JI6203 4.7 11.2 0.7
CG A:ASP87 4.7 11.2 1.0
C11 A:JI6203 4.7 10.8 0.7
N A:THR89 4.7 7.1 1.0
CZ A:ARG14 4.8 19.1 0.6
HD1 A:HIS15 4.8 11.5 1.0
HH22 A:ARG14 4.9 23.0 0.6
OD2 A:ASP87 4.9 12.9 1.0
O A:HOH420 4.9 16.5 1.0
HD3 A:ARG14 5.0 16.4 0.4

Reference:

T.Furuya, D.Nakane, K.Kitanishi, N.Katsuumi, A.Tsaturyan, I.N.Shcherbakov, M.Unno, T.Akitsu. A Novel Hybrid Protein Composed of Superoxide-Dismutase-Active Cu(II) Complex and Lysozyme. Sci Rep V. 13 6892 2023.
ISSN: ESSN 2045-2322
PubMed: 37106030
DOI: 10.1038/S41598-023-33926-1
Page generated: Wed Jul 31 09:24:53 2024

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