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Sodium 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:

Chlorine (Cl) 4 atoms
Copper (Cu) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex, PDB code: 7yrk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7yrk

Go back to Sodium Binding Sites List in 7yrk
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na208

b:27.4
occ:0.32
 O A:HOH423 2.1 15.2 0.6
HG1 A:THR43 2.1 14.0 1.0
OG1 A:THR43 2.5 11.7 1.0
HB A:THR43 2.6 11.7 1.0
O A:HOH423 2.9 26.4 0.4
CB A:THR43 3.1 9.7 1.0
HG21 A:THR51 3.6 7.9 1.0
HG23 A:THR51 3.7 7.9 1.0
HG21 A:THR43 3.8 12.2 1.0
HH22 A:ARG68 4.0 8.8 0.5
CG2 A:THR43 4.0 10.2 1.0
C A:THR43 4.1 9.6 1.0
CG2 A:THR51 4.1 6.6 1.0
CA A:THR43 4.2 8.9 1.0
N A:ASN44 4.3 8.3 1.0
HH21 A:ARG45 4.3 12.1 0.5
O A:THR43 4.3 12.5 1.0
HB2 A:ARG45 4.3 14.7 0.5
HB2 A:ARG45 4.4 11.1 0.5
HA A:ASN44 4.4 10.9 0.1
H A:ASN44 4.4 10.0 0.4
H A:ASN44 4.5 10.0 0.1
HG22 A:THR51 4.5 7.9 1.0
NH2 A:ARG45 4.5 10.1 0.5
HG22 A:THR43 4.6 12.2 1.0
H A:ARG45 4.6 9.4 0.5
H A:ARG45 4.6 9.4 0.5
HH22 A:ARG45 4.6 12.1 0.5
NH2 A:ARG68 4.6 7.4 0.5
HA A:ASN44 4.7 9.3 0.4
HG23 A:THR43 4.7 12.2 1.0
CA A:ASN44 4.7 9.1 0.4
HH21 A:ARG68 4.7 8.8 0.5
O A:HOH398 4.7 20.1 1.0
CA A:ASN44 4.7 9.1 0.1
N A:ARG45 4.8 7.9 1.0
HA A:THR43 4.8 10.7 1.0
CA A:ASN44 4.9 7.7 0.4
C A:ASN44 4.9 7.1 1.0
O A:HOH360 4.9 8.4 1.0

Sodium binding site 2 out of 3 in 7yrk

Go back to Sodium Binding Sites List in 7yrk
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na binding site number 2 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:Na209

b:42.7
occ:1.00
 O A:HOH494 2.2 27.6 1.0
O A:HOH316 2.2 33.9 1.0
O A:GLU35 3.1 7.1 1.0
O A:HOH480 3.2 35.2 1.0
C A:74C211 3.4 22.3 0.3
ND2 A:ASN44 3.4 17.7 0.1
O A:HOH455 3.4 48.4 1.0
OD1 A:ASN44 3.5 13.8 0.4
HD22 A:ASN44 3.6 21.2 0.1
O A:HOH372 4.0 10.7 1.0
C A:74C211 4.1 21.4 0.5
C A:GLU35 4.1 6.2 1.0
CG A:ASN44 4.2 14.3 0.1
O A:HOH357 4.3 14.4 1.0
HG3 A:GLN57 4.3 7.7 1.0
CG A:ASN44 4.3 13.2 0.4
O A:HOH338 4.4 13.8 1.0
HA A:GLU35 4.4 7.5 1.0
HA A:SER36 4.4 8.3 1.0
O A:PHE34 4.5 9.3 1.0
OD1 A:ASN44 4.5 14.5 0.1
HB2 A:ASN44 4.6 10.6 0.4
OE1 A:GLN57 4.6 8.2 1.0
O A:HOH486 4.7 19.8 1.0
ND2 A:ASN44 4.8 15.7 0.4
CA A:GLU35 4.9 6.3 1.0

Sodium binding site 3 out of 3 in 7yrk

Go back to Sodium Binding Sites List in 7yrk
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na binding site number 3 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:Na210

b:29.8
occ:0.20
 HD22 A:ASN44 1.8 18.8 0.4
OD1 A:ASN44 2.3 12.7 0.4
O A:HOH312 2.4 38.5 1.0
OD1 A:ASN44 2.5 14.5 0.1
ND2 A:ASN44 2.6 15.7 0.4
O A:HOH398 2.7 20.1 1.0
HB3 A:ASN44 2.9 13.6 0.4
C A:74C211 3.1 21.4 0.5
HA A:ASN44 3.2 9.3 0.4
HB3 A:ASN44 3.2 14.2 0.1
HA A:ASN44 3.3 10.9 0.1
CG A:ASN44 3.4 11.5 0.4
CG A:ASN44 3.4 14.3 0.1
CG A:ASN44 3.4 13.2 0.4
CB A:ASN44 3.5 11.3 0.4
H A:ARG45 3.6 9.4 0.5
H A:ARG45 3.6 9.4 0.5
CB A:ASN44 3.7 11.8 0.1
CA A:ASN44 3.9 9.1 0.4
CA A:ASN44 3.9 9.1 0.1
CA A:ASN44 4.0 7.7 0.4
CB A:ASN44 4.1 8.9 0.4
HB2 A:ASN44 4.1 10.6 0.4
N A:ARG45 4.2 7.9 1.0
O A:HOH455 4.3 48.4 1.0
HD22 A:ASN44 4.3 19.1 0.4
ND2 A:ASN44 4.3 15.9 0.4
HB2 A:ASN44 4.4 13.6 0.4
O A:HOH423 4.4 26.4 0.4
OD1 A:ASN44 4.5 13.8 0.4
C A:ASN44 4.6 7.1 1.0
O A:ARG45 4.6 11.2 1.0
HB2 A:ASN44 4.6 14.2 0.1
O A:HOH512 4.6 29.8 0.5
ND2 A:ASN44 4.7 17.7 0.1
O A:THR43 4.7 12.5 1.0
HB3 A:ARG45 4.9 11.1 0.5
HB3 A:ASN44 5.0 10.6 0.4
O A:HOH423 5.0 15.2 0.6

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 Oct 9 09:58:50 2024

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