Chlorine 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
Copper (Cu) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Hen Egg Lysozyme-2-Oxidobenzylidene- Threoninato-Copper (II) Complex, PDB code: 7yrk:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7yrk

Go back to Chlorine Binding Sites List in 7yrk
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl202

b:9.8
occ:1.00
HH A:TYR23 2.3 9.4 1.0
OH A:TYR23 3.0 7.8 1.0
HE2 A:TYR23 3.2 8.0 1.0
O A:HOH371 3.2 9.6 1.0
HA3 A:GLY104 3.3 8.4 1.0
CZ A:TYR23 3.7 6.9 1.0
CE2 A:TYR23 3.7 6.6 1.0
HA2 A:GLY104 4.1 8.4 1.0
CA A:GLY104 4.1 7.0 1.0
HD2 A:ARG21 4.3 17.3 0.1
HD3 A:ARG21 4.5 17.3 0.1
N A:GLY104 4.6 7.3 1.0
O A:ARG21 4.6 9.4 1.0
O A:HOH417 4.7 39.0 1.0
H A:MET105 4.7 7.2 1.0
H A:GLY104 4.8 8.8 1.0
CD A:ARG21 4.9 14.4 0.1
CE1 A:TYR23 4.9 7.0 1.0
CD2 A:TYR23 4.9 6.5 1.0
HB3 A:ARG21 4.9 9.8 0.5

Chlorine binding site 2 out of 4 in 7yrk

Go back to Chlorine Binding Sites List in 7yrk
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl204

b:22.5
occ:1.00
HZ3 A:LYS33 2.7 18.8 1.0
HE2 A:PHE38 2.8 10.4 1.0
HZ3 A:TRP123 3.0 16.8 1.0
HD3 A:ARG5 3.2 14.2 1.0
HD3 A:LYS33 3.4 13.4 1.0
HB2 A:ARG5 3.5 12.3 1.0
NZ A:LYS33 3.6 15.6 1.0
CE2 A:PHE38 3.7 8.7 1.0
HZ1 A:LYS33 3.9 18.8 1.0
HE2 A:LYS33 3.9 16.6 1.0
CZ3 A:TRP123 3.9 14.0 1.0
O A:HOH419 4.0 34.6 1.0
HZ A:PHE38 4.1 9.3 1.0
O A:HOH443 4.1 35.9 0.5
CE A:LYS33 4.1 13.8 1.0
HZ2 A:LYS33 4.2 18.8 1.0
CD A:LYS33 4.2 11.2 1.0
CD A:ARG5 4.2 11.8 1.0
CZ A:PHE38 4.3 7.8 1.0
CB A:ARG5 4.4 10.3 1.0
HE A:ARG5 4.4 15.5 1.0
HE3 A:TRP123 4.5 13.3 1.0
HD2 A:PHE38 4.6 9.5 1.0
CD2 A:PHE38 4.6 7.9 1.0
HG3 A:ARG5 4.7 12.6 1.0
CG A:ARG5 4.7 10.5 1.0
HB3 A:ARG5 4.7 12.3 1.0
HD2 A:LYS33 4.7 13.4 1.0
HH2 A:TRP123 4.7 17.2 1.0
CE3 A:TRP123 4.7 11.1 1.0
NE A:ARG5 4.7 12.9 1.0
HD2 A:ARG5 4.8 14.2 1.0
CH2 A:TRP123 4.8 14.3 1.0

Chlorine binding site 3 out of 4 in 7yrk

Go back to Chlorine Binding Sites List in 7yrk
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl205

b:9.8
occ:0.74
H A:THR69 2.4 9.0 1.0
O A:HOH465 3.1 33.8 1.0
HG A:SER72 3.1 12.8 1.0
HA2 A:GLY67 3.2 10.1 1.0
O A:HOH406 3.2 7.8 1.0
H A:GLY67 3.2 9.2 1.0
N A:THR69 3.2 7.5 1.0
O A:THR69 3.3 9.4 1.0
H A:ARG68 3.4 9.1 0.5
H A:ARG68 3.5 9.1 0.5
C A:GLY67 3.5 7.8 1.0
N A:ARG68 3.5 7.6 1.0
CA A:GLY67 3.6 8.4 1.0
HB A:THR69 3.6 9.0 1.0
N A:GLY67 3.6 7.6 1.0
C A:THR69 3.6 8.1 1.0
O A:HOH366 3.6 28.5 1.0
OG A:SER72 3.7 10.6 1.0
OD1 A:ASN65 3.7 9.4 1.0
CA A:THR69 3.9 7.6 1.0
O A:HOH409 4.1 10.9 1.0
O A:GLY67 4.1 10.2 1.0
CB A:THR69 4.2 7.5 1.0
H A:ASP66 4.2 7.6 1.0
C A:ARG68 4.2 9.0 1.0
OD1 A:ASP66 4.3 6.8 1.0
CA A:ARG68 4.3 8.6 0.5
CA A:ARG68 4.4 8.0 0.5
HA A:PRO70 4.4 12.3 1.0
HA A:ARG68 4.4 10.3 0.5
HG1 A:THR69 4.4 8.9 1.0
N A:PRO70 4.5 9.1 1.0
HA3 A:GLY67 4.5 10.1 1.0
HA A:ARG68 4.6 9.6 0.5
H A:SER72 4.6 15.3 1.0
O A:HOH302 4.7 5.3 1.0
C A:ASP66 4.7 6.9 1.0
HA A:THR69 4.8 9.1 1.0
OG1 A:THR69 4.9 7.4 1.0
O A:HOH374 4.9 18.3 0.5
CG A:ASN65 4.9 8.6 1.0
CB A:SER72 4.9 10.8 1.0
N A:ASP66 4.9 6.3 1.0
HA A:ASN65 4.9 8.1 1.0
HB3 A:SER72 4.9 12.9 1.0
CA A:PRO70 4.9 10.2 1.0

Chlorine binding site 4 out of 4 in 7yrk

Go back to Chlorine Binding Sites List in 7yrk
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl206

b:13.6
occ:0.74
HG A:SER24 2.3 14.1 1.0
H A:GLY26 2.4 8.2 1.0
O A:HOH457 2.7 33.9 1.0
HA A:GLN121 2.9 16.4 1.0
HA3 A:GLY26 2.9 8.1 1.0
HB2 A:SER24 3.0 11.8 1.0
OG A:SER24 3.1 11.7 1.0
N A:GLY26 3.2 6.9 1.0
HG23 A:VAL120 3.3 14.8 1.0
HD11 A:ILE124 3.4 20.4 1.0
CA A:GLY26 3.5 6.8 1.0
HD13 A:ILE124 3.5 20.4 1.0
CB A:SER24 3.5 9.8 1.0
CA A:GLN121 3.7 13.7 1.0
HG12 A:ILE124 3.7 16.5 1.0
HG2 A:GLN121 3.7 26.4 1.0
HB2 A:GLN121 3.8 21.9 1.0
CD1 A:ILE124 3.8 17.0 1.0
N A:GLN121 4.0 11.9 1.0
HB3 A:SER24 4.1 11.8 1.0
H A:ASN27 4.1 7.7 1.0
CB A:GLN121 4.1 18.3 1.0
HA2 A:GLY26 4.1 8.1 1.0
O A:VAL120 4.2 10.7 1.0
H A:LEU25 4.2 9.2 1.0
C A:VAL120 4.2 10.6 1.0
CG2 A:VAL120 4.2 12.3 1.0
N A:LEU25 4.3 7.7 1.0
H A:GLN121 4.3 14.2 1.0
CG1 A:ILE124 4.3 13.8 1.0
C A:LEU25 4.4 6.9 1.0
CG A:GLN121 4.4 22.0 1.0
C A:SER24 4.4 7.8 1.0
HB3 A:LEU25 4.4 9.2 1.0
HG21 A:VAL120 4.5 14.8 1.0
C A:GLY26 4.5 6.5 1.0
N A:ASN27 4.6 6.4 1.0
CA A:SER24 4.6 8.1 1.0
HD12 A:ILE124 4.7 20.4 1.0
HG3 A:GLN121 4.7 26.4 1.0
CA A:LEU25 4.8 7.4 1.0
HB A:VAL120 4.8 12.9 1.0
HG22 A:VAL120 4.8 14.8 1.0
O A:SER24 4.8 8.4 1.0
HG13 A:ILE124 4.8 16.5 1.0
HG23 A:ILE124 4.9 14.6 1.0
C A:GLN121 4.9 11.2 1.0
HG21 A:ILE124 4.9 14.6 1.0
HD22 A:ASN27 5.0 9.8 1.0
O A:HOH505 5.0 31.9 1.0

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 26 15:17:25 2023

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