Atomistry » Chlorine » PDB 7y7v-7yuz » 7yrk
Atomistry »
  Chlorine »
    PDB 7y7v-7yuz »
      7yrk »

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: Tue Jul 30 06:02:24 2024

Last articles

Zn in 2YRC
Zn in 2YQP
Zn in 2YR2
Zn in 2YQL
Zn in 2YPT
Zn in 2YPA
Zn in 2YPU
Zn in 2YNW
Zn in 2YNT
Zn in 2YNV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy