Atomistry » Chlorine » PDB 5z42-5zkn » 5z5c
Atomistry »
  Chlorine »
    PDB 5z42-5zkn »
      5z5c »

Chlorine in PDB 5z5c: Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form

Enzymatic activity of Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form

All present enzymatic activity of Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form:
2.5.1.47;

Protein crystallography data

The structure of Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form, PDB code: 5z5c was solved by Y.Kezuka, Y.Yoshida, T.Nonaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.93 / 2.07
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.760, 136.160, 171.680, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 24.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form (pdb code 5z5c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form, PDB code: 5z5c:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5z5c

Go back to Chlorine Binding Sites List in 5z5c
Chlorine binding site 1 out of 3 in the Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form


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 Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:32.4
occ:1.00
 OG A:SER74 2.9 22.1 1.0
OG1 A:THR73 3.1 22.2 1.0
N A:SER74 3.2 22.3 1.0
OG1 A:THR77 3.3 21.4 1.0
O A:HOH508 3.4 26.8 1.0
NZ A:LYS46 3.4 21.0 1.0
CB A:THR77 3.4 21.1 1.0
OE1 A:GLN147 3.5 25.7 1.0
N A:THR77 3.7 21.0 1.0
NE2 A:GLN147 3.9 24.4 1.0
CB A:SER74 3.9 22.4 1.0
C4A A:PLP401 4.0 21.0 1.0
N A:GLY75 4.0 21.7 1.0
CA A:SER74 4.0 22.1 1.0
CA A:THR73 4.0 22.6 1.0
CD A:GLN147 4.1 24.6 1.0
C A:THR73 4.1 22.6 1.0
CB A:THR73 4.1 22.4 1.0
CA A:THR77 4.2 21.0 1.0
N A:ASN76 4.2 21.4 1.0
O A:HOH552 4.3 19.5 1.0
C A:SER74 4.3 22.0 1.0
O3 A:PLP401 4.6 21.4 1.0
CG2 A:THR77 4.6 21.4 1.0
CE A:LYS46 4.7 20.9 1.0
C A:ASN76 4.7 20.9 1.0
C A:GLY75 4.8 21.6 1.0
CD A:LYS46 4.9 20.6 1.0
CA A:ASN76 4.9 21.3 1.0

Chlorine binding site 2 out of 3 in 5z5c

Go back to Chlorine Binding Sites List in 5z5c
Chlorine binding site 2 out of 3 in the Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form


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 Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:48.5
occ:1.00
 OG C:SER74 2.9 32.8 1.0
N C:SER74 3.2 32.0 1.0
OG1 C:THR73 3.2 32.2 1.0
OG1 C:THR77 3.3 28.5 1.0
OE1 C:GLN147 3.3 30.6 1.0
CB C:THR77 3.3 28.0 1.0
O C:HOH512 3.5 29.1 1.0
NZ C:LYS46 3.5 24.9 1.0
N C:THR77 3.6 26.0 1.0
CB C:SER74 3.8 32.2 1.0
NE2 C:GLN147 3.9 30.9 1.0
CA C:SER74 3.9 32.2 1.0
CD C:GLN147 4.0 30.6 1.0
C4A C:PLP401 4.1 24.9 1.0
N C:GLY75 4.1 30.6 1.0
CA C:THR77 4.1 26.9 1.0
CA C:THR73 4.2 32.5 1.0
C C:THR73 4.2 32.8 1.0
CB C:THR73 4.2 31.8 1.0
O C:HOH538 4.3 20.9 1.0
C C:SER74 4.4 31.8 1.0
N C:ASN76 4.4 26.9 1.0
CG2 C:THR77 4.5 28.8 1.0
C C:ASN76 4.7 26.0 1.0
O3 C:PLP401 4.8 24.6 1.0
C C:GLY75 4.8 28.2 1.0
CE C:LYS46 4.8 24.6 1.0
CA C:ASN76 5.0 25.9 1.0

Chlorine binding site 3 out of 3 in 5z5c

Go back to Chlorine Binding Sites List in 5z5c
Chlorine binding site 3 out of 3 in the Crystal Structure of Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form


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 Hydrogen Sulfide-Producing Enzyme (FN1055) From Fusobacterium Nucleatum: Lysine-Dimethylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:47.2
occ:1.00
 OG D:SER74 2.9 33.9 1.0
OG1 D:THR77 3.2 31.4 1.0
OG1 D:THR73 3.2 32.7 1.0
N D:SER74 3.3 35.0 1.0
CB D:THR77 3.4 31.1 1.0
OE1 D:GLN147 3.4 37.2 1.0
NZ D:LYS46 3.6 30.0 1.0
N D:THR77 3.6 29.9 1.0
O D:HOH503 3.6 53.8 1.0
CB D:SER74 3.9 35.1 1.0
N D:GLY75 3.9 33.3 1.0
C4A D:PLP401 4.0 31.4 1.0
CA D:SER74 4.0 35.1 1.0
NE2 D:GLN147 4.1 36.4 1.0
CA D:THR77 4.1 30.3 1.0
CD D:GLN147 4.2 37.0 1.0
CA D:THR73 4.2 35.2 1.0
CB D:THR73 4.2 33.8 1.0
C D:THR73 4.2 35.2 1.0
N D:ASN76 4.3 30.1 1.0
O D:HOH506 4.3 24.5 1.0
C D:SER74 4.3 34.6 1.0
O3 D:PLP401 4.6 31.0 1.0
CG2 D:THR77 4.7 31.5 1.0
C D:ASN76 4.7 29.5 1.0
C D:GLY75 4.8 30.9 1.0
CA D:ASN76 4.9 29.4 1.0
CE D:LYS46 4.9 28.9 1.0
CA D:GLY75 5.0 32.3 1.0

Reference:

Y.Kezuka, T.Ishida, Y.Yoshida, T.Nonaka. Structural Insights Into the Catalytic Mechanism of Cysteine (Hydroxyl) Lyase From the Hydrogen Sulfide-Producing Oral Pathogen, Biochem. J. V. 475 733 2018.
ISSN: ESSN 1470-8728
PubMed: 29343611
DOI: 10.1042/BCJ20170838
Page generated: Fri Jul 26 21:40:24 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy