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: Sat Dec 12 12:41:50 2020

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