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Chlorine in PDB 2ygy: Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II

Enzymatic activity of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II

All present enzymatic activity of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II:
4.1.3.3;

Protein crystallography data

The structure of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II, PDB code: 2ygy was solved by I.Campeotto, A.Nelson, A.Berry, S.E.V.Phillips, A.R.Pearson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.59 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.260, 95.870, 91.380, 90.00, 115.33, 90.00
R / Rfree (%) 19.4 / 22.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II (pdb code 2ygy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II, PDB code: 2ygy:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2ygy

Go back to Chlorine Binding Sites List in 2ygy
Chlorine binding site 1 out of 4 in the Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1298

b:25.3
occ:1.00
 NZ A:LYS165 3.1 23.1 1.0
OG1 A:THR48 3.1 16.2 1.0
N A:SER47 3.2 17.7 1.0
N A:THR48 3.3 16.8 1.0
OH A:TYR137 3.6 30.2 1.0
CB A:THR48 3.7 16.5 1.0
CA A:GLY46 3.7 16.7 1.0
C A:GLY46 3.7 16.8 1.0
CE2 A:TYR43 3.8 14.1 1.0
OG A:SER47 3.9 22.7 1.0
CB A:ALA11 3.9 14.8 1.0
CD2 A:TYR43 4.0 14.1 1.0
CA A:SER47 4.0 18.7 1.0
CB A:SER47 4.0 19.5 1.0
CA A:THR48 4.1 16.3 1.0
C A:SER47 4.2 17.4 1.0
O A:HOH2007 4.2 16.6 1.0
CZ A:TYR137 4.3 29.8 1.0
CE A:LYS165 4.4 22.1 1.0
CE2 A:TYR137 4.5 29.5 1.0
O A:GLY46 4.7 16.1 1.0
N A:GLY46 4.8 16.4 1.0
CZ A:TYR43 5.0 14.3 1.0

Chlorine binding site 2 out of 4 in 2ygy

Go back to Chlorine Binding Sites List in 2ygy
Chlorine binding site 2 out of 4 in the Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1297

b:19.4
occ:1.00
 OG1 B:THR48 3.0 15.0 1.0
N B:THR48 3.3 15.6 1.0
N B:SER47 3.5 16.4 1.0
NZ B:LYS165 3.5 22.1 1.0
CB B:THR48 3.6 15.3 1.0
CB B:ALA11 3.8 13.0 1.0
CE2 B:TYR43 3.9 11.7 1.0
CA B:GLY46 3.9 14.9 1.0
C B:GLY46 3.9 15.5 1.0
CD2 B:TYR43 4.0 11.9 1.0
CA B:THR48 4.0 15.1 1.0
CB B:SER47 4.1 18.5 1.0
CA B:SER47 4.1 17.3 1.0
C B:SER47 4.2 15.9 1.0
O B:HOH2007 4.4 15.6 1.0
OG B:SER47 4.6 21.8 1.0
OH B:TYR137 4.7 19.1 1.0
CE B:LYS165 4.7 21.2 1.0
O B:GLY46 4.8 14.9 1.0
N B:GLY46 4.9 14.7 1.0
CG2 B:THR48 4.9 14.3 1.0

Chlorine binding site 3 out of 4 in 2ygy

Go back to Chlorine Binding Sites List in 2ygy
Chlorine binding site 3 out of 4 in the Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1298

b:17.3
occ:1.00
 OG1 C:THR48 3.1 14.3 1.0
N C:THR48 3.3 14.2 1.0
NZ C:LYS165 3.3 22.9 1.0
N C:SER47 3.5 14.6 1.0
CB C:THR48 3.6 14.0 1.0
O C:HOH2031 3.8 33.3 1.0
CE2 C:TYR43 3.8 13.7 1.0
CB C:ALA11 3.8 13.0 1.0
CA C:GLY46 3.8 13.8 1.0
C C:GLY46 3.9 14.0 1.0
CD2 C:TYR43 4.0 13.8 1.0
CA C:THR48 4.1 14.1 1.0
CB C:SER47 4.1 16.4 1.0
CA C:SER47 4.1 15.2 1.0
C C:SER47 4.2 14.3 1.0
O C:HOH2006 4.4 13.7 1.0
OH C:TYR137 4.5 18.2 1.0
OG C:SER47 4.6 19.3 1.0
CE C:LYS165 4.6 22.1 1.0
O C:GLY46 4.8 13.4 1.0
N C:GLY46 4.9 13.6 1.0

Chlorine binding site 4 out of 4 in 2ygy

Go back to Chlorine Binding Sites List in 2ygy
Chlorine binding site 4 out of 4 in the Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Wild Type E. Coli N-Acetylneuraminic Acid Lyase in Space Group P21 Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1298

b:19.5
occ:1.00
 OG1 D:THR48 3.0 13.7 1.0
NZ D:LYS165 3.2 21.3 1.0
N D:THR48 3.4 14.6 1.0
N D:SER47 3.4 14.7 1.0
CB D:THR48 3.6 13.9 1.0
O D:HOH2042 3.6 23.6 1.0
CA D:GLY46 3.9 13.3 1.0
C D:GLY46 3.9 13.6 1.0
CB D:ALA11 3.9 10.3 1.0
OG D:SER47 3.9 20.1 1.0
CE2 D:TYR43 3.9 12.1 1.0
CB D:SER47 4.0 16.6 1.0
CD2 D:TYR43 4.1 12.4 1.0
CA D:SER47 4.1 15.6 1.0
CA D:THR48 4.1 14.0 1.0
C D:SER47 4.3 14.4 1.0
O D:HOH2043 4.4 25.9 1.0
CE D:LYS165 4.4 20.3 1.0
O D:HOH2008 4.5 9.6 1.0
OH D:TYR137 4.6 22.2 1.0
O D:GLY46 4.8 12.6 1.0
N D:GLY46 4.9 13.2 1.0
CG2 D:THR48 5.0 13.8 1.0

Reference:

I.Campeotto, A.Lebedev, A.M.M.Schreurs, L.M.J.Kroon-Batenburg, E.Lowe, S.E.V.Phillips, G.N.Murshudov, A.R.Pearson. Pathological Macromolecular Crystallographic Data Affected By Twinning, Partial-Disorder and Exhibiting Multiple Lattices For Testing of Data Processing and Refinement Tools. Sci Rep V. 8 14876 2018.
ISSN: ESSN 2045-2322
PubMed: 30291262
DOI: 10.1038/S41598-018-32962-6
Page generated: Sat Jul 20 15:01:33 2024

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