Chlorine in PDB 8dcw: Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)

Enzymatic activity of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)

All present enzymatic activity of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands), PDB code: 8dcw was solved by A.S.Soares, Y.Yamada, J.Jakoncic, D.K.Schneider, H.J.Bernstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.42 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.78, 78.78, 37.57, 90, 90, 90
R / Rfree (%) 18.7 / 23.7

Other elements in 8dcw:

The structure of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) (pdb code 8dcw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands), PDB code: 8dcw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8dcw

Go back to Chlorine Binding Sites List in 8dcw
Chlorine binding site 1 out of 5 in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:41.8
occ:1.00
 O A:HOH344 2.6 32.8 0.5
O A:HOH323 3.3 22.1 1.0
O A:HOH455 3.3 40.3 1.0
N A:ILE88 3.3 21.5 1.0
CG1 A:ILE88 3.7 21.8 1.0
CA A:ASP87 3.7 23.4 1.0
O A:HOH382 3.8 61.4 1.0
NE2 A:HIS15 3.8 26.1 1.0
OD1 A:ASP87 4.0 24.6 1.0
C A:ASP87 4.0 22.4 1.0
O A:SER86 4.1 25.0 1.0
CG A:ASP87 4.2 29.4 1.0
CB A:ILE88 4.3 22.1 1.0
CA A:ILE88 4.4 21.3 1.0
CB A:ASP87 4.4 26.7 1.0
CB A:ALA11 4.4 16.7 1.0
CD1 A:ILE88 4.4 22.7 1.0
CG2 A:ILE88 4.4 22.3 1.0
CZ A:PHE3 4.5 20.3 1.0
CD2 A:HIS15 4.5 25.5 1.0
N A:ASP87 4.7 22.4 1.0
OD2 A:ASP87 4.8 35.9 1.0
CE1 A:HIS15 4.9 25.2 1.0
C A:SER86 4.9 22.8 1.0
N A:THR89 4.9 20.2 1.0
CE2 A:PHE3 5.0 19.9 1.0

Chlorine binding site 2 out of 5 in 8dcw

Go back to Chlorine Binding Sites List in 8dcw
Chlorine binding site 2 out of 5 in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:19.1
occ:1.00
 OH A:TYR23 2.9 14.8 1.0
CE2 A:TYR23 3.6 14.3 1.0
CZ A:TYR23 3.6 14.5 1.0
CA A:GLY104 4.0 15.1 1.0
N A:GLY104 4.7 16.7 1.0
O A:ARG21 4.7 17.1 1.0
O A:HOH322 4.8 26.1 1.0
CE1 A:TYR23 4.9 14.4 1.0
CD2 A:TYR23 4.9 15.4 1.0

Chlorine binding site 3 out of 5 in 8dcw

Go back to Chlorine Binding Sites List in 8dcw
Chlorine binding site 3 out of 5 in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:30.0
occ:1.00
 OG A:SER24 3.1 16.4 1.0
N A:GLY26 3.1 12.7 1.0
O A:HOH365 3.3 36.2 1.0
CB A:SER24 3.4 15.6 1.0
CA A:GLN121 3.5 26.4 1.0
CA A:GLY26 3.7 12.1 1.0
N A:GLN121 3.8 22.9 1.0
CD1 A:ILE124 3.8 26.5 1.0
N A:LEU25 4.0 14.9 1.0
O A:HOH303 4.0 38.6 1.0
CB A:GLN121 4.1 33.1 1.0
CG1 A:ILE124 4.1 24.7 1.0
C A:SER24 4.1 14.8 1.0
C A:VAL120 4.2 22.4 1.0
C A:LEU25 4.3 14.6 1.0
O A:VAL120 4.4 21.8 1.0
CA A:SER24 4.4 15.0 1.0
CG A:GLN121 4.5 41.0 1.0
CG2 A:VAL120 4.5 21.7 1.0
CA A:LEU25 4.6 14.5 1.0
O A:SER24 4.7 14.4 1.0
CB A:LEU25 4.7 15.8 1.0
C A:GLY26 4.7 11.7 1.0
C A:GLN121 4.8 22.3 1.0
N A:ASN27 4.8 11.8 1.0

Chlorine binding site 4 out of 5 in 8dcw

Go back to Chlorine Binding Sites List in 8dcw
Chlorine binding site 4 out of 5 in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:37.0
occ:1.00
 O A:HOH457 3.1 61.8 1.0
O A:HOH428 3.2 39.8 1.0
O A:HOH425 3.5 37.2 1.0
CE A:LYS33 3.9 17.2 1.0
CE2 A:PHE38 3.9 15.8 1.0
NZ A:LYS33 4.1 18.9 1.0
CZ3 A:TRP123 4.1 25.6 1.0
CD A:ARG5 4.2 17.5 1.0
CB A:ARG5 4.2 17.8 1.0
CD A:LYS33 4.4 15.4 1.0
CZ A:PHE38 4.5 15.6 1.0
NE A:ARG5 4.6 18.6 1.0
CG A:ARG5 4.7 17.1 1.0
CD2 A:PHE38 4.8 15.6 1.0
CE3 A:TRP123 4.9 23.6 1.0
CH2 A:TRP123 4.9 24.9 1.0

Chlorine binding site 5 out of 5 in 8dcw

Go back to Chlorine Binding Sites List in 8dcw
Chlorine binding site 5 out of 5 in the Lysozyme Cluster 0062 (Nag and Benzamidine Ligands)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme Cluster 0062 (Nag and Benzamidine Ligands) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:24.0
occ:1.00
 O A:HOH451 3.0 29.5 1.0
O A:HOH389 3.1 12.9 1.0
O A:THR69 3.3 19.7 1.0
N A:THR69 3.3 19.4 1.0
O A:HOH454 3.3 31.5 1.0
O A:HOH396 3.4 23.5 1.0
N A:ARG68 3.5 17.4 1.0
C A:THR69 3.6 20.1 1.0
CA A:GLY67 3.6 16.4 1.0
C A:GLY67 3.7 17.2 1.0
OD1 A:ASN65 3.7 15.9 1.0
N A:GLY67 3.8 16.1 1.0
OG A:SER72 3.8 22.8 1.0
CA A:THR69 3.9 18.5 1.0
O A:HOH436 4.1 19.4 1.0
CB A:THR69 4.3 17.5 1.0
C A:ARG68 4.3 18.5 1.0
OD1 A:ASP66 4.3 13.4 1.0
N A:PRO70 4.3 20.6 1.0
O A:GLY67 4.4 18.4 1.0
CA A:ARG68 4.4 18.1 1.0
NA A:NA201 4.6 17.8 1.0
O A:HOH375 4.8 21.2 0.5
CA A:PRO70 4.8 22.4 1.0
C A:ASP66 4.8 14.3 1.0
N A:ASP66 4.9 13.6 1.0
CB A:SER72 4.9 22.5 1.0
CG A:ASN65 4.9 16.8 1.0
OG1 A:THR69 4.9 15.2 1.0

Reference:

A.S.Soares, Y.Yamada, J.Jakoncic, S.Mcsweeney, R.M.Sweet, J.Skinner, J.Foadi, M.R.Fuchs, D.K.Schneider, W.Shi, B.Andi, L.C.Andrews, H.J.Bernstein. Serial Crystallography with Multi-Stage Merging of Thousands of Images. Acta Crystallogr.,Sect.F V. 78 281 2022.
ISSN: ESSN 2053-230X
PubMed: 35787556
DOI: 10.1107/S2053230X22006422
Page generated: Tue Jul 30 08:43:05 2024

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