Chlorine in PDB 8c4q: Cdaa-Apo

Enzymatic activity of Cdaa-Apo

All present enzymatic activity of Cdaa-Apo:
2.7.7.85;

Protein crystallography data

The structure of Cdaa-Apo, PDB code: 8c4q was solved by P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.87 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.7, 64.52, 129.48, 90, 90, 90
R / Rfree (%) 19 / 21.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cdaa-Apo (pdb code 8c4q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Cdaa-Apo, PDB code: 8c4q:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8c4q

Go back to Chlorine Binding Sites List in 8c4q
Chlorine binding site 1 out of 5 in the Cdaa-Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cdaa-Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:44.0
occ:0.90
 O A:HOH387 3.3 52.9 0.9
N A:GLU123 3.3 36.9 1.0
NH1 A:ARG103 3.4 44.6 1.0
CA A:SER122 3.7 34.4 1.0
CG A:GLU123 3.8 46.2 1.0
CE1 A:HIS104 4.0 33.4 1.0
C A:SER122 4.0 35.1 1.0
OG A:SER122 4.0 37.5 1.0
O A:HOH398 4.1 59.5 1.0
CB A:SER122 4.2 34.6 1.0
CD A:ARG103 4.3 37.8 1.0
ND1 A:HIS104 4.3 34.0 1.0
CB A:GLU123 4.3 41.9 1.0
CA A:GLU123 4.3 40.6 1.0
O A:VAL121 4.4 35.7 1.0
OE2 A:GLU123 4.5 55.1 1.0
N A:GLU124 4.5 43.5 1.0
CZ A:ARG103 4.5 41.5 1.0
CB A:ARG103 4.6 35.3 1.0
CG A:ARG103 4.6 37.3 1.0
CD A:GLU123 4.7 52.2 1.0
O A:HOH302 4.8 121.0 0.0
N A:SER122 4.8 35.2 1.0
NE A:ARG103 4.9 39.8 1.0
CG A:GLU124 4.9 56.2 1.0
O A:HOH322 4.9 48.2 1.0
C A:GLU123 4.9 43.6 1.0

Chlorine binding site 2 out of 5 in 8c4q

Go back to Chlorine Binding Sites List in 8c4q
Chlorine binding site 2 out of 5 in the Cdaa-Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cdaa-Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:50.9
occ:0.80
 OG B:SER56 2.9 38.3 1.0
CG B:GLN57 3.7 32.2 1.0
CB B:SER56 3.7 33.4 1.0
CD1 B:ILE60 3.8 27.6 1.0
N B:GLN57 4.0 29.0 1.0
CD B:GLN57 4.0 36.6 1.0
C B:SER56 4.2 29.5 1.0
CA B:GLN57 4.2 30.0 1.0
OE1 B:GLN57 4.4 33.4 1.0
NZ B:LYS18 4.4 57.1 1.0
NE2 B:GLN57 4.4 41.3 1.0
CB B:GLN57 4.6 31.9 1.0
CA B:SER56 4.6 28.5 1.0
O B:SER56 4.6 30.0 1.0
CG A:PRO68 4.8 38.5 1.0
CE B:LYS18 4.9 54.1 1.0
CB A:PRO68 4.9 38.9 1.0

Chlorine binding site 3 out of 5 in 8c4q

Go back to Chlorine Binding Sites List in 8c4q
Chlorine binding site 3 out of 5 in the Cdaa-Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cdaa-Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:43.0
occ:0.84
 O B:HOH380 3.1 50.6 1.0
NH1 B:ARG103 3.2 45.8 1.0
N B:GLU123 3.3 38.7 1.0
CA B:SER122 3.7 36.0 1.0
CE1 B:HIS104 3.7 36.8 1.0
CG B:GLU123 3.7 48.9 1.0
OG B:SER122 3.9 39.8 1.0
C B:SER122 4.0 38.4 1.0
ND1 B:HIS104 4.1 35.2 1.0
CB B:SER122 4.2 38.0 1.0
CA B:GLU123 4.3 41.1 1.0
CB B:GLU123 4.3 44.6 1.0
CZ B:ARG103 4.4 48.7 1.0
CA B:GLY101 4.5 48.8 1.0
N B:GLU124 4.5 43.9 1.0
N B:GLY101 4.5 52.1 1.0
O B:VAL121 4.5 34.8 1.0
OE2 B:GLU123 4.6 53.6 1.0
CD B:ARG103 4.6 48.9 1.0
CD B:GLU123 4.7 51.8 1.0
O B:HOH324 4.7 53.5 1.0
N B:SER122 4.8 33.8 1.0
O B:HOH369 4.8 60.3 1.0
CG B:GLU124 4.8 52.9 1.0
C B:GLU123 4.9 43.6 1.0
O B:HOH372 4.9 57.5 1.0
NE2 B:HIS104 4.9 37.5 1.0
CB B:ARG103 4.9 38.8 1.0
NE B:ARG103 5.0 51.2 1.0

Chlorine binding site 4 out of 5 in 8c4q

Go back to Chlorine Binding Sites List in 8c4q
Chlorine binding site 4 out of 5 in the Cdaa-Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cdaa-Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:110.5
occ:1.00
 N B:LYS98 3.5 47.9 1.0
CA B:SER97 3.9 47.5 1.0
CG B:LYS98 3.9 56.4 1.0
CD B:LYS98 4.0 59.7 1.0
OG B:SER97 4.1 53.6 1.0
C B:SER97 4.2 47.3 1.0
CB B:LYS98 4.2 54.2 1.0
CB B:SER97 4.4 50.1 1.0
CA B:LYS98 4.5 52.0 1.0
NZ B:LYS98 4.6 64.1 1.0
CE B:LYS98 4.7 61.9 1.0
O B:LEU96 4.8 45.0 1.0
N B:SER97 4.9 44.3 1.0

Chlorine binding site 5 out of 5 in 8c4q

Go back to Chlorine Binding Sites List in 8c4q
Chlorine binding site 5 out of 5 in the Cdaa-Apo


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cdaa-Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:85.3
occ:1.00
 O B:HOH381 3.0 58.1 1.0
CG B:ARG7 3.7 47.9 1.0
CD B:ARG7 3.7 50.1 1.0
CB B:HIS11 4.0 32.7 1.0
O B:HOH311 4.2 65.3 1.0
O B:ARG7 4.2 34.7 1.0
O B:HOH310 4.2 60.8 1.0
CG B:HIS11 4.3 33.4 1.0
O B:HOH353 4.5 48.3 1.0
C B:ARG7 4.5 35.6 1.0
O B:HOH401 4.7 59.0 1.0
CA B:GLU8 4.7 35.3 1.0
N B:GLU8 4.7 35.9 1.0
CB B:ARG7 4.8 43.4 1.0
CD2 B:HIS11 4.8 34.7 1.0
ND1 B:HIS11 4.8 35.8 1.0
CG B:GLU8 4.9 45.9 1.0

Reference:

P.Neumann, P.Kloskowski, R.Ficner. Computer-Aided Design of A Cyclic Di-Amp Synthesizing Enzyme Cdaa Inhibitor. Microlife V. 4 AD021 2023.
ISSN: ISSN 2633-6693
PubMed: 37223749
DOI: 10.1093/FEMSML/UQAD021
Page generated: Wed Jul 26 15:46:38 2023

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