Chlorine in PDB 8c4p: Cdaa-Compound 7 Complex

Enzymatic activity of Cdaa-Compound 7 Complex

All present enzymatic activity of Cdaa-Compound 7 Complex:
2.7.7.85;

Protein crystallography data

The structure of Cdaa-Compound 7 Complex, PDB code: 8c4p 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) 45.46 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 41.76, 64.2, 128.78, 90, 90, 90
R / Rfree (%) 13.9 / 16.2

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Cdaa-Compound 7 Complex (pdb code 8c4p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Cdaa-Compound 7 Complex, PDB code: 8c4p:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in 8c4p

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Chlorine binding site 1 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:29.2
occ:0.80
 O A:HOH363 3.0 33.8 1.0
N A:GLU123 3.3 18.1 0.5
N A:GLU123 3.3 19.9 0.5
O A:HOH465 3.4 38.2 1.0
CG A:GLU123 3.5 29.9 0.5
NH1 A:ARG103 3.5 29.1 1.0
CA A:SER122 3.7 16.9 1.0
O A:HOH457 3.9 51.5 1.0
CE1 A:HIS104 4.0 20.2 1.0
C A:SER122 4.0 19.8 1.0
OG A:SER122 4.2 19.3 1.0
OE2 A:GLU123 4.2 38.5 0.5
CB A:GLU123 4.2 22.8 0.5
CD A:GLU123 4.2 36.4 0.5
O A:VAL121 4.3 16.3 1.0
CB A:GLU123 4.3 24.0 0.5
CD A:ARG103 4.3 22.5 1.0
ND1 A:HIS104 4.3 19.8 1.0
CA A:GLU123 4.3 20.9 0.5
CA A:GLU123 4.4 22.8 0.5
CB A:SER122 4.4 18.3 1.0
CZ A:ARG103 4.6 25.2 1.0
N A:GLU124 4.6 22.0 1.0
CB A:ARG103 4.7 20.7 1.0
CG A:GLU124 4.7 38.7 1.0
CG A:ARG103 4.7 22.4 1.0
N A:SER122 4.8 15.7 1.0
NE A:ARG103 4.9 26.9 1.0
C A:VAL121 4.9 15.5 1.0
O A:HOH372 5.0 37.7 1.0

Chlorine binding site 2 out of 14 in 8c4p

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Chlorine binding site 2 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:16.0
occ:0.89
 OG A:SER162 3.1 15.2 1.0
O A:HOH380 3.3 20.3 1.0
CB A:SER162 3.7 15.5 1.0
CA A:SER162 4.1 14.4 1.0
CD2 A:PHE164 4.1 19.6 1.0
CE2 A:PHE164 4.3 22.0 1.0
O A:PRO161 4.5 16.4 1.0
N A:ILE163 4.7 14.2 1.0
C A:SER162 4.9 14.5 1.0

Chlorine binding site 3 out of 14 in 8c4p

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Chlorine binding site 3 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:17.8
occ:0.80
 NE A:ARG7 2.8 34.1 0.4
NH2 A:ARG7 3.0 34.8 0.4
N A:ARG4 3.3 16.0 1.0
CZ A:ARG7 3.3 36.0 0.4
O A:HOH477 3.3 38.5 0.7
NH1 A:ARG4 3.3 16.4 1.0
O A:HOH453 3.6 46.1 1.0
CA A:SER3 3.6 18.3 0.5
CA A:SER3 3.6 17.1 0.5
CD A:ARG4 3.7 16.0 1.0
OG A:SER3 3.9 20.9 0.5
C A:SER3 3.9 17.8 0.5
CD A:ARG7 3.9 28.3 0.4
CB A:ARG4 3.9 15.6 1.0
C A:SER3 3.9 16.9 0.5
CB A:SER3 4.0 24.1 0.5
CG A:ARG4 4.0 18.0 1.0
CG A:ARG7 4.2 19.8 0.6
CA A:ARG4 4.2 16.0 1.0
CB A:SER3 4.3 19.3 0.5
O A:GLY2 4.3 19.1 1.0
CZ A:ARG4 4.3 14.1 1.0
CB A:ARG7 4.3 16.2 0.6
CB A:ARG7 4.3 16.4 0.4
NE A:ARG4 4.4 15.4 1.0
CG A:ARG7 4.5 20.0 0.4
NH1 A:ARG7 4.6 38.6 0.4
O A:ARG4 4.7 14.9 1.0
N A:SER3 4.7 18.7 0.5
N A:SER3 4.8 18.8 0.5
CA A:GLY-1 5.0 17.8 1.0
C A:GLY2 5.0 17.6 1.0
C A:ARG4 5.0 14.8 1.0

Chlorine binding site 4 out of 14 in 8c4p

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Chlorine binding site 4 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:21.2
occ:0.77
 O A:HOH509 3.2 48.2 1.0
NE A:ARG27 3.3 19.8 1.0
NH2 A:ARG27 3.4 21.3 1.0
CZ A:ARG27 3.8 19.6 1.0
O A:GLU124 4.2 30.7 1.0
CD A:ARG27 4.3 19.5 1.0
CG A:ARG27 4.6 17.5 1.0
O A:HOH358 4.9 47.9 1.0

Chlorine binding site 5 out of 14 in 8c4p

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Chlorine binding site 5 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:15.8
occ:0.80
 N A:GLY-1 3.2 15.8 1.0
NH2 A:ARG4 3.2 14.9 1.0
N A:TYR1 3.3 18.7 1.0
N A:SER0 3.5 19.2 1.0
O A:HOH452 3.7 30.6 1.0
CB A:TYR1 3.8 19.3 1.0
N A:GLY2 3.9 19.4 1.0
CA A:GLY-1 3.9 17.8 1.0
C A:GLY-1 3.9 19.4 1.0
CA A:TYR1 3.9 19.6 1.0
CD2 A:TYR1 4.0 21.5 1.0
CA A:LEU-2 4.0 15.4 1.0
NH1 A:ARG4 4.1 16.4 1.0
C A:LEU-2 4.1 16.3 1.0
CG2 A:ILE163 4.1 16.2 1.0
CZ A:ARG4 4.1 14.1 1.0
O A:PRO-3 4.1 18.8 1.0
O A:GLY2 4.2 19.1 1.0
C A:TYR1 4.2 20.2 1.0
C A:SER0 4.3 21.2 1.0
CA A:SER0 4.4 21.5 1.0
CG A:TYR1 4.4 19.8 1.0
CD2 A:LEU-2 4.6 17.0 1.0
CB A:SER0 4.7 23.3 1.0
O A:GLY-1 4.7 23.6 1.0
CA A:GLY2 4.9 18.7 1.0
C A:GLY2 4.9 17.6 1.0
CB A:LEU-2 4.9 15.9 1.0
C A:PRO-3 5.0 17.4 1.0

Chlorine binding site 6 out of 14 in 8c4p

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Chlorine binding site 6 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:31.9
occ:0.86
 O A:HOH532 2.4 46.1 1.0
O A:HOH527 3.1 47.2 1.0
OG A:SER56 3.2 17.0 0.8
OG A:SER56 3.3 11.5 0.2
CD1 A:ILE60 3.8 13.9 1.0
CB A:SER56 4.0 11.5 0.2
CB A:SER56 4.0 16.9 0.8
CG A:GLN57 4.1 14.9 1.0
CD A:GLN57 4.1 15.4 1.0
NE2 A:GLN57 4.1 18.5 1.0
O A:HOH379 4.2 51.1 0.9
N A:GLN57 4.4 12.9 1.0
C A:SER56 4.6 11.7 0.2
C A:SER56 4.6 13.7 0.8
OE1 A:GLN57 4.7 16.3 1.0
O A:HOH537 4.7 45.1 1.0
CA A:GLN57 4.7 13.2 1.0
CL A:CL208 4.8 24.9 0.8
CD2 A:TYR22 4.9 18.2 1.0
O A:SER56 4.9 10.7 0.2
CA A:SER56 4.9 12.2 0.2
CA A:SER56 4.9 14.0 0.8
O A:SER56 5.0 15.2 0.8

Chlorine binding site 7 out of 14 in 8c4p

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Chlorine binding site 7 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:24.9
occ:0.81
 NE2 A:GLN57 3.2 18.5 1.0
O A:HOH532 3.6 46.1 1.0
CG A:GLN57 3.8 14.9 1.0
CD A:GLN57 4.0 15.4 1.0
O A:HOH516 4.5 33.4 1.0
CB B:PRO68 4.7 17.7 1.0
CL A:CL207 4.8 31.9 0.9

Chlorine binding site 8 out of 14 in 8c4p

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Chlorine binding site 8 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:25.1
occ:0.72
 N A:LEU90 3.2 19.9 1.0
OH A:TYR87 3.2 33.1 0.6
O A:HOH521 3.4 33.1 0.5
C6 A:TJ9201 3.6 36.1 0.8
O A:HOH525 3.7 49.7 1.0
CA A:PRO89 3.8 19.5 1.0
C A:PRO89 4.0 19.4 1.0
CB A:LEU90 4.0 23.0 1.0
CE2 A:TYR87 4.1 33.6 0.6
CZ A:TYR87 4.1 32.2 0.6
CA A:LEU90 4.1 19.9 1.0
O A:LEU90 4.2 22.4 1.0
CG A:LEU90 4.2 25.1 1.0
CB A:PRO89 4.4 23.2 1.0
C A:LEU90 4.6 20.5 1.0
O A:LEU88 4.7 21.8 1.0
C5 A:TJ9201 4.7 32.1 0.8
CD1 A:LEU90 4.9 30.9 1.0
N A:PRO89 5.0 18.3 1.0

Chlorine binding site 9 out of 14 in 8c4p

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Chlorine binding site 9 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:36.1
occ:1.00
 N A:GLU142 3.2 20.8 0.4
N A:GLU142 3.2 18.9 0.6
O A:HOH468 3.5 41.2 1.0
O A:HOH502 3.5 42.1 1.0
CG A:GLU142 3.6 26.1 0.4
CA A:SER141 3.7 19.8 1.0
CG A:GLU142 3.7 22.4 0.6
O A:HOH456 3.7 27.0 1.0
CB A:SER141 3.8 20.9 1.0
C A:SER141 3.9 18.9 1.0
CB A:GLU142 4.1 24.7 0.4
CB A:GLU142 4.1 21.6 0.6
CD A:GLU142 4.2 29.5 0.6
O A:HOH538 4.2 50.1 1.0
CA A:GLU142 4.2 22.5 0.4
CA A:GLU142 4.2 19.9 0.6
OE2 A:GLU142 4.3 28.9 0.4
O A:HOH505 4.4 22.0 1.0
CD A:GLU142 4.5 27.7 0.4
OE2 A:GLU142 4.6 33.7 0.6
OE1 A:GLU142 4.7 30.1 0.6
O A:HOH442 4.9 36.5 0.7
O A:HOH540 4.9 53.4 1.0
N A:SER141 5.0 19.0 1.0
OG A:SER141 5.0 21.8 1.0
O A:HOH393 5.0 39.1 1.0

Chlorine binding site 10 out of 14 in 8c4p

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Chlorine binding site 10 out of 14 in the Cdaa-Compound 7 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Cdaa-Compound 7 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:38.5
occ:0.81
 OG B:SER56 3.0 21.6 1.0
CB B:SER56 3.8 17.7 1.0
CD1 B:ILE60 3.8 15.7 1.0
CG B:GLN57 3.8 17.7 1.0
CD B:GLN57 4.0 20.1 1.0
N B:GLN57 4.1 14.1 1.0
C B:SER56 4.2 14.0 1.0
CA B:GLN57 4.3 14.9 1.0
NE2 B:GLN57 4.3 24.8 1.0
CE B:LYS18 4.3 44.5 1.0
OE1 B:GLN57 4.4 19.9 1.0
O B:SER56 4.6 14.2 1.0
CA B:SER56 4.6 14.7 1.0
CG A:PRO68 4.7 23.1 1.0
CB B:GLN57 4.7 16.9 1.0
NZ B:LYS18 4.7 48.5 1.0
O A:HOH531 4.9 58.3 1.0
CB A:PRO68 4.9 22.2 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: Tue Jul 30 07:40:24 2024

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