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Chlorine in PDB 6hvn: Cdaa-Apo Y187A Mutant

Enzymatic activity of Cdaa-Apo Y187A Mutant

All present enzymatic activity of Cdaa-Apo Y187A Mutant:
2.7.7.85;

Protein crystallography data

The structure of Cdaa-Apo Y187A Mutant, PDB code: 6hvn was solved by J.L.Heidemann, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.94 / 2.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.490, 65.130, 131.320, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cdaa-Apo Y187A Mutant (pdb code 6hvn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Cdaa-Apo Y187A Mutant, PDB code: 6hvn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6hvn

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Chlorine binding site 1 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:39.8
occ:1.00
 N A:GLU123 3.3 30.6 1.0
O A:HOH367 3.4 43.8 1.0
NH1 A:ARG103 3.5 35.2 1.0
CA A:SER122 3.7 26.1 1.0
CG A:GLU123 3.9 49.3 1.0
C A:SER122 4.0 29.3 1.0
OG A:SER122 4.0 32.0 1.0
CE1 A:HIS104 4.0 29.5 1.0
CD A:ARG103 4.0 28.7 1.0
CB A:SER122 4.3 29.6 1.0
O A:VAL121 4.3 30.1 1.0
CA A:GLU123 4.3 34.5 1.0
ND1 A:HIS104 4.3 30.3 1.0
CB A:GLU123 4.3 40.8 1.0
CG A:ARG103 4.5 24.2 1.0
CB A:ARG103 4.6 26.9 1.0
CZ A:ARG103 4.6 40.3 1.0
N A:GLU124 4.6 36.0 1.0
OE1 A:GLU123 4.7 59.5 1.0
N A:SER122 4.7 26.2 1.0
NE A:ARG103 4.8 37.4 1.0
CD A:GLU123 4.8 59.5 1.0
O A:HOH302 4.8 46.3 1.0
C A:VAL121 4.9 27.3 1.0
CG A:GLU124 4.9 51.3 1.0
C A:GLU123 5.0 36.8 1.0

Chlorine binding site 2 out of 8 in 6hvn

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Chlorine binding site 2 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:60.6
occ:1.00
 N A:GLU142 3.4 29.2 1.0
CA A:SER141 3.8 33.5 1.0
CL A:CL204 3.9 56.8 1.0
CB A:SER141 3.9 31.3 1.0
CG A:GLU142 4.0 48.5 1.0
C A:SER141 4.1 29.9 1.0
CB A:GLU142 4.2 37.0 1.0
CA A:GLU142 4.4 30.5 1.0
CD A:GLU142 4.6 55.0 1.0
OE2 A:GLU142 5.0 58.2 1.0

Chlorine binding site 3 out of 8 in 6hvn

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Chlorine binding site 3 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:59.1
occ:1.00
 O A:HOH383 3.1 44.1 1.0
NH1 A:ARG26 3.1 37.5 1.0
NH2 A:ARG26 3.2 33.5 1.0
NZ A:LYS25 3.5 40.4 1.0
CZ A:ARG26 3.6 35.9 1.0
CD A:LYS25 3.6 51.1 1.0
CD2 A:TYR22 3.6 31.7 1.0
CE A:LYS25 4.1 44.3 1.0
CE2 A:TYR22 4.2 34.5 1.0
CG A:TYR22 4.3 33.9 1.0
CA A:TYR22 4.4 30.0 1.0
CB A:TYR22 4.5 31.6 1.0
CG A:LYS25 4.6 49.7 1.0
NE A:ARG26 4.9 32.0 1.0

Chlorine binding site 4 out of 8 in 6hvn

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Chlorine binding site 4 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:56.8
occ:1.00
 N A:GLU143 3.2 30.9 1.0
CB A:GLU143 3.5 46.2 1.0
N A:GLU142 3.7 29.2 1.0
CB A:GLU142 3.9 37.0 1.0
CB A:SER141 3.9 31.3 1.0
CL A:CL202 3.9 60.6 1.0
OG A:SER141 4.0 31.0 1.0
CA A:GLU143 4.0 35.8 1.0
C A:GLU142 4.1 32.2 1.0
CA A:GLU142 4.1 30.5 1.0
C A:SER141 4.5 29.9 1.0
OE1 A:GLU143 4.5 84.9 1.0
CA A:SER141 4.7 33.5 1.0
CG A:GLU143 4.9 64.3 1.0
CG A:GLU142 4.9 48.5 1.0

Chlorine binding site 5 out of 8 in 6hvn

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Chlorine binding site 5 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:49.1
occ:1.00
 NH2 A:ARG7 3.2 31.5 1.0
NE A:ARG7 3.3 40.8 1.0
O A:HOH347 3.3 35.6 1.0
N A:LEU-2 3.4 53.2 1.0
CB A:LEU-2 3.5 43.7 1.0
CD A:PRO-3 3.6 65.3 1.0
CA A:GLY-4 3.6 60.8 1.0
N A:PRO-3 3.7 65.0 1.0
CZ A:ARG7 3.7 37.3 1.0
C A:GLY-4 3.8 63.1 1.0
CG A:LEU-2 3.9 40.0 1.0
CA A:LEU-2 4.0 52.1 1.0
CG A:PRO-3 4.0 64.0 1.0
CD1 A:LEU-2 4.2 38.2 1.0
CG A:ARG4 4.2 41.6 1.0
N A:GLY-4 4.2 61.4 1.0
N A:GLY-1 4.2 45.5 1.0
O A:GLY-1 4.4 40.8 1.0
CD A:ARG7 4.4 34.4 1.0
C A:PRO-3 4.5 59.4 1.0
CA A:PRO-3 4.6 63.6 1.0
C A:LEU-2 4.6 53.8 1.0
O A:GLY-4 4.6 64.6 1.0
CB A:ARG7 4.8 29.6 1.0
CA A:ARG4 4.9 37.9 1.0
CB A:PRO-3 4.9 65.2 1.0
CB A:ARG4 5.0 39.0 1.0

Chlorine binding site 6 out of 8 in 6hvn

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Chlorine binding site 6 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:38.4
occ:1.00
 N B:GLU123 3.2 33.1 1.0
NH2 B:ARG103 3.3 34.4 1.0
O B:HOH307 3.6 57.4 1.0
CA B:SER122 3.7 29.8 1.0
CG B:GLU123 3.8 54.3 1.0
CE1 B:HIS104 3.9 29.9 1.0
CD B:ARG103 3.9 35.1 1.0
C B:SER122 3.9 30.0 1.0
OG B:SER122 4.1 29.8 1.0
ND1 B:HIS104 4.2 28.2 1.0
CA B:GLU123 4.2 41.6 1.0
CB B:GLU123 4.2 46.0 1.0
CB B:SER122 4.3 29.6 1.0
O B:VAL121 4.3 29.0 1.0
CZ B:ARG103 4.4 36.1 1.0
CB B:ARG103 4.4 29.6 1.0
OE2 B:GLU123 4.4 62.1 1.0
N B:GLU124 4.6 43.2 1.0
NE B:ARG103 4.6 36.3 1.0
CD B:GLU123 4.6 59.4 1.0
CG B:ARG103 4.7 33.5 1.0
N B:SER122 4.8 29.9 1.0
C B:GLU123 4.9 42.5 1.0
C B:VAL121 5.0 32.2 1.0
CG B:GLU124 5.0 65.8 1.0
O B:HOH311 5.0 52.1 1.0

Chlorine binding site 7 out of 8 in 6hvn

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Chlorine binding site 7 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:55.5
occ:1.00
 CD B:ARG7 3.3 72.0 1.0
NH2 B:ARG7 3.5 69.9 1.0
CB B:ARG7 3.7 61.0 1.0
NE B:ARG7 4.0 74.3 1.0
CZ B:ARG7 4.0 73.1 1.0
CG B:ARG7 4.1 69.2 1.0
CA B:ARG7 4.6 55.6 1.0
N B:ARG7 4.7 57.5 1.0

Chlorine binding site 8 out of 8 in 6hvn

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Chlorine binding site 8 out of 8 in the Cdaa-Apo Y187A Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Cdaa-Apo Y187A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:65.2
occ:1.00
 O B:HOH316 3.3 25.5 1.0
NE B:ARG138 3.3 42.1 1.0
OG1 B:THR125 3.6 45.1 1.0
NH2 B:ARG138 3.8 41.3 1.0
CB B:ASP139 4.0 45.9 1.0
CA B:GLY127 4.0 34.4 1.0
CZ B:ARG138 4.0 46.5 1.0
CG B:ARG138 4.1 34.6 1.0
O B:HOH311 4.2 52.1 1.0
CD B:ARG138 4.3 43.3 1.0
C B:GLY127 4.4 36.8 1.0
OG B:SER129 4.4 34.6 1.0
CA B:ASP139 4.4 35.8 1.0
N B:ASP139 4.5 32.7 1.0
CB B:SER122 4.5 29.6 1.0
CG B:ASP139 4.5 54.9 1.0
N B:GLY127 4.5 25.5 1.0
O B:GLY127 4.6 35.3 1.0
OD1 B:ASP139 4.6 60.6 1.0
CD2 B:LEU100 4.7 38.2 1.0
CB B:THR125 4.8 35.0 1.0
OG B:SER122 4.9 29.8 1.0
NE2 B:HIS104 5.0 29.1 1.0

Reference:

J.L.Heidemann, P.Neumann, A.Dickmanns, R.Ficner. Crystal Structures of the C-Di-Amp-Synthesizing Enzyme Cdaa. J.Biol.Chem. V. 294 10463 2019.
ISSN: ESSN 1083-351X
PubMed: 31118276
DOI: 10.1074/JBC.RA119.009246
Page generated: Sat Jul 12 15:27:19 2025

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