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Chlorine in PDB 4dzi: Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10

Protein crystallography data

The structure of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10, PDB code: 4dzi was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.106, 136.131, 93.229, 90.00, 113.09, 90.00
R / Rfree (%) 16.6 / 20.3

Other elements in 4dzi:

The structure of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 also contains other interesting chemical elements:

Cadmium (Cd) 8 atoms
Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 (pdb code 4dzi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10, PDB code: 4dzi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4dzi

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Chlorine binding site 1 out of 6 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:25.4
occ:1.00
 O A:HOH1000 3.0 36.3 1.0
O A:HOH671 3.0 27.2 1.0
O A:HOH999 3.2 37.4 1.0
N A:LYS285 3.2 17.3 1.0
CD A:PRO284 3.5 19.0 1.0
N A:PRO284 3.5 18.6 1.0
C A:HIS283 3.5 16.6 1.0
CA A:HIS283 3.5 13.4 1.0
CB A:LYS285 3.6 17.6 1.0
CB A:ALA220 3.8 19.4 1.0
CG A:LYS285 3.9 22.7 1.0
CA A:LYS285 3.9 16.9 1.0
CG A:PRO284 4.1 22.5 1.0
O A:HIS283 4.1 17.2 1.0
CB A:HIS283 4.1 18.7 1.0
C A:PRO284 4.3 14.8 1.0
CA A:PRO284 4.4 19.4 1.0
O A:HOH810 4.5 37.8 1.0
CD A:LYS285 4.6 28.9 1.0
N A:LEU286 4.6 18.1 1.0
C A:LYS285 4.6 13.8 1.0
O A:ARG282 4.7 21.4 1.0
N A:HIS283 4.8 16.3 1.0
CB A:PRO284 4.9 22.8 1.0

Chlorine binding site 2 out of 6 in 4dzi

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Chlorine binding site 2 out of 6 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:21.5
occ:1.00
 O A:HOH1020 2.8 33.9 1.0
O A:HOH632 2.9 15.3 1.0
N A:SER233 3.0 11.7 1.0
N A:TYR235 3.2 13.3 1.0
N A:GLY234 3.4 13.2 1.0
CB A:TYR235 3.6 14.1 1.0
CA A:SER233 3.6 11.1 1.0
CB A:SER233 3.7 11.1 1.0
C A:SER233 3.7 13.8 1.0
O A:HOH815 3.8 28.9 1.0
O A:SER231 3.8 12.3 1.0
CA A:TYR235 3.9 12.8 1.0
OD1 A:ASP232 4.0 15.2 1.0
C A:ASP232 4.0 12.4 1.0
CD1 A:LEU262 4.0 27.9 1.0
CA A:ASP232 4.1 11.6 1.0
C A:GLY234 4.2 17.1 1.0
CD2 A:LEU262 4.3 36.7 1.0
CA A:GLY234 4.3 15.2 1.0
O A:HOH761 4.4 26.6 1.0
CD1 A:TYR235 4.5 13.5 1.0
CG A:TYR235 4.5 15.4 1.0
OG A:SER233 4.5 11.0 1.0
O A:HOH1021 4.6 42.9 1.0
N A:LEU236 4.6 17.7 1.0
O A:SER233 4.6 13.7 1.0
O A:HOH885 4.6 30.0 1.0
C A:TYR235 4.6 20.4 1.0
O A:HOH610 4.7 12.0 1.0
CG A:LEU262 4.8 44.8 1.0
C A:SER231 4.8 14.1 1.0
CG A:ASP232 4.9 19.0 1.0
O A:HOH609 5.0 12.1 1.0

Chlorine binding site 3 out of 6 in 4dzi

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Chlorine binding site 3 out of 6 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:53.0
occ:1.00
 O A:HOH828 2.7 40.0 1.0
CB A:GLU335 3.1 37.7 1.0
CG A:ARG75 3.2 46.4 1.0
N A:GLU335 3.5 21.2 1.0
CG A:GLU335 3.5 98.0 1.0
CB A:TYR333 3.5 16.5 1.0
CA A:GLU335 3.8 31.6 1.0
CD A:ARG75 4.1 46.7 1.0
CB A:ARG75 4.1 40.1 1.0
CG A:TYR333 4.2 29.7 1.0
NE A:ARG75 4.3 0.6 1.0
CA A:ARG75 4.3 38.2 1.0
N A:TYR334 4.4 23.4 1.0
C A:TYR333 4.5 22.9 1.0
CA A:TYR333 4.6 13.2 1.0
C A:GLU335 4.6 30.0 1.0
C A:TYR334 4.6 26.0 1.0
CD2 A:TYR333 4.6 28.5 1.0
O A:PHE74 4.7 37.1 1.0
O A:HOH1028 4.7 40.0 1.0
CB A:TYR334 4.8 35.2 1.0
CA A:TYR334 4.9 29.8 1.0
N A:ASP336 4.9 21.0 1.0
O A:HOH923 4.9 42.3 1.0
N A:ARG75 4.9 38.1 1.0
O A:HOH1018 4.9 42.3 1.0
CD1 A:TYR333 5.0 23.1 1.0

Chlorine binding site 4 out of 6 in 4dzi

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Chlorine binding site 4 out of 6 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:23.0
occ:1.00
 O B:HOH662 3.0 24.0 1.0
O B:HOH895 3.2 30.9 1.0
N B:LYS285 3.3 16.6 1.0
N B:PRO284 3.5 20.6 1.0
C B:HIS283 3.5 19.4 1.0
CA B:HIS283 3.6 16.4 1.0
CB B:LYS285 3.6 20.0 1.0
CD B:PRO284 3.6 18.9 1.0
CG B:LYS285 3.7 22.8 1.0
CB B:ALA220 3.8 17.1 1.0
CA B:LYS285 3.9 20.4 1.0
CG B:PRO284 4.0 23.0 1.0
CB B:HIS283 4.1 17.2 1.0
O B:HIS283 4.2 17.6 1.0
CD B:LYS285 4.2 29.0 1.0
C B:PRO284 4.3 15.3 1.0
O B:HOH1000 4.3 34.6 1.0
CA B:PRO284 4.4 18.1 1.0
N B:LEU286 4.5 16.5 1.0
C B:LYS285 4.6 18.1 1.0
O B:ARG282 4.7 22.4 1.0
N B:HIS283 4.8 15.9 1.0
CB B:PRO284 4.9 21.2 1.0
ND1 B:HIS283 4.9 17.6 1.0
CG B:HIS283 5.0 16.2 1.0

Chlorine binding site 5 out of 6 in 4dzi

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Chlorine binding site 5 out of 6 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:26.1
occ:1.00
 O C:HOH754 3.1 26.4 1.0
N C:LYS285 3.3 18.2 1.0
N C:PRO284 3.5 22.5 1.0
CD C:PRO284 3.5 21.7 1.0
CB C:LYS285 3.6 23.5 1.0
C C:HIS283 3.6 21.7 1.0
CA C:HIS283 3.6 20.1 1.0
CG C:LYS285 3.7 27.9 1.0
CB C:ALA220 3.8 20.3 1.0
CA C:LYS285 4.0 22.4 1.0
CG C:PRO284 4.1 26.7 1.0
CB C:HIS283 4.2 16.0 1.0
OE1 C:GLU221 4.2 0.5 1.0
O C:HIS283 4.3 18.6 1.0
C C:PRO284 4.4 22.3 1.0
CD C:LYS285 4.4 43.0 1.0
CA C:PRO284 4.5 25.9 1.0
N C:LEU286 4.6 19.7 1.0
CE C:LYS285 4.6 60.7 1.0
O C:ARG282 4.7 20.8 1.0
C C:LYS285 4.7 18.0 1.0
N C:HIS283 4.8 21.9 1.0
ND1 C:HIS283 4.9 19.5 1.0
CB C:PRO284 5.0 25.9 1.0

Chlorine binding site 6 out of 6 in 4dzi

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Chlorine binding site 6 out of 6 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl503

b:25.8
occ:1.00
 O D:HOH912 3.1 35.8 1.0
O D:HOH688 3.2 27.5 1.0
N D:LYS285 3.4 21.7 1.0
CB D:LYS285 3.6 19.1 1.0
CA D:HIS283 3.6 22.7 1.0
C D:HIS283 3.6 19.0 1.0
N D:PRO284 3.6 18.2 1.0
CD D:PRO284 3.6 23.2 1.0
CG D:LYS285 3.9 22.6 1.0
CB D:ALA220 3.9 22.8 1.0
CA D:LYS285 4.0 23.1 1.0
CD D:LYS285 4.0 37.2 1.0
CB D:HIS283 4.1 18.6 1.0
CG D:PRO284 4.1 24.8 1.0
O D:HIS283 4.2 19.0 1.0
C D:PRO284 4.4 16.7 1.0
CA D:PRO284 4.5 19.8 1.0
N D:LEU286 4.6 20.4 1.0
O D:ARG282 4.7 29.2 1.0
C D:LYS285 4.7 22.1 1.0
CE D:LYS285 4.8 97.7 1.0
N D:HIS283 4.8 18.5 1.0
CB D:PRO284 4.9 25.7 1.0
ND1 D:HIS283 4.9 27.0 1.0
CG D:HIS283 5.0 23.8 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo. Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium To Be Published.
Page generated: Fri Jul 11 14:34:20 2025

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