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Chlorine in PDB 5e2h: Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis

Enzymatic activity of Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis

All present enzymatic activity of Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis, PDB code: 5e2h was solved by Y.Kim, C.Hatzos-Skintges, M.Endres, G.Babnigg, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.55 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.779, 73.682, 113.413, 90.00, 90.19, 90.00
R / Rfree (%) 16.4 / 19.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis (pdb code 5e2h). 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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis, PDB code: 5e2h:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5e2h

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Chlorine binding site 1 out of 6 in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis


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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:45.4
occ:1.00
 O A:HOH590 3.1 46.3 1.0
N A:VAL185 3.2 27.3 1.0
CG2 A:VAL185 3.8 25.1 1.0
CB A:VAL185 3.8 27.6 1.0
NZ A:LYS219 3.9 30.9 1.0
CE A:LYS219 3.9 31.5 1.0
CA A:ASP184 4.0 32.0 1.0
C A:ASP184 4.1 29.9 1.0
CA A:VAL185 4.1 28.7 1.0
O A:VAL183 4.1 34.6 1.0
CE2 A:TYR193 4.3 27.8 1.0
O A:VAL185 4.6 33.5 1.0
CE A:MSE190 4.8 41.4 1.0
C A:VAL185 4.9 33.3 1.0
OD1 A:ASP184 4.9 41.0 1.0
CB A:ASP184 4.9 37.5 1.0
C A:VAL183 4.9 32.4 1.0
N A:ASP184 4.9 29.3 1.0
CD2 A:TYR193 5.0 28.5 1.0

Chlorine binding site 2 out of 6 in 5e2h

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Chlorine binding site 2 out of 6 in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis


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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:37.0
occ:1.00
 O A:HOH550 3.0 31.9 1.0
N A:PHE115 3.3 33.4 1.0
CA A:GLN114 3.5 35.4 1.0
CB A:GLN114 3.7 39.8 1.0
CB A:ASN146 3.8 24.8 1.0
CD2 A:PHE115 3.9 35.5 1.0
C A:GLN114 4.0 35.8 1.0
CG A:GLN114 4.1 43.2 1.0
CD A:PRO147 4.3 30.7 1.0
CB A:PHE115 4.3 35.9 1.0
ND2 A:ASN146 4.4 31.5 1.0
CA A:PHE115 4.4 35.5 1.0
CE2 A:TYR216 4.4 29.8 1.0
CG A:ASN146 4.5 29.1 1.0
CG A:PHE115 4.5 33.2 1.0
O A:LEU113 4.6 30.9 1.0
CG A:PRO147 4.7 35.5 1.0
O A:VAL210 4.7 30.3 1.0
CE2 A:PHE115 4.7 37.3 1.0
N A:GLN114 4.8 33.8 1.0
OH A:TYR216 4.8 29.8 1.0
N A:PRO147 4.9 30.6 1.0

Chlorine binding site 3 out of 6 in 5e2h

Go back to Chlorine Binding Sites List in 5e2h
Chlorine binding site 3 out of 6 in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis


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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:39.2
occ:1.00
 N B:VAL185 3.2 29.4 1.0
NZ B:LYS219 3.7 29.4 1.0
CG2 B:VAL185 3.9 26.8 1.0
CB B:VAL185 3.9 28.0 1.0
CA B:ASP184 4.0 35.2 1.0
C B:ASP184 4.1 31.9 1.0
O B:VAL183 4.1 34.5 1.0
CA B:VAL185 4.1 28.4 1.0
CE B:LYS219 4.2 32.0 1.0
CD B:LYS219 4.2 34.5 1.0
CE2 B:TYR193 4.3 28.2 1.0
OD1 B:ASP184 4.6 47.8 1.0
O B:VAL185 4.7 33.6 1.0
CE B:MSE190 4.8 39.3 1.0
CB B:ASP184 4.9 41.2 1.0
N B:ASP184 4.9 31.5 1.0
C B:VAL183 4.9 33.5 1.0
C B:VAL185 4.9 31.5 1.0
OH B:TYR193 5.0 24.9 1.0

Chlorine binding site 4 out of 6 in 5e2h

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Chlorine binding site 4 out of 6 in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis


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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:36.8
occ:1.00
 O B:HOH529 3.1 30.6 1.0
N B:PHE115 3.3 34.5 1.0
CA B:GLN114 3.5 35.7 1.0
CB B:GLN114 3.7 40.1 1.0
CB B:ASN146 3.8 29.1 1.0
C B:GLN114 3.9 35.4 1.0
CG B:GLN114 4.0 46.2 1.0
CD2 B:PHE115 4.0 35.2 1.0
CB B:PHE115 4.4 36.9 1.0
ND2 B:ASN146 4.4 33.6 1.0
CD B:PRO147 4.4 29.3 1.0
CA B:PHE115 4.4 36.1 1.0
CE2 B:TYR216 4.4 30.2 1.0
CG B:ASN146 4.5 32.9 1.0
O B:LEU113 4.5 30.1 1.0
CG B:PHE115 4.6 34.9 1.0
CG B:PRO147 4.8 31.1 1.0
N B:GLN114 4.8 35.4 1.0
O B:VAL210 4.8 31.1 1.0
OH B:TYR216 4.9 28.2 1.0
CD B:GLN114 4.9 54.8 1.0
OE1 B:GLN114 4.9 58.9 1.0
CE2 B:PHE115 4.9 34.6 1.0
N B:PRO147 4.9 30.5 1.0

Chlorine binding site 5 out of 6 in 5e2h

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Chlorine binding site 5 out of 6 in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis


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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:43.3
occ:1.00
 N C:VAL185 3.2 29.3 1.0
CB C:VAL185 3.8 26.9 1.0
CG2 C:VAL185 3.8 26.5 1.0
NZ C:LYS219 3.9 30.0 1.0
CA C:ASP184 4.0 33.9 1.0
C C:ASP184 4.0 31.8 1.0
CA C:VAL185 4.0 28.4 1.0
O C:VAL183 4.1 34.4 1.0
CE C:LYS219 4.1 33.2 1.0
CE2 C:TYR193 4.3 27.1 1.0
CD C:LYS219 4.4 31.7 1.0
O C:VAL185 4.6 36.2 1.0
C C:VAL185 4.8 34.0 1.0
OD1 C:ASP184 4.9 46.0 1.0
CB C:ASP184 4.9 40.3 1.0
N C:ASP184 4.9 31.3 1.0
C C:VAL183 4.9 33.3 1.0
CE C:MSE190 4.9 41.6 1.0
CD2 C:TYR193 5.0 26.3 1.0

Chlorine binding site 6 out of 6 in 5e2h

Go back to Chlorine Binding Sites List in 5e2h
Chlorine binding site 6 out of 6 in the Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis


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 D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:38.5
occ:1.00
 O C:HOH640 3.0 46.4 1.0
O C:HOH549 3.1 31.7 1.0
N C:PHE115 3.2 34.1 1.0
CA C:GLN114 3.5 36.5 1.0
CB C:GLN114 3.6 40.4 1.0
C C:GLN114 3.8 38.0 1.0
CB C:ASN146 3.9 29.3 1.0
CD2 C:PHE115 3.9 35.7 1.0
CG C:GLN114 4.1 45.4 1.0
CB C:PHE115 4.2 36.2 1.0
CA C:PHE115 4.3 36.9 1.0
ND2 C:ASN146 4.4 34.7 1.0
CG C:PHE115 4.4 35.6 1.0
CD C:PRO147 4.4 35.0 1.0
CG C:ASN146 4.5 32.3 1.0
O C:LEU113 4.5 29.2 1.0
CE2 C:TYR216 4.6 30.4 1.0
CG C:PRO147 4.7 38.7 1.0
N C:GLN114 4.7 33.7 1.0
CE2 C:PHE115 4.8 37.8 1.0
O C:VAL210 4.8 33.9 1.0
NE2 C:GLN114 4.8 54.6 1.0
OH C:TYR216 4.9 25.6 1.0
N C:PRO147 4.9 34.4 1.0
O C:PHE115 4.9 38.7 1.0
CD C:GLN114 5.0 52.5 1.0

Reference:

Y.Kim, C.Hatzos-Skintges, M.Endres, G.Babnigg, A.Joachimiak. Crystal Structure of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis To Be Published.
Page generated: Sat Dec 12 11:40:18 2020

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