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Chlorine in PDB 4pi8: Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam

Protein crystallography data

The structure of Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam, PDB code: 4pi8 was solved by M.Mihelic, M.Renko, A.Jakas, D.Turk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.40 / 1.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.011, 69.720, 73.540, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.6

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam (pdb code 4pi8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam, PDB code: 4pi8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in 4pi8

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Chlorine binding site 1 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


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 Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:23.1
occ:1.00
 NZ A:LYS243 3.1 19.8 1.0
O A:HOH513 3.1 34.2 1.0
CE A:LYS243 3.7 18.2 1.0
CD A:LYS243 4.0 16.6 1.0

Chlorine binding site 2 out of 14 in 4pi8

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Chlorine binding site 2 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


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 Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:20.8
occ:1.00
 OG A:SER98 3.0 22.3 0.5
O A:HOH506 3.1 36.2 1.0
N A:SER98 3.4 14.5 1.0
OE2 A:GLU97 3.4 18.0 0.3
OG A:SER98 3.4 18.6 0.5
CG A:GLU97 3.6 14.2 0.3
CB A:SER96 3.6 15.1 1.0
CB A:SER98 3.6 18.4 0.5
CB A:SER98 3.7 17.6 0.5
OG A:SER96 3.7 15.2 1.0
N A:GLU97 3.8 13.2 1.0
CD A:GLU97 3.8 16.2 0.3
CA A:SER98 4.1 16.4 1.0
CB A:GLU97 4.3 17.3 0.7
C A:GLU97 4.3 14.2 1.0
CA A:GLU97 4.3 14.6 0.7
CA A:GLU97 4.4 13.8 0.3
C A:SER96 4.4 13.2 1.0
CB A:GLU97 4.5 14.1 0.3
CA A:SER96 4.6 14.1 1.0
OE1 A:GLU97 4.9 16.3 0.3

Chlorine binding site 3 out of 14 in 4pi8

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Chlorine binding site 3 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


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 Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:22.6
occ:1.00
 O A:HOH576 3.1 33.3 1.0
O A:HOH568 3.2 35.2 1.0
N A:TYR256 3.2 17.2 1.0
N A:TYR257 3.4 16.9 1.0
O A:HOH574 3.4 44.2 1.0
CA A:THR255 3.8 19.6 1.0
CD2 A:TYR257 3.8 17.0 1.0
CB A:TYR257 4.0 17.8 1.0
C A:THR255 4.0 17.4 1.0
CA A:TYR256 4.1 16.5 1.0
O A:TYR257 4.1 21.6 1.0
O A:GLN254 4.1 22.2 1.0
CG1 A:ILE77 4.2 34.9 1.0
CA A:TYR257 4.2 17.8 1.0
O A:HOH651 4.2 52.8 1.0
C A:TYR256 4.2 18.5 1.0
CG2 A:THR255 4.3 22.3 1.0
CB A:TYR256 4.3 17.0 1.0
CG A:TYR257 4.4 16.7 1.0
CD2 A:TYR256 4.6 17.8 1.0
CB A:THR255 4.6 21.7 1.0
C A:TYR257 4.6 20.1 1.0
O A:HOH573 4.8 34.5 1.0
N A:THR255 4.8 19.1 1.0
CD1 A:ILE77 4.9 31.7 1.0
CE2 A:TYR257 4.9 15.6 1.0
OG1 A:THR255 4.9 26.2 1.0
C A:GLN254 4.9 20.6 1.0
CG A:TYR256 5.0 17.1 1.0

Chlorine binding site 4 out of 14 in 4pi8

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Chlorine binding site 4 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


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 Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:17.8
occ:1.00
 O A:HOH549 3.1 17.7 1.0
NZ A:LYS85 3.2 20.6 0.5
NE1 A:TRP214 3.2 13.8 1.0
O A:HOH541 3.2 26.6 1.0
NZ A:LYS85 3.3 19.3 0.5
O A:HOH551 3.4 29.3 1.0
CD A:LYS85 3.6 21.5 0.5
O A:ALA74 3.7 21.1 1.0
CD A:LYS85 3.7 16.0 0.5
CD1 A:TRP214 3.9 13.5 1.0
CB A:ALA231 3.9 13.3 1.0
CE A:LYS85 3.9 22.2 0.5
CE A:LYS85 3.9 18.3 0.5
CD1 A:TYR210 4.1 13.1 1.0
OD2 A:ASP232 4.1 25.0 1.0
CE2 A:TRP214 4.3 13.4 1.0
CE1 A:TYR210 4.4 13.8 1.0
O A:ILE228 4.6 15.4 1.0
OD1 A:ASP232 4.7 23.5 1.0
CG A:ASP232 4.7 20.6 1.0
C A:ALA74 4.8 18.9 1.0
CZ2 A:TRP214 4.8 14.5 1.0
CA A:ALA231 5.0 12.4 1.0
CG A:LYS85 5.0 19.3 0.5

Chlorine binding site 5 out of 14 in 4pi8

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Chlorine binding site 5 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


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 Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:21.9
occ:1.00
 O A:HOH601 3.1 21.7 1.0
O A:HOH416 3.2 40.2 1.0
O A:HOH468 3.3 31.3 1.0
ND2 A:ASN215 3.3 13.5 1.0
ND2 A:ASN204 3.3 17.6 1.0
O A:HOH629 3.4 33.1 1.0
CB A:HIS222 4.0 13.7 1.0
OD1 A:ASN218 4.2 18.2 1.0
CB A:ASN218 4.2 13.0 1.0
CG A:ASN204 4.2 17.6 1.0
OD1 A:ASN204 4.3 19.4 1.0
CG A:ASN215 4.4 13.3 1.0
CG A:ASN218 4.5 14.9 1.0
OD1 A:ASN215 4.6 14.2 1.0
CG A:HIS222 4.6 14.3 1.0
O A:HOH627 4.7 33.3 1.0
CB A:GLN221 4.7 17.0 1.0
O A:GLN221 4.9 13.3 1.0
OE1 A:GLN206 4.9 14.0 1.0
ND1 A:HIS222 5.0 14.7 1.0

Chlorine binding site 6 out of 14 in 4pi8

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Chlorine binding site 6 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


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 Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:47.7
occ:1.00
 N A:GLY52 3.1 18.9 1.0
O A:HOH485 3.4 42.8 1.0
O A:HOH550 3.5 36.4 1.0
O A:HOH585 3.8 29.0 1.0
CA A:LYS51 3.9 16.9 1.0
CA A:GLY52 3.9 19.9 1.0
C A:LYS51 4.0 18.7 1.0
CG A:LYS51 4.1 20.8 1.0
CB A:LYS51 4.6 18.9 1.0
O A:GLY50 4.6 16.0 1.0
O A:HOH457 4.9 38.1 1.0
C A:GLY52 4.9 20.9 1.0
NZ A:LYS51 5.0 30.4 1.0
N A:LYS51 5.0 15.6 1.0

Chlorine binding site 7 out of 14 in 4pi8

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Chlorine binding site 7 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:34.9
occ:1.00
 N A:ALA165 3.2 21.9 1.0
O A:HOH583 3.2 47.3 1.0
N A:TYR177 3.3 24.0 1.0
O A:HOH634 3.4 48.1 1.0
O A:LYS175 3.6 44.2 1.0
CA A:GLY164 3.7 20.3 1.0
CB A:TYR177 3.8 24.6 1.0
C A:GLY164 3.9 19.4 1.0
CA A:SER176 4.0 29.6 1.0
CB A:ALA165 4.0 23.4 1.0
C A:SER176 4.0 26.3 1.0
CA A:TYR177 4.1 23.6 1.0
CA A:ALA165 4.1 23.6 1.0
C A:LYS175 4.3 41.6 1.0
O A:ALA165 4.3 24.2 1.0
N A:SER176 4.4 32.6 1.0
O A:HOH602 4.7 22.8 1.0
C A:ALA165 4.7 19.5 1.0
CG A:TYR177 4.9 25.8 1.0
N A:GLY164 5.0 17.8 1.0

Chlorine binding site 8 out of 14 in 4pi8

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Chlorine binding site 8 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:51.3
occ:1.00
 N A:GLU145 3.2 26.2 1.0
O A:HOH561 3.5 33.1 1.0
CA A:SER144 3.8 22.5 1.0
CB A:SER144 4.0 22.1 1.0
C A:SER144 4.0 24.1 1.0
CB A:GLU145 4.2 35.4 1.0
CA A:GLU145 4.3 27.5 1.0

Chlorine binding site 9 out of 14 in 4pi8

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Chlorine binding site 9 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:34.1
occ:1.00
 O A:HOH580 2.9 35.9 1.0
O A:HOH530 3.1 32.0 1.0
N A:LYS248 3.2 21.4 1.0
CG A:PRO94 3.6 17.5 1.0
CB A:LYS248 3.8 31.1 1.0
CA A:ILE247 3.9 18.8 1.0
CG2 A:ILE247 3.9 18.9 1.0
CD A:PRO94 4.0 16.1 1.0
C A:ILE247 4.0 19.3 1.0
CA A:LYS248 4.1 24.5 1.0
O A:GLY246 4.4 23.8 1.0
O A:LYS248 4.5 23.9 1.0
CB A:ILE247 4.5 18.6 1.0
CD1 A:ILE247 4.6 20.3 1.0
C A:LYS248 4.8 23.4 1.0

Chlorine binding site 10 out of 14 in 4pi8

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Chlorine binding site 10 out of 14 in the Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Catalytic Mutant E138A of S. Aureus Autolysin E in Complex with Disaccharide Nag-Nam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:16.6
occ:1.00
 O A:HOH599 3.2 18.9 1.0
NE1 A:TRP230 3.2 13.1 1.0
NE2 A:HIS134 3.2 12.6 1.0
O A:PHE161 3.5 14.4 1.0
CE1 A:TYR224 3.8 11.7 1.0
CD2 A:HIS134 3.9 13.1 1.0
CD1 A:TRP230 3.9 12.6 1.0
C A:PHE161 3.9 15.0 1.0
O A:HOH514 4.0 40.2 1.0
CA A:GLY162 4.1 14.9 1.0
CB A:ALA138 4.1 16.8 1.0
CD1 A:TYR224 4.1 12.5 1.0
O1 A:SO4314 4.2 26.6 0.7
N A:GLY162 4.2 14.3 1.0
CE1 A:HIS134 4.3 13.2 1.0
CE2 A:TRP230 4.4 12.6 1.0
O A:GLY162 4.8 16.5 1.0
CA A:ALA138 4.8 15.6 1.0
O A:HOH647 4.8 36.5 1.0
C A:GLY162 4.8 14.4 1.0
CZ2 A:TRP230 4.9 12.6 1.0
CA A:PHE161 4.9 13.3 1.0
CZ A:TYR224 4.9 12.5 1.0

Reference:

M.Mihelic, K.Vlahovicek-Kahlina, M.Renko, S.Mesnage, A.Dobersek, A.Taler-Vercic, A.Jakas, D.Turk. The Mechanism Behind the Selection of Two Different Cleavage Sites in Nag-Nam Polymers Iucrj V. 4 185 2017.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252517000367
Page generated: Thu Jul 25 23:58:04 2024

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