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Chlorine in PDB 4pi9: Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu

Protein crystallography data

The structure of Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu, PDB code: 4pi9 was solved by M.Mihelic, M.Renko, D.Turk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.75 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.626, 69.312, 73.424, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu (pdb code 4pi9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu, PDB code: 4pi9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4pi9

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Chlorine binding site 1 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:49.0
occ:1.00
 N A:ILE252 3.2 25.9 1.0
O A:HOH471 3.2 41.9 1.0
CA A:ASP251 3.8 31.3 1.0
CB A:ILE252 3.9 28.7 1.0
O A:ILE252 3.9 28.9 1.0
C A:ASP251 4.0 30.1 1.0
CG1 A:ILE252 4.0 32.0 1.0
CA A:ILE252 4.0 27.3 1.0
C A:ILE252 4.5 29.6 1.0
O A:ASP250 4.5 26.4 1.0
OD1 A:ASP251 4.5 49.4 1.0
CB A:ASP251 4.6 35.9 1.0
N A:ASP251 4.9 28.0 1.0
CG A:ASP251 4.9 44.3 1.0

Chlorine binding site 2 out of 7 in 4pi9

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Chlorine binding site 2 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:29.6
occ:1.00
 NZ A:LYS243 3.1 23.6 1.0
CE A:LYS243 3.6 23.8 1.0
CD A:LYS243 3.9 24.0 1.0
CG A:LYS243 5.0 22.0 1.0

Chlorine binding site 3 out of 7 in 4pi9

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Chlorine binding site 3 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:24.4
occ:1.00
 OG A:SER98 3.0 26.2 0.6
OG A:SER98 3.2 23.3 0.4
N A:SER98 3.4 19.6 1.0
CB A:SER96 3.5 20.3 1.0
CB A:SER98 3.6 21.5 0.6
CB A:SER98 3.6 21.1 0.4
OG A:SER96 3.7 20.5 1.0
N A:GLU97 3.8 19.7 1.0
CA A:SER98 4.1 19.9 0.6
CA A:SER98 4.1 19.8 0.4
C A:GLU97 4.3 19.3 1.0
CB A:GLU97 4.4 25.8 1.0
CA A:GLU97 4.4 20.4 1.0
C A:SER96 4.5 19.2 1.0
CA A:SER96 4.5 18.4 1.0
O A:HOH502 4.7 30.7 1.0

Chlorine binding site 4 out of 7 in 4pi9

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Chlorine binding site 4 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:63.1
occ:1.00
 O A:HOH457 3.1 37.4 1.0
N A:VAL54 3.2 37.8 1.0
O A:HOH507 3.2 53.8 1.0
O A:HOH585 3.6 35.2 1.0
CB A:VAL54 3.7 39.3 1.0
CG2 A:VAL54 3.8 43.6 1.0
CA A:VAL54 4.0 38.0 1.0
CAE A:3LT311 4.0 35.5 1.0
CA A:ILE53 4.1 41.4 1.0
C A:ILE53 4.2 43.4 1.0
O A:VAL54 4.2 30.7 1.0
CG2 A:ILE53 4.4 38.4 1.0
O A:GLY52 4.5 43.3 1.0
C A:VAL54 4.6 32.3 1.0
CB A:ILE53 4.8 40.5 1.0
O A:HOH508 4.9 45.1 1.0
OAH A:3LT311 4.9 29.6 1.0
OAF A:3LT311 4.9 41.2 1.0
CAD A:3LT311 5.0 31.5 1.0
OG A:SER226 5.0 21.4 0.6

Chlorine binding site 5 out of 7 in 4pi9

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Chlorine binding site 5 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:23.4
occ:1.00
 O A:HOH480 3.2 20.3 1.0
NE1 A:TRP214 3.2 17.1 1.0
O A:HOH474 3.2 27.0 1.0
NZ A:LYS85 3.3 27.1 1.0
O A:HOH416 3.4 34.9 1.0
O A:ALA74 3.6 24.8 1.0
CD A:LYS85 3.8 25.9 1.0
CD1 A:TRP214 3.9 17.0 1.0
CE A:LYS85 3.9 27.3 1.0
CB A:ALA231 3.9 16.2 1.0
OD2 A:ASP232 4.0 27.8 1.0
CD1 A:TYR210 4.1 17.4 1.0
CE2 A:TRP214 4.3 17.3 1.0
CE1 A:TYR210 4.5 18.3 1.0
O A:ILE228 4.7 19.0 1.0
CG A:ASP232 4.7 26.0 1.0
C A:ALA74 4.7 22.5 1.0
CZ2 A:TRP214 4.8 17.1 1.0
OD1 A:ASP232 4.8 29.0 1.0
N A:ASP232 5.0 15.8 1.0
CA A:ALA231 5.0 15.6 1.0

Chlorine binding site 6 out of 7 in 4pi9

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Chlorine binding site 6 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:32.0
occ:1.00
 O A:HOH550 3.1 52.4 1.0
N A:TYR256 3.1 22.4 1.0
O A:HOH637 3.2 49.2 1.0
N A:TYR257 3.3 22.5 1.0
O A:HOH420 3.5 44.5 1.0
O A:GLN254 3.8 29.5 1.0
CD2 A:TYR257 3.8 22.1 1.0
CA A:THR255 3.8 26.8 1.0
O A:TYR257 3.9 27.9 1.0
C A:THR255 4.0 23.4 1.0
CB A:TYR257 4.0 23.6 1.0
CA A:TYR256 4.0 21.8 1.0
CD1 A:ILE77 4.1 34.4 0.7
CA A:TYR257 4.1 22.9 1.0
C A:TYR256 4.1 22.7 1.0
CG A:TYR257 4.3 22.7 1.0
CG2 A:THR255 4.3 31.0 1.0
C A:TYR257 4.4 26.7 1.0
CB A:TYR256 4.5 21.5 1.0
C A:GLN254 4.7 27.7 1.0
CB A:THR255 4.7 30.2 1.0
N A:THR255 4.8 26.4 1.0
CE2 A:TYR257 4.8 23.8 1.0

Chlorine binding site 7 out of 7 in 4pi9

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Chlorine binding site 7 out of 7 in the Crystal Structure of S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu


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 S. Aureus Autolysin E in Complex with Muropeptide Nam-L-Ala-D-Iglu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:30.2
occ:1.00
 OE1 A:GLU138 2.3 41.8 1.0
NE1 A:TRP230 3.1 16.4 1.0
NE2 A:HIS134 3.2 17.6 1.0
O A:HOH450 3.4 25.8 1.0
CD A:GLU138 3.4 39.3 1.0
O A:PHE161 3.5 18.2 1.0
CE1 A:TYR224 3.7 15.5 1.0
CD1 A:TRP230 3.8 15.8 1.0
CD2 A:HIS134 3.8 15.8 1.0
C A:PHE161 4.0 19.6 1.0
CD1 A:TYR224 4.1 17.1 1.0
O A:HOH549 4.1 40.7 1.0
CG A:GLU138 4.1 33.7 1.0
CA A:GLY162 4.2 21.1 1.0
CE1 A:HIS134 4.2 17.9 1.0
CE2 A:TRP230 4.2 14.9 1.0
O1 A:SO4301 4.2 45.4 0.6
CB A:GLU138 4.3 26.8 1.0
OE2 A:GLU138 4.3 45.7 1.0
N A:GLY162 4.4 19.8 1.0
CZ2 A:TRP230 4.7 14.9 1.0
CZ A:TYR224 4.8 15.8 1.0
O A:GLY162 4.9 20.8 1.0
O A:HOH610 4.9 49.4 1.0
CA A:PHE161 4.9 17.9 1.0
C A:GLY162 5.0 20.7 1.0
CB A:ALA225 5.0 18.8 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
PubMed: 28250957
DOI: 10.1107/S2052252517000367
Page generated: Thu Jul 25 23:58:12 2024

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