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Chlorine in PDB 4eof: Lysozyme in the Presence of Arginine

Enzymatic activity of Lysozyme in the Presence of Arginine

All present enzymatic activity of Lysozyme in the Presence of Arginine:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme in the Presence of Arginine, PDB code: 4eof was solved by P.Sharma, Ashish, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.33 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 30.524, 55.509, 72.426, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.6

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 8 in 4eof

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Chlorine binding site 1 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:22.1
occ:1.00
 N A:SER81 3.2 17.4 1.0
CB A:SER81 3.6 24.6 1.0
O A:ASN65 3.6 18.5 1.0
N A:CYS80 3.7 15.7 1.0
CA A:ASP66 3.7 21.5 1.0
OG A:SER81 3.8 24.9 1.0
CA A:SER81 4.0 21.1 1.0
CB A:ASP66 4.0 20.4 1.0
CB A:CYS80 4.1 17.0 1.0
C A:CYS80 4.1 16.9 1.0
CA A:CYS80 4.1 16.2 1.0
O A:ASP66 4.3 26.5 1.0
C A:ASP66 4.4 18.6 1.0
C A:PRO79 4.4 19.2 1.0
CB A:PRO79 4.5 22.6 1.0
C A:ASN65 4.5 21.4 1.0
N A:ASP66 4.6 19.2 1.0
CA A:PRO79 4.7 20.7 1.0

Chlorine binding site 2 out of 8 in 4eof

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Chlorine binding site 2 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:28.1
occ:1.00
 O A:HOH307 3.2 20.5 1.0
ND2 A:ASN93 3.3 22.8 1.0
CA A:ALA90 3.7 15.6 1.0
CB A:ASN93 3.9 13.6 1.0
CB A:ALA90 4.1 17.2 1.0
CG A:ASN93 4.1 23.4 1.0
CD1 A:ILE78 4.4 24.2 1.0
N A:ALA90 4.4 14.4 1.0
O A:THR89 4.5 11.7 1.0
O A:ALA90 4.6 14.8 1.0
O A:HOH308 4.7 25.9 1.0
C A:ALA90 4.7 13.0 1.0
C A:THR89 4.7 13.2 1.0
CG2 A:THR89 4.8 21.9 1.0

Chlorine binding site 3 out of 8 in 4eof

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Chlorine binding site 3 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:31.9
occ:1.00
 O A:HOH372 2.8 41.1 1.0
ND2 A:ASN39 3.2 16.1 1.0
ND2 A:ASN37 3.7 27.7 1.0
O3 A:GOL210 3.8 29.2 1.0
CB A:ASN39 4.0 16.2 1.0
CB A:ASN37 4.0 18.6 1.0
CG A:ASN39 4.1 17.5 1.0
O A:ASN37 4.2 16.3 1.0
CG A:ASN37 4.3 28.9 1.0
O A:HOH327 4.4 26.1 1.0
CG2 A:VAL2 4.5 17.9 1.0
O A:SER36 4.5 16.9 1.0
C3 A:GOL210 4.8 44.3 1.0
CG1 A:VAL2 4.9 15.8 1.0
O A:HOH313 4.9 20.4 1.0
C A:ASN37 5.0 16.6 1.0

Chlorine binding site 4 out of 8 in 4eof

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Chlorine binding site 4 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:23.5
occ:1.00
 O A:HOH301 3.1 20.8 1.0
N A:ILE88 3.3 17.3 1.0
CA A:ASP87 3.7 16.1 1.0
CG1 A:ILE88 3.8 18.8 1.0
CZ A:PHE3 4.0 16.9 1.0
C A:ASP87 4.0 16.3 1.0
NH2 A:ARG14 4.0 29.5 0.5
OD1 A:ASP87 4.1 21.3 1.0
O A:SER86 4.2 19.3 1.0
CG2 A:ILE88 4.2 11.4 1.0
CG A:ASP87 4.2 23.2 1.0
CB A:ILE88 4.3 14.3 1.0
CA A:ILE88 4.4 14.6 1.0
CB A:ASP87 4.5 20.4 1.0
CB A:ALA11 4.5 17.6 1.0
CE1 A:HIS15 4.6 23.2 1.0
CD1 A:ILE88 4.6 16.2 1.0
NH1 A:ARG14 4.6 23.4 0.5
OD2 A:ASP87 4.6 20.2 1.0
CE2 A:PHE3 4.7 18.2 1.0
O1 A:GOL209 4.8 32.0 0.9
N A:ASP87 4.8 17.9 1.0
CZ A:ARG14 4.8 23.0 0.5
O A:HOH357 4.9 28.7 1.0
CE1 A:PHE3 4.9 18.3 1.0
C A:SER86 4.9 18.8 1.0
O2 A:GOL209 5.0 36.5 0.9

Chlorine binding site 5 out of 8 in 4eof

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Chlorine binding site 5 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:46.4
occ:1.00
 O A:HOH310 2.9 22.8 1.0
N A:THR69 2.9 34.0 1.0
N A:ARG68 3.1 33.6 1.0
O A:THR69 3.1 34.9 1.0
N A:GLY67 3.4 27.1 1.0
OD1 A:ASN65 3.5 39.0 1.0
OG A:SER72 3.5 35.5 1.0
CA A:GLY67 3.5 36.0 1.0
C A:GLY67 3.7 44.4 1.0
CA A:THR69 3.7 30.2 1.0
C A:THR69 3.8 35.8 1.0
C A:ARG68 3.9 40.1 1.0
OD1 A:ASP66 3.9 24.5 1.0
CB A:THR69 3.9 28.3 1.0
CA A:ARG68 4.0 36.4 1.0
CB A:SER72 4.0 38.5 1.0
O A:HOH337 4.2 35.3 1.0
C A:ASP66 4.4 18.6 1.0
N A:ASP66 4.4 19.2 1.0
OG1 A:THR69 4.5 22.7 1.0
O A:HOH311 4.6 24.1 1.0
CG A:ASN65 4.6 31.4 1.0
O A:GLY67 4.7 45.4 1.0
CA A:ASP66 5.0 21.5 1.0

Chlorine binding site 6 out of 8 in 4eof

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Chlorine binding site 6 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:56.6
occ:1.00
 NH1 A:ARG114 2.7 25.1 1.0
NH2 A:ARG114 3.2 27.0 1.0
ND2 A:ASN113 3.3 33.3 1.0
CZ A:ARG114 3.3 26.7 1.0
CG1 A:VAL109 3.7 31.8 1.0
CA A:ALA110 3.7 22.1 1.0
N A:ALA110 3.9 21.1 1.0
O A:VAL109 4.0 25.7 1.0
C A:VAL109 4.0 19.9 1.0
CB A:ALA110 4.2 25.1 1.0
CB A:ASN113 4.2 26.2 1.0
CG A:ASN113 4.2 29.0 1.0
CB A:VAL109 4.5 30.3 1.0
NE A:ARG114 4.6 23.3 1.0
C A:ALA110 4.9 20.9 1.0
O A:HOH321 4.9 27.1 1.0
CA A:VAL109 5.0 27.4 1.0

Chlorine binding site 7 out of 8 in 4eof

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Chlorine binding site 7 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:28.3
occ:1.00
 OG A:SER24 3.0 19.6 1.0
N A:GLY26 3.1 14.0 1.0
CB A:SER24 3.4 17.9 1.0
CA A:GLN121 3.5 21.9 1.0
CA A:GLY26 3.5 13.6 1.0
CD1 A:ILE124 3.9 29.4 1.0
CB A:GLN121 4.0 24.8 1.0
N A:GLN121 4.0 18.4 1.0
N A:LEU25 4.1 15.3 1.0
CG A:GLN121 4.1 30.7 0.7
C A:SER24 4.2 16.0 1.0
C A:LEU25 4.3 15.4 1.0
O A:VAL120 4.3 15.2 1.0
C A:VAL120 4.3 17.3 1.0
CG1 A:ILE124 4.4 22.6 1.0
CA A:SER24 4.5 16.3 1.0
CG2 A:VAL120 4.6 21.3 1.0
CA A:LEU25 4.6 15.9 1.0
C A:GLY26 4.6 16.0 1.0
C A:GLN121 4.6 17.1 1.0
O A:SER24 4.7 14.8 1.0
N A:ASN27 4.7 14.7 1.0
O A:GLN121 4.8 15.9 1.0
CB A:LEU25 4.9 13.2 1.0

Chlorine binding site 8 out of 8 in 4eof

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Chlorine binding site 8 out of 8 in the Lysozyme in the Presence of Arginine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Lysozyme in the Presence of Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:70.7
occ:1.00
 NZ A:LYS13 3.0 37.2 1.0
CD1 A:LEU129 3.8 28.0 1.0
CD1 A:ILE124 3.9 29.4 1.0
CE A:LYS13 4.0 38.5 1.0
CD A:LYS13 4.1 27.5 1.0
OD2 A:ASP18 4.1 32.2 1.0
CB A:LEU129 4.1 29.3 1.0
CD2 A:LEU25 4.2 14.4 1.0
CG A:LEU129 4.5 30.3 1.0
CG A:ASP18 4.9 28.0 1.0

Reference:

P.Sharma, N.Verma, P.K.Singh, S.Korpole, Ashish. Characterization of Heat Induced Spherulites of Lysozyme Reveals New Insight on Amyloid Initiation. Sci Rep V. 6 22475 2016.
ISSN: ESSN 2045-2322
PubMed: 26926993
DOI: 10.1038/SREP22475
Page generated: Sat Dec 12 10:35:15 2020

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