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Chlorine in PDB 4xji: X-Ray Structure of LYSOZYMES2

Enzymatic activity of X-Ray Structure of LYSOZYMES2

All present enzymatic activity of X-Ray Structure of LYSOZYMES2:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of LYSOZYMES2, PDB code: 4xji was solved by C.Y.Huang, V.Olieric, K.Diederichs, M.Wang, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.36 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.710, 78.710, 37.330, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21

Other elements in 4xji:

The structure of X-Ray Structure of LYSOZYMES2 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of LYSOZYMES2 (pdb code 4xji). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Structure of LYSOZYMES2, PDB code: 4xji:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4xji

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Chlorine binding site 1 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:18.3
occ:1.00
 OH A:TYR23 3.0 13.8 1.0
O A:HOH320 3.4 17.6 1.0
CZ A:TYR23 3.6 14.0 1.0
CE2 A:TYR23 3.7 14.1 1.0
CA A:GLY104 4.1 15.8 1.0
O A:ARG21 4.6 15.2 1.0
N A:GLY104 4.7 13.2 1.0
CE1 A:TYR23 4.8 12.7 1.0
CD2 A:TYR23 4.9 11.1 1.0

Chlorine binding site 2 out of 8 in 4xji

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Chlorine binding site 2 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:22.6
occ:1.00
 OG A:SER24 3.0 17.9 1.0
N A:GLY26 3.2 12.6 1.0
CA A:GLY26 3.4 14.4 1.0
CB A:SER24 3.4 23.8 1.0
CA A:GLN121 3.7 18.9 1.0
CD1 A:ILE124 3.8 28.6 1.0
N A:GLN121 4.1 20.1 1.0
CB A:GLN121 4.1 25.3 1.0
CG1 A:ILE124 4.2 20.3 1.0
N A:LEU25 4.3 16.2 1.0
CG A:GLN121 4.3 25.8 1.0
C A:SER24 4.4 19.0 1.0
C A:LEU25 4.4 15.6 1.0
C A:VAL120 4.4 18.8 1.0
CG2 A:VAL120 4.4 18.1 1.0
O A:VAL120 4.4 19.1 1.0
C A:GLY26 4.5 14.5 1.0
CA A:SER24 4.5 15.0 1.0
N A:ASN27 4.7 12.4 1.0
CA A:LEU25 4.8 16.6 1.0
O A:SER24 4.8 14.2 1.0
C A:GLN121 4.9 19.1 1.0

Chlorine binding site 3 out of 8 in 4xji

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Chlorine binding site 3 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:23.9
occ:1.00
 O A:HOH348 3.0 30.4 1.0
N A:THR69 3.0 17.6 1.0
O A:HOH358 3.2 14.6 1.0
O A:THR69 3.2 21.6 1.0
C A:THR69 3.5 22.4 1.0
N A:ARG68 3.5 15.9 1.0
C A:GLY67 3.6 20.2 1.0
OG A:SER72 3.6 26.3 1.0
CA A:THR69 3.7 21.2 1.0
OD1 A:ASN65 3.7 23.4 1.0
CA A:GLY67 3.7 17.9 1.0
N A:GLY67 3.8 15.5 1.0
O A:HOH394 3.8 26.1 0.9
O A:HOH357 4.0 18.1 1.0
C A:ARG68 4.1 21.4 1.0
CB A:THR69 4.1 18.1 1.0
O A:GLY67 4.1 22.3 1.0
CA A:ARG68 4.2 15.2 1.0
OD1 A:ASP66 4.3 15.4 1.0
N A:PRO70 4.3 19.4 1.0
OG1 A:THR69 4.7 15.1 1.0
NA A:NA209 4.8 24.8 1.0
CB A:SER72 4.8 23.1 1.0
CA A:PRO70 4.8 27.8 1.0
CG A:ASN65 4.9 22.4 1.0
C A:ASP66 4.9 16.2 1.0
N A:ASP66 4.9 15.1 1.0

Chlorine binding site 4 out of 8 in 4xji

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Chlorine binding site 4 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:35.5
occ:1.00
 N A:ILE88 3.3 18.1 1.0
O A:HOH371 3.5 22.7 0.9
CG1 A:ILE88 3.7 16.9 1.0
CA A:ASP87 3.8 20.7 1.0
O A:SER86 4.0 25.2 1.0
CE1 A:HIS15 4.0 20.9 1.0
OD1 A:ASP87 4.0 30.6 1.0
C A:ASP87 4.0 19.2 1.0
CG2 A:ILE88 4.1 20.2 1.0
CB A:ALA11 4.2 19.1 1.0
O A:HOH339 4.2 31.2 0.7
CB A:ILE88 4.2 17.7 1.0
CZ A:PHE3 4.2 23.7 1.0
CA A:ILE88 4.3 16.9 1.0
CG A:ASP87 4.4 37.0 1.0
CD1 A:ILE88 4.5 15.5 1.0
ND1 A:HIS15 4.7 24.9 1.0
CB A:ASP87 4.7 26.8 1.0
N A:ASP87 4.8 21.1 1.0
C A:SER86 4.8 23.4 1.0
NE2 A:HIS15 4.8 27.3 1.0
CE2 A:PHE3 4.9 20.1 1.0
NH1 A:ARG14 4.9 40.5 1.0

Chlorine binding site 5 out of 8 in 4xji

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Chlorine binding site 5 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:45.0
occ:1.00
 CE2 A:PHE38 3.7 20.6 1.0
CZ3 A:TRP123 3.8 19.6 1.0
CB A:ARG5 4.1 20.3 1.0
CD A:ARG5 4.1 19.0 1.0
NZ A:LYS33 4.3 24.2 1.0
CZ A:PHE38 4.5 14.9 1.0
CE A:LYS33 4.5 21.5 1.0
CG A:ARG5 4.6 19.2 1.0
CD A:LYS33 4.6 17.4 1.0
NE A:ARG5 4.6 18.7 1.0
CD2 A:PHE38 4.6 15.3 1.0
CE3 A:TRP123 4.7 19.4 1.0
CH2 A:TRP123 4.7 24.9 1.0

Chlorine binding site 6 out of 8 in 4xji

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Chlorine binding site 6 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:64.3
occ:1.00
 O A:HOH381 2.8 25.7 1.0
ND2 A:ASN65 3.2 20.4 1.0
CB A:PRO79 3.7 15.3 1.0
CA A:PRO79 3.7 17.4 1.0
N A:PRO79 3.9 19.3 1.0
CB A:ASN65 3.9 13.7 1.0
CG A:ASN65 4.0 22.4 1.0
CD A:PRO79 4.1 19.5 1.0
O A:ASN65 4.3 14.8 1.0
CG A:PRO79 4.4 20.4 1.0
C A:ILE78 4.5 16.8 1.0
O A:ILE78 4.7 14.8 1.0
ND2 A:ASN74 4.8 17.4 1.0
C A:ASN65 4.9 11.7 1.0
CA A:ASN65 4.9 14.6 1.0
O A:HOH338 5.0 14.4 1.0

Chlorine binding site 7 out of 8 in 4xji

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Chlorine binding site 7 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:49.8
occ:1.00
 N A:ASN74 2.8 20.0 1.0
NH1 A:ARG73 3.0 48.9 1.0
C A:ASN74 3.4 14.8 1.0
CB A:ARG73 3.6 25.7 1.0
O A:ASN74 3.6 18.1 1.0
CA A:ASN74 3.6 16.6 1.0
CA A:ARG73 3.7 24.9 1.0
C A:ARG73 3.7 24.9 1.0
CD A:ARG73 3.8 36.3 1.0
N A:LEU75 3.9 18.3 1.0
CD2 A:LEU75 3.9 27.3 1.0
CZ A:ARG73 4.0 45.8 1.0
CB A:ASN74 4.0 16.8 1.0
CG A:ARG73 4.3 31.1 1.0
NE A:ARG73 4.3 45.2 1.0
CA A:LEU75 4.4 21.7 1.0
CG A:LEU75 4.7 21.6 1.0
O A:ARG73 4.9 23.8 1.0

Chlorine binding site 8 out of 8 in 4xji

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Chlorine binding site 8 out of 8 in the X-Ray Structure of LYSOZYMES2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure of LYSOZYMES2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:41.0
occ:1.00
 NH1 A:ARG68 2.9 20.5 1.0
CD A:ARG68 3.5 21.1 1.0
CZ A:ARG68 3.9 25.9 1.0
NE A:ARG68 4.1 21.2 1.0
CG A:ARG68 4.8 20.5 1.0
NH1 A:ARG45 4.9 26.4 1.0
CB A:ARG68 4.9 17.3 1.0

Reference:

C.Y.Huang, V.Olieric, P.Ma, E.Panepucci, K.Diederichs, M.Wang, M.Caffrey. In Meso in Situ Serial X-Ray Crystallography of Soluble and Membrane Proteins. Acta Crystallogr.,Sect.D V. 71 1238 2015.
ISSN: ESSN 1399-0047
PubMed: 26057665
DOI: 10.1107/S1399004715005210
Page generated: Fri Jul 26 03:29:42 2024

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