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Chlorine in PDB 3agg: X-Ray Analysis of Lysozyme in the Absence of Arg

Enzymatic activity of X-Ray Analysis of Lysozyme in the Absence of Arg

All present enzymatic activity of X-Ray Analysis of Lysozyme in the Absence of Arg:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Analysis of Lysozyme in the Absence of Arg, PDB code: 3agg was solved by L.Ito, K.Shiraki, K.Hasegawa, S.Baba, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.31 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.609, 78.609, 37.289, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.8

Other elements in 3agg:

The structure of X-Ray Analysis of Lysozyme in the Absence of Arg also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Analysis of Lysozyme in the Absence of Arg (pdb code 3agg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the X-Ray Analysis of Lysozyme in the Absence of Arg, PDB code: 3agg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 3agg

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Chlorine binding site 1 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl130

b:12.3
occ:1.00
 O G:HOH300 3.0 32.7 1.0
OH G:TYR23 3.0 7.5 1.0
O G:HOH176 3.3 10.3 1.0
CE2 G:TYR23 3.7 6.1 1.0
CZ G:TYR23 3.7 6.7 1.0
CA G:GLY104 4.1 7.0 1.0
O G:ARG21 4.6 9.2 0.5
O G:ARG21 4.6 9.4 0.5
N G:GLY104 4.7 7.5 1.0
CE1 G:TYR23 4.9 8.0 1.0
CD2 G:TYR23 5.0 6.1 1.0

Chlorine binding site 2 out of 9 in 3agg

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Chlorine binding site 2 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl131

b:13.1
occ:1.00
 O G:HOH173 3.1 9.1 1.0
O G:HOH251 3.2 19.1 1.0
N G:THR69 3.3 10.6 1.0
O G:HOH244 3.4 19.6 1.0
O G:THR69 3.4 11.1 1.0
C G:GLY67 3.5 10.8 1.0
N G:ARG68 3.6 9.6 1.0
OG G:SER72 3.6 13.6 1.0
CA G:GLY67 3.6 10.9 1.0
N G:GLY67 3.7 9.7 1.0
OD1 G:ASN65 3.7 10.7 1.0
C G:THR69 3.7 11.1 1.0
CA G:THR69 3.9 10.9 1.0
O G:HOH209 4.0 11.2 1.0
O G:GLY67 4.2 12.2 1.0
CB G:THR69 4.3 10.9 1.0
C G:ARG68 4.3 10.4 1.0
OD1 G:ASP66 4.3 8.3 1.0
CA G:ARG68 4.4 10.4 1.0
N G:PRO70 4.5 12.6 1.0
O G:HOH154 4.6 20.0 1.0
NA G:NA139 4.7 11.3 1.0
C G:ASP66 4.8 8.6 1.0
CB G:SER72 4.8 14.1 1.0
OG1 G:THR69 4.9 9.6 1.0
CG G:ASN65 4.9 9.8 1.0
N G:ASP66 4.9 7.8 1.0
CA G:PRO70 5.0 13.8 1.0

Chlorine binding site 3 out of 9 in 3agg

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Chlorine binding site 3 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl132

b:16.5
occ:1.00
 OG G:SER24 3.0 12.1 1.0
O G:HOH292 3.0 29.4 1.0
N G:GLY26 3.2 8.6 1.0
CA G:GLY26 3.5 8.4 1.0
CB G:SER24 3.5 10.4 1.0
CA G:GLN121 3.6 13.8 1.0
CD1 G:ILE124 3.7 20.5 1.0
N G:GLN121 3.9 13.1 1.0
CB G:GLN121 4.0 15.4 1.0
O G:VAL120 4.2 11.7 1.0
C G:VAL120 4.2 12.4 1.0
CG1 G:ILE124 4.2 14.1 1.0
CG2 G:VAL120 4.2 14.4 1.0
CG G:GLN121 4.3 20.6 1.0
N G:LEU25 4.4 9.7 1.0
C G:LEU25 4.4 9.0 1.0
C G:SER24 4.4 9.8 1.0
C G:GLY26 4.5 6.4 1.0
N G:ASN27 4.6 7.1 1.0
CA G:SER24 4.6 8.8 1.0
O G:SER24 4.8 10.7 1.0
O G:HOH169 4.8 32.8 1.0
CA G:LEU25 4.8 9.5 1.0
C G:GLN121 4.8 12.7 1.0
CB G:VAL120 5.0 12.3 1.0

Chlorine binding site 4 out of 9 in 3agg

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Chlorine binding site 4 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl133

b:17.9
occ:1.00
 O G:HOH163 2.8 21.6 1.0
ND2 G:ASN65 3.1 11.3 1.0
CA G:GLY67 3.7 10.9 1.0
N G:GLY67 4.0 9.7 1.0
CG G:ASN65 4.1 9.8 1.0
OD1 G:ASN65 4.3 10.7 1.0
O G:HOH244 4.4 19.6 1.0
C G:ASP66 4.6 8.6 1.0
O G:ASP66 4.9 9.9 1.0
C G:GLY67 5.0 10.8 1.0

Chlorine binding site 5 out of 9 in 3agg

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Chlorine binding site 5 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl134

b:23.7
occ:1.00
 O G:HOH265 3.0 17.6 1.0
ND2 G:ASN65 3.3 11.3 1.0
CB G:PRO79 3.7 10.5 1.0
CA G:PRO79 3.7 9.9 1.0
CB G:ASN65 3.9 7.3 1.0
N G:PRO79 3.9 10.3 1.0
CG G:ASN65 4.1 9.8 1.0
CD G:PRO79 4.3 11.4 1.0
CG G:PRO79 4.3 11.8 1.0
O G:ASN65 4.3 8.6 1.0
C G:ILE78 4.5 10.4 1.0
O G:ILE78 4.7 10.7 1.0
ND2 G:ASN74 4.8 11.4 1.0
C G:ASN65 5.0 8.3 1.0
CA G:ASN65 5.0 8.7 1.0

Chlorine binding site 6 out of 9 in 3agg

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Chlorine binding site 6 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl135

b:21.3
occ:1.00
 O G:HOH207 3.2 26.0 1.0
N G:ILE88 3.3 11.7 1.0
O G:HOH242 3.3 19.3 1.0
CG1 G:ILE88 3.7 11.8 1.0
CA G:ASP87 3.7 13.5 1.0
CE1 G:HIS15 3.9 17.2 1.0
C G:ASP87 4.0 12.2 1.0
O G:SER86 4.0 12.8 0.5
CG G:ASP87 4.1 20.8 1.0
CB G:ALA11 4.2 10.8 1.0
O G:SER86 4.2 12.7 0.5
OD1 G:ASP87 4.2 17.2 1.0
CB G:ILE88 4.3 10.9 1.0
CZ G:PHE3 4.3 12.3 1.0
CA G:ILE88 4.3 11.6 1.0
CG2 G:ILE88 4.3 14.5 1.0
OD2 G:ASP87 4.4 26.6 1.0
CB G:ASP87 4.5 15.3 1.0
CD1 G:ILE88 4.5 13.2 1.0
NE2 G:HIS15 4.6 17.9 1.0
ND1 G:HIS15 4.7 15.2 1.0
O G:HOH285 4.7 24.8 1.0
N G:ASP87 4.8 11.7 1.0
CE2 G:PHE3 4.8 10.5 1.0
C G:SER86 4.8 12.0 0.5
C G:SER86 4.9 12.4 0.5

Chlorine binding site 7 out of 9 in 3agg

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Chlorine binding site 7 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl136

b:19.9
occ:1.00
 O G:TYR53 2.9 8.8 1.0
N G:LEU56 2.9 9.9 1.0
OG G:SER91 3.0 8.7 1.0
N G:ILE55 3.4 8.3 1.0
C G:GLY54 3.4 8.1 1.0
N G:GLN57 3.5 6.7 1.0
CA G:LEU56 3.5 8.5 1.0
CA G:GLY54 3.5 7.5 1.0
C G:LEU56 3.6 9.2 1.0
CB G:SER91 3.6 10.1 1.0
CB G:LEU56 3.7 9.9 1.0
CD1 G:ILE58 3.8 13.5 1.0
CG1 G:ILE58 3.8 9.3 1.0
C G:TYR53 3.8 7.7 1.0
C G:ILE55 3.9 10.5 1.0
O G:HOH275 4.0 18.8 1.0
O G:GLY54 4.0 7.5 1.0
N G:ILE58 4.0 7.0 1.0
CA G:ILE55 4.2 10.3 1.0
CG2 G:ILE55 4.2 13.6 1.0
N G:GLY54 4.2 7.1 1.0
O G:LEU83 4.2 11.4 1.0
CB G:ILE58 4.2 8.8 1.0
O G:LEU56 4.5 8.3 1.0
CD2 G:LEU83 4.5 13.5 1.0
CA G:GLN57 4.5 7.1 1.0
CB G:LEU83 4.5 9.2 1.0
CA G:SER91 4.5 9.1 1.0
C G:GLN57 4.8 7.5 1.0
CG G:LEU56 4.8 8.5 1.0
CB G:ILE55 4.8 12.8 1.0
CA G:ILE58 4.8 7.6 1.0
CG G:LEU83 5.0 11.8 1.0

Chlorine binding site 8 out of 9 in 3agg

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Chlorine binding site 8 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl137

b:21.2
occ:1.00
 NE G:ARG114 2.9 7.7 1.0
O G:HOH210 2.9 16.4 1.0
NH2 G:ARG114 3.5 9.7 1.0
CZ G:ARG114 3.6 8.3 1.0
CB G:ARG114 3.7 8.2 1.0
CG G:ARG114 3.8 9.3 1.0
CD G:ARG114 3.9 9.0 1.0
CZ G:PHE34 4.0 11.9 1.0
CE1 G:PHE34 4.2 10.2 1.0
CE2 G:PHE34 4.3 10.4 1.0
CA G:ARG114 4.4 8.2 1.0
O G:ARG114 4.5 10.3 1.0
CD1 G:PHE34 4.8 9.0 1.0
CD2 G:PHE34 4.9 9.1 1.0
NH1 G:ARG114 4.9 9.5 1.0
O G:HOH280 5.0 15.4 1.0

Chlorine binding site 9 out of 9 in 3agg

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Chlorine binding site 9 out of 9 in the X-Ray Analysis of Lysozyme in the Absence of Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of X-Ray Analysis of Lysozyme in the Absence of Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl138

b:21.1
occ:1.00
 OG1 G:THR51 2.6 7.5 1.0
OD2 G:ASP66 2.7 9.1 1.0
O G:GLY49 2.9 12.7 1.0
NE G:ARG68 2.9 8.6 1.0
OG1 G:THR69 3.1 9.6 1.0
N G:THR51 3.3 6.8 1.0
C G:SER50 3.4 9.4 1.0
CB G:THR51 3.4 7.4 1.0
CD G:ARG68 3.5 10.8 1.0
CG G:ASP66 3.6 9.7 1.0
O G:ARG68 3.6 12.3 1.0
CG G:ARG68 3.7 10.2 1.0
CA G:SER50 3.7 10.4 1.0
OG G:SER60 3.7 8.4 1.0
OD1 G:ASP66 3.8 8.3 1.0
CZ G:ARG68 3.8 10.1 1.0
C G:GLY49 3.9 12.3 1.0
NH2 G:ARG68 4.0 8.2 1.0
CA G:THR51 4.0 7.0 1.0
O G:SER50 4.0 8.9 1.0
NE G:ARG45 4.1 15.0 1.0
C G:ARG68 4.2 10.4 1.0
OH G:TYR53 4.3 7.1 1.0
N G:SER50 4.3 9.7 1.0
NH2 G:ARG45 4.3 15.0 1.0
CB G:THR69 4.4 10.9 1.0
CZ G:ARG45 4.6 19.4 1.0
CB G:ARG68 4.6 9.8 1.0
CB G:SER60 4.7 9.0 1.0
N G:THR69 4.7 10.6 1.0
CG2 G:THR51 4.8 9.2 1.0
CA G:THR69 4.8 10.9 1.0
CB G:SER50 4.9 10.6 1.0
CA G:ARG68 4.9 10.4 1.0
CG2 G:THR69 4.9 11.7 1.0
CD G:ARG45 4.9 11.4 1.0
CB G:ASP66 5.0 8.5 1.0

Reference:

L.Ito, K.Shiraki, T.Matsuura, M.Okumura, K.Hasegawa, S.Baba, H.Yamaguchi, T.Kumasaka. High-Resolution X-Ray Analysis Reveals Binding of Arginine to Aromatic Residues of Lysozyme Surface: Implication of Suppression of Protein Aggregation By Arginine Protein Eng.Des.Sel. V. 24 269 2011.
ISSN: ISSN 1741-0126
PubMed: 21084280
DOI: 10.1093/PROTEIN/GZQ101
Page generated: Fri Jul 11 03:05:02 2025

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