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Chlorine in PDB 3agi: High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg

Enzymatic activity of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg

All present enzymatic activity of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg:
3.2.1.17;

Protein crystallography data

The structure of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg, PDB code: 3agi 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) 39.02 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.033, 78.033, 37.752, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 16.7

Other elements in 3agi:

The structure of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg (pdb code 3agi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg, PDB code: 3agi:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3agi

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Chlorine binding site 1 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl135

b:16.7
occ:1.00
 O A:HOH307 3.1 26.9 1.0
O A:HOH197 3.2 11.1 1.0
O A:HOH289 3.2 27.6 1.0
N A:THR69 3.3 13.1 1.0
O A:THR69 3.3 14.2 1.0
O A:HOH287 3.3 24.0 1.0
N A:ARG68 3.5 13.0 0.5
C A:THR69 3.6 13.5 1.0
C A:GLY67 3.6 13.6 1.0
OD1 A:ASN65 3.6 13.5 1.0
N A:ARG68 3.7 13.0 0.5
CA A:GLY67 3.7 14.3 1.0
OG A:SER72 3.7 14.0 1.0
N A:GLY67 3.7 12.3 1.0
CA A:THR69 3.9 12.8 1.0
O A:HOH215 3.9 13.2 1.0
O A:GLY67 4.2 16.7 1.0
C A:ARG68 4.2 13.4 0.5
CB A:THR69 4.2 11.9 1.0
CA A:ARG68 4.3 13.0 0.5
N A:PRO70 4.3 16.1 1.0
OD1 A:ASP66 4.3 9.8 1.0
C A:ARG68 4.3 11.8 0.5
CA A:ARG68 4.5 11.8 0.5
O A:HOH297 4.6 31.0 1.0
NA A:NA134 4.7 10.8 1.0
CA A:PRO70 4.8 16.6 1.0
C A:ASP66 4.9 11.3 1.0
CG A:ASN65 4.9 11.6 1.0
OG1 A:THR69 4.9 11.7 1.0
N A:ASP66 4.9 9.5 1.0
CB A:SER72 4.9 13.4 1.0

Chlorine binding site 2 out of 8 in 3agi

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Chlorine binding site 2 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl136

b:13.2
occ:0.80
 NE2 A:GLN121 2.9 21.6 0.2
O A:HOH250 2.9 33.8 1.0
OG A:SER24 3.1 13.3 1.0
N A:GLY26 3.2 8.5 1.0
O A:HOH144 3.3 28.9 1.0
CB A:SER24 3.5 11.2 1.0
CA A:GLY26 3.5 9.1 1.0
CA A:GLN121 3.6 13.7 0.8
CA A:GLN121 3.7 13.1 0.2
CB A:GLN121 3.9 14.5 0.8
N A:GLN121 3.9 11.6 0.8
CD1 A:ILE124 3.9 20.8 1.0
N A:GLN121 4.0 12.0 0.2
CD A:GLN121 4.0 19.3 0.2
CG A:GLN121 4.1 17.7 0.8
N A:LEU25 4.2 8.9 1.0
CG1 A:ILE124 4.3 15.3 1.0
C A:VAL120 4.3 11.4 1.0
CG2 A:VAL120 4.3 13.0 1.0
O A:VAL120 4.3 10.8 1.0
C A:LEU25 4.3 8.2 1.0
CB A:GLN121 4.3 13.6 0.2
C A:SER24 4.4 9.1 1.0
C A:GLY26 4.6 7.8 1.0
CA A:SER24 4.6 8.6 1.0
N A:ASN27 4.6 7.9 1.0
CA A:LEU25 4.7 9.1 1.0
OE1 A:GLN121 4.7 19.8 0.2
CG A:GLN121 4.8 16.4 0.2
O A:SER24 4.8 9.7 1.0
C A:GLN121 4.8 12.6 0.8
C A:GLN121 4.9 12.7 0.2

Chlorine binding site 3 out of 8 in 3agi

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Chlorine binding site 3 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl137

b:18.1
occ:0.80
 OD1 A:ASN19 2.6 11.1 0.3
O A:HOH144 2.9 28.9 1.0
O A:HOH268 2.9 22.3 1.0
N A:LEU25 3.0 8.9 1.0
CG A:ASN19 3.3 10.8 0.3
CA A:SER24 3.5 8.6 1.0
ND2 A:ASN19 3.6 12.4 0.3
CB A:LEU25 3.7 10.2 1.0
CB A:SER24 3.8 11.2 1.0
C A:SER24 3.8 9.1 1.0
N A:ASN19 3.9 11.5 0.7
CB A:ASP18 3.9 13.6 1.0
CA A:LEU25 4.0 9.1 1.0
N A:ASN19 4.0 11.0 0.3
O A:HOH180 4.2 31.3 1.0
C A:ASP18 4.3 12.8 1.0
CA A:ASP18 4.4 13.0 1.0
CB A:ASN19 4.4 14.3 0.7
CB A:ASN19 4.6 10.8 0.3
CA A:ASN19 4.6 12.2 0.7
CA A:ASN19 4.6 10.6 0.3
OD2 A:ASP18 4.7 15.1 1.0
N A:SER24 4.8 9.2 1.0
CG A:ASP18 4.9 13.4 1.0
OG A:SER24 5.0 13.3 1.0
O A:ASP18 5.0 14.8 1.0

Chlorine binding site 4 out of 8 in 3agi

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Chlorine binding site 4 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl138

b:18.3
occ:0.70
 O A:HOH209 2.8 15.3 1.0
O A:ASP87 2.9 11.0 1.0
O A:HOH254 2.9 31.8 1.0
N A:ALA90 2.9 10.4 1.0
OG A:SER85 3.3 15.0 0.5
N A:THR89 3.4 9.9 1.0
OD1 A:ASP87 3.5 16.4 1.0
O A:HOH190 3.5 13.2 1.0
CB A:ALA90 3.6 11.5 1.0
CB A:THR89 3.6 12.7 1.0
C A:ASP87 3.7 10.5 1.0
CA A:THR89 3.8 10.8 1.0
C A:THR89 3.8 10.4 1.0
CA A:ALA90 3.8 10.6 1.0
CG A:ASP87 4.0 15.5 1.0
CB A:ASP87 4.1 13.7 1.0
C A:ILE88 4.1 9.6 1.0
CB A:SER85 4.3 11.2 0.5
O A:ALA82 4.3 12.0 1.0
CB A:SER85 4.4 11.9 0.5
OG1 A:THR89 4.4 13.2 1.0
OG A:SER85 4.4 11.7 0.5
O A:HOH288 4.4 22.9 1.0
N A:ILE88 4.5 9.9 1.0
CA A:ASP87 4.5 12.3 1.0
CA A:ILE88 4.6 9.5 1.0
CG2 A:THR89 4.7 14.5 1.0
O A:ILE88 4.8 9.1 1.0
O A:THR89 5.0 10.6 1.0
N A:SER91 5.0 8.9 0.8
C A:ALA90 5.0 9.7 1.0
N A:SER91 5.0 9.9 0.2

Chlorine binding site 5 out of 8 in 3agi

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Chlorine binding site 5 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl139

b:16.3
occ:0.70
 O A:HOH152 2.7 22.0 1.0
NH2 A:ARG114 2.9 9.7 1.0
NH1 A:ARG114 3.6 9.6 1.0
CZ A:ARG114 3.7 8.8 1.0
O A:HOH216 4.0 17.7 1.0
O A:HOH207 4.1 15.6 1.0
CD1 A:PHE34 4.4 8.7 1.0
CE1 A:PHE34 4.6 10.1 1.0
NE A:ARG114 5.0 8.7 1.0

Chlorine binding site 6 out of 8 in 3agi

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Chlorine binding site 6 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl140

b:16.0
occ:0.70
 NH2 A:ARG14 3.2 14.8 0.3
O A:HOH233 3.2 19.4 1.0
N A:ILE88 3.3 9.9 1.0
CG1 A:ILE88 3.7 10.5 1.0
CA A:ASP87 3.8 12.3 1.0
CE1 A:HIS15 3.8 18.6 1.0
NH1 A:ARG14 4.0 16.5 0.3
CZ A:ARG14 4.0 13.3 0.3
C A:ASP87 4.1 10.5 1.0
O A:SER86 4.1 13.6 0.5
CB A:ALA11 4.2 12.7 1.0
CZ A:PHE3 4.2 12.6 1.0
O A:SER86 4.2 12.8 0.5
OD1 A:ASP87 4.2 16.4 1.0
CG A:ASP87 4.3 15.5 1.0
CB A:ILE88 4.3 10.3 1.0
CG2 A:ILE88 4.3 11.6 1.0
CA A:ILE88 4.4 9.5 1.0
O A:HOH310 4.4 25.7 1.0
OD2 A:ASP87 4.5 23.4 1.0
CB A:ASP87 4.6 13.7 1.0
CD1 A:ILE88 4.6 12.5 1.0
NH2 A:ARG14 4.7 26.6 0.7
ND1 A:HIS15 4.7 16.4 1.0
NE2 A:HIS15 4.7 18.4 1.0
CE2 A:PHE3 4.7 11.8 1.0
N A:ASP87 4.8 11.3 1.0
C A:SER86 4.9 12.3 0.5
C A:SER86 5.0 11.6 0.5

Chlorine binding site 7 out of 8 in 3agi

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Chlorine binding site 7 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl141

b:14.6
occ:0.70
 O A:HOH218 2.8 13.4 1.0
O A:HOH177 2.9 11.9 1.0
CZ2 A:TRP111 3.6 8.2 1.0
CH2 A:TRP111 3.7 8.4 1.0
CG A:LYS116 3.9 8.2 1.0
N A:GLY117 4.3 10.4 1.0
O A:HOH224 4.4 15.6 1.0
CA A:LYS116 4.5 8.4 1.0
O A:HOH211 4.5 14.5 1.0
CB A:LYS116 4.7 7.7 1.0
OD1 A:ASN27 4.8 8.4 1.0
CE A:LYS116 4.8 9.0 1.0
CE2 A:TRP111 4.9 7.7 1.0
CE1 A:TYR23 4.9 8.1 1.0
CD A:LYS116 4.9 8.1 1.0
C A:LYS116 4.9 9.3 1.0
CZ3 A:TRP111 5.0 8.3 1.0

Chlorine binding site 8 out of 8 in 3agi

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Chlorine binding site 8 out of 8 in the High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of High Resolution X-Ray Analysis of Arg-Lysozyme Complex in the Presence of 500 Mm Arg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl142

b:11.8
occ:1.00
 OH A:TYR23 3.0 8.7 1.0
O A:HOH185 3.2 10.3 1.0
CE2 A:TYR23 3.7 7.7 1.0
CZ A:TYR23 3.7 8.2 1.0
CA A:GLY104 4.0 8.4 1.0
O A:HOH143 4.5 24.6 1.0
O A:ARG21 4.6 10.6 1.0
N A:GLY104 4.6 8.2 1.0
CE1 A:TYR23 4.9 8.1 1.0
CD2 A:TYR23 4.9 7.9 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: Sat Jul 20 15:53:11 2024

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