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Chlorine in PDB 1gwd: Tri-Iodide Derivative of Hen Egg-White Lysozyme

Enzymatic activity of Tri-Iodide Derivative of Hen Egg-White Lysozyme

All present enzymatic activity of Tri-Iodide Derivative of Hen Egg-White Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Tri-Iodide Derivative of Hen Egg-White Lysozyme, PDB code: 1gwd was solved by G.Evans, G.Bricogne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.09 / 1.77
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.050, 79.050, 36.820, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.1

Other elements in 1gwd:

The structure of Tri-Iodide Derivative of Hen Egg-White Lysozyme also contains other interesting chemical elements:

Iodine (I) 5 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Tri-Iodide Derivative of Hen Egg-White Lysozyme (pdb code 1gwd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Tri-Iodide Derivative of Hen Egg-White Lysozyme, PDB code: 1gwd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 1gwd

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Chlorine binding site 1 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1137

b:3.0
occ:0.77
 OH A:TYR23 3.1 6.9 1.0
O A:HOH2019 3.3 6.9 1.0
CE2 A:TYR23 3.7 4.3 1.0
CZ A:TYR23 3.7 8.6 1.0
CA A:GLY104 4.2 4.3 1.0
O A:ARG21 4.5 10.1 1.0
N A:GLY104 4.8 4.5 1.0
CD2 A:TYR23 4.9 3.9 1.0
CE1 A:TYR23 4.9 6.0 1.0
O A:HOH2083 5.0 15.8 1.0

Chlorine binding site 2 out of 7 in 1gwd

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Chlorine binding site 2 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1138

b:8.1
occ:0.85
 O A:HOH2053 3.0 5.5 1.0
N A:THR69 3.2 7.5 1.0
O A:HOH2063 3.3 25.9 1.0
O A:HOH2058 3.3 15.2 1.0
O A:THR69 3.4 10.8 1.0
C A:GLY67 3.5 11.4 1.0
O A:HOH2052 3.5 19.6 1.0
N A:ARG68 3.5 7.8 1.0
OG A:SER72 3.6 13.9 1.0
CA A:GLY67 3.6 6.8 1.0
N A:GLY67 3.7 6.8 1.0
C A:THR69 3.7 12.0 1.0
OD1 A:ASN65 3.8 10.8 1.0
CA A:THR69 3.9 7.2 1.0
O A:HOH2051 4.0 9.6 1.0
O A:GLY67 4.1 11.6 1.0
C A:ARG68 4.1 11.5 1.0
CA A:ARG68 4.2 8.0 1.0
OD1 A:ASP66 4.3 7.9 1.0
CB A:THR69 4.3 11.0 1.0
N A:PRO70 4.6 9.8 1.0
NA A:NA1144 4.7 9.6 1.0
O A:HOH2060 4.8 17.4 0.5
OG1 A:THR69 4.8 9.1 1.0
C A:ASP66 4.8 8.8 1.0
CB A:SER72 4.8 11.4 1.0
N A:ASP66 4.9 5.5 1.0
CG A:ASN65 5.0 18.1 1.0

Chlorine binding site 3 out of 7 in 1gwd

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Chlorine binding site 3 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1139

b:10.2
occ:0.85
 OG A:SER24 3.0 13.6 1.0
N A:GLY26 3.1 5.4 1.0
CA A:GLY26 3.5 4.7 1.0
CB A:SER24 3.5 9.3 1.0
CA A:GLN121 3.6 8.4 1.0
CD1 A:ILE124 3.7 19.8 1.0
N A:GLN121 4.0 8.9 1.0
CB A:GLN121 4.0 9.5 0.5
N A:LEU25 4.1 6.9 1.0
CG1 A:ILE124 4.2 12.4 1.0
C A:LEU25 4.3 9.1 1.0
O A:VAL120 4.3 9.7 1.0
C A:VAL120 4.3 11.2 1.0
C A:SER24 4.3 9.9 1.0
CG2 A:VAL120 4.4 10.1 1.0
C A:GLY26 4.5 8.2 1.0
CA A:SER24 4.6 6.7 1.0
CA A:LEU25 4.6 6.3 1.0
N A:ASN27 4.6 4.8 1.0
O A:SER24 4.7 8.7 1.0
C A:GLN121 4.8 12.2 1.0
CG A:GLN121 4.9 23.9 0.5
CG2 A:ILE124 4.9 13.0 1.0
CB A:LEU25 5.0 6.3 1.0

Chlorine binding site 4 out of 7 in 1gwd

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Chlorine binding site 4 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1140

b:13.1
occ:0.81
 N A:ILE88 3.4 7.2 1.0
O A:HOH2073 3.4 19.2 1.0
O A:HOH2103 3.5 18.9 1.0
CG1 A:ILE88 3.7 9.5 1.0
CA A:ASP87 3.8 7.8 1.0
CE1 A:HIS15 3.8 16.8 1.0
O A:SER86 4.0 13.1 1.0
C A:ASP87 4.1 10.8 1.0
OD1 A:ASP87 4.1 18.4 1.0
CB A:ALA11 4.2 7.6 1.0
CG2 A:ILE88 4.3 10.0 1.0
CZ A:PHE3 4.3 9.6 1.0
CB A:ILE88 4.4 9.4 1.0
CA A:ILE88 4.4 6.6 1.0
CG A:ASP87 4.6 19.7 1.0
CD1 A:ILE88 4.6 15.5 1.0
NE2 A:HIS15 4.7 17.2 1.0
ND1 A:HIS15 4.7 17.3 1.0
CB A:ASP87 4.7 9.8 1.0
N A:ASP87 4.8 8.1 1.0
CE2 A:PHE3 4.8 11.5 1.0
C A:SER86 4.8 12.3 1.0

Chlorine binding site 5 out of 7 in 1gwd

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Chlorine binding site 5 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1141

b:17.0
occ:0.82
 CE2 A:PHE38 3.7 9.5 1.0
NZ A:LYS33 3.7 16.4 1.0
CZ3 A:TRP123 3.8 9.9 1.0
CE A:LYS33 4.0 15.4 1.0
CD A:ARG5 4.1 12.4 1.0
CD A:LYS33 4.2 9.6 1.0
CB A:ARG5 4.2 7.0 1.0
CZ A:PHE38 4.3 7.4 1.0
C2 A:EDO1136 4.3 33.1 1.0
CG A:ARG5 4.6 11.3 1.0
O A:HOH2006 4.7 25.2 1.0
CE3 A:TRP123 4.7 8.4 1.0
CH2 A:TRP123 4.7 10.6 1.0
NE A:ARG5 4.7 12.2 1.0
CD2 A:PHE38 4.8 6.8 1.0

Chlorine binding site 6 out of 7 in 1gwd

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Chlorine binding site 6 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1142

b:13.8
occ:0.72
 O A:HOH2065 3.0 15.3 1.0
ND2 A:ASN65 3.2 11.0 1.0
CA A:PRO79 3.7 6.4 1.0
CB A:PRO79 3.7 8.1 1.0
CB A:ASN65 3.8 6.3 1.0
N A:PRO79 4.0 7.2 1.0
CG A:ASN65 4.0 18.1 1.0
O A:ASN65 4.2 7.3 1.0
CD A:PRO79 4.4 8.0 1.0
C A:ILE78 4.5 10.8 1.0
CG A:PRO79 4.5 12.7 1.0
O A:ILE78 4.6 10.2 1.0
ND2 A:ASN74 4.8 8.8 1.0
C A:ASN65 4.9 8.7 1.0
CA A:ASN65 4.9 6.1 1.0

Chlorine binding site 7 out of 7 in 1gwd

Go back to Chlorine Binding Sites List in 1gwd
Chlorine binding site 7 out of 7 in the Tri-Iodide Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Tri-Iodide Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1143

b:14.3
occ:0.61
 N A:ASN74 3.2 9.9 1.0
NE A:ARG73 3.3 22.9 1.0
O A:ASN74 3.8 11.8 1.0
C A:ASN74 3.9 12.8 1.0
CA A:ARG73 4.0 9.5 1.0
CA A:ASN74 4.0 9.2 1.0
CB A:ARG73 4.0 9.8 1.0
C A:ARG73 4.1 13.6 1.0
NH2 A:ARG73 4.1 20.7 1.0
CZ A:ARG73 4.2 31.9 1.0
CD2 A:LEU75 4.2 19.3 1.0
CB A:ASN74 4.2 7.7 1.0
CD A:ARG73 4.2 18.0 1.0
O A:HOH2064 4.2 35.0 1.0
N A:LEU75 4.3 10.0 1.0
CG A:ARG73 4.7 15.8 1.0
CA A:LEU75 4.8 9.9 1.0
O A:HOH2061 4.9 23.2 1.0

Reference:

G.Evans, G.Bricogne. Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods For Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Acta Crystallogr.,Sect.D V. 58 976 2002.
ISSN: ISSN 0907-4449
PubMed: 12037300
DOI: 10.1107/S0907444902005486
Page generated: Fri Jul 19 22:19:53 2024

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