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Chlorine in PDB 3tmx: X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)

Enzymatic activity of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)

All present enzymatic activity of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY), PDB code: 3tmx was solved by J.Kmetko, M.A.Warkentin, U.Englich, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.04 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.678, 79.678, 37.655, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 21

Other elements in 3tmx:

The structure of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) (pdb code 3tmx). 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 Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY), PDB code: 3tmx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3tmx

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Chlorine binding site 1 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1130

b:13.2
occ:1.00
 OH A:TYR23 3.1 8.3 1.0
O A:HOH2031 3.3 11.3 1.0
CZ A:TYR23 3.8 7.5 1.0
CE2 A:TYR23 3.8 5.6 1.0
CA A:GLY104 4.2 9.3 1.0
O A:ARG21 4.7 9.5 1.0
N A:GLY104 4.8 10.1 1.0
O A:HOH2168 4.9 39.6 1.0
CE1 A:TYR23 5.0 5.6 1.0

Chlorine binding site 2 out of 8 in 3tmx

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Chlorine binding site 2 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1131

b:21.6
occ:1.00
 O A:HOH2150 2.9 39.4 1.0
OG A:SER24 3.1 14.1 1.0
N A:GLY26 3.2 9.5 1.0
CA A:GLY26 3.5 10.4 1.0
CB A:SER24 3.5 12.3 1.0
CA A:GLN121 3.7 14.5 1.0
CD1 A:ILE124 3.7 20.0 1.0
N A:GLN121 4.0 12.6 1.0
CB A:GLN121 4.2 17.0 1.0
CG1 A:ILE124 4.3 14.2 1.0
CG A:GLN121 4.3 23.9 1.0
C A:VAL120 4.3 12.6 1.0
O A:VAL120 4.4 12.6 1.0
C A:LEU25 4.4 10.2 1.0
N A:LEU25 4.4 10.4 1.0
C A:SER24 4.5 11.3 1.0
CG2 A:VAL120 4.5 13.1 1.0
C A:GLY26 4.6 9.9 1.0
CA A:SER24 4.6 10.9 1.0
N A:ASN27 4.7 7.9 1.0
CA A:LEU25 4.8 10.4 1.0
C A:GLN121 4.8 13.0 1.0
O A:SER24 4.9 10.9 1.0

Chlorine binding site 3 out of 8 in 3tmx

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Chlorine binding site 3 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1132

b:23.5
occ:1.00
 O A:HOH2078 2.9 31.9 1.0
O A:HOH2076 3.1 10.3 1.0
N A:THR69 3.2 15.5 1.0
O A:THR69 3.4 17.3 1.0
O A:HOH2184 3.4 34.5 1.0
O A:HOH2075 3.4 32.7 1.0
N A:ARG68 3.6 11.8 1.0
OD1 A:ASN65 3.6 17.5 1.0
C A:THR69 3.7 18.9 1.0
C A:GLY67 3.7 13.7 1.0
CA A:GLY67 3.8 12.7 1.0
OG A:SER72 3.8 25.3 1.0
N A:GLY67 3.8 11.3 1.0
CA A:THR69 3.8 17.2 1.0
O A:HOH2079 4.0 32.6 1.0
O A:HOH2081 4.1 14.3 1.0
C A:ARG68 4.2 14.7 1.0
CB A:THR69 4.2 18.4 1.0
CA A:ARG68 4.3 13.0 1.0
OD1 A:ASP66 4.3 9.9 1.0
O A:GLY67 4.4 14.0 1.0
N A:PRO70 4.6 20.8 1.0
NA A:NA1138 4.8 18.5 1.0
OG1 A:THR69 4.8 14.3 1.0
CG A:ASN65 4.8 10.8 1.0
C A:ASP66 4.9 11.7 1.0
N A:ASP66 5.0 8.6 1.0
CB A:SER72 5.0 24.3 1.0

Chlorine binding site 4 out of 8 in 3tmx

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Chlorine binding site 4 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1133

b:32.4
occ:1.00
 N A:ILE88 3.3 14.6 1.0
O A:HOH2096 3.4 20.4 1.0
O A:HOH2018 3.7 48.0 1.0
CG1 A:ILE88 3.8 13.7 1.0
CA A:ASP87 3.8 16.5 1.0
CE1 A:HIS15 3.9 22.4 1.0
O A:HOH2099 4.0 37.8 1.0
C A:ASP87 4.1 14.0 1.0
O A:SER86 4.1 16.3 1.0
OD1 A:ASP87 4.2 19.5 1.0
CB A:ILE88 4.3 12.5 1.0
CA A:ILE88 4.3 13.4 1.0
CB A:ALA11 4.3 13.2 1.0
CG A:ASP87 4.3 24.9 1.0
CZ A:PHE3 4.4 13.6 1.0
CG2 A:ILE88 4.4 13.6 1.0
CB A:ASP87 4.7 16.8 1.0
ND1 A:HIS15 4.7 22.2 1.0
CD1 A:ILE88 4.7 11.1 1.0
OD2 A:ASP87 4.8 31.0 1.0
NE2 A:HIS15 4.8 24.3 1.0
N A:ASP87 4.9 15.4 1.0
C A:SER86 4.9 16.1 1.0
NH1 A:ARG14 5.0 41.1 1.0

Chlorine binding site 5 out of 8 in 3tmx

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Chlorine binding site 5 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1134

b:31.9
occ:1.00
 O A:HOH2190 3.7 36.9 1.0
CE2 A:PHE38 3.7 16.4 1.0
O A:HOH2180 3.8 43.9 1.0
NZ A:LYS33 3.9 18.2 1.0
CZ3 A:TRP123 4.0 14.1 1.0
O A:HOH2008 4.1 41.7 1.0
CD A:ARG5 4.3 19.3 1.0
CE A:LYS33 4.3 19.0 1.0
CD A:LYS33 4.4 11.1 1.0
CZ A:PHE38 4.5 9.3 1.0
CB A:ARG5 4.5 14.8 1.0
O A:HOH2143 4.5 35.1 1.0
CD2 A:PHE38 4.7 11.3 1.0
CG A:ARG5 4.8 14.7 1.0
CH2 A:TRP123 4.9 14.8 1.0
NE A:ARG5 4.9 22.2 1.0
CE3 A:TRP123 4.9 13.6 1.0

Chlorine binding site 6 out of 8 in 3tmx

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Chlorine binding site 6 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1135

b:34.6
occ:1.00
 O A:HOH2084 2.9 24.0 1.0
O A:HOH2158 3.1 51.3 1.0
ND2 A:ASN65 3.5 17.9 1.0
CB A:PRO79 3.7 11.6 1.0
CA A:PRO79 3.8 11.4 1.0
CB A:ASN65 4.0 7.8 1.0
N A:PRO79 4.0 11.3 1.0
CG A:ASN65 4.2 10.8 1.0
CD A:PRO79 4.3 12.8 1.0
CG A:PRO79 4.3 13.6 1.0
O A:ASN65 4.4 9.0 1.0
C A:ILE78 4.5 11.7 1.0
O A:ILE78 4.7 11.3 1.0
ND2 A:ASN74 4.9 15.5 1.0

Chlorine binding site 7 out of 8 in 3tmx

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Chlorine binding site 7 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1136

b:43.0
occ:1.00
 O A:HOH2174 2.9 39.3 1.0
N A:ASN74 3.1 14.2 1.0
NE A:ARG73 3.2 34.1 1.0
C A:ASN74 3.7 13.3 1.0
O A:ASN74 3.7 13.7 1.0
CB A:ARG73 3.9 19.1 1.0
CA A:ASN74 3.9 12.9 1.0
CA A:ARG73 3.9 18.5 1.0
C A:ARG73 4.0 17.7 1.0
NH2 A:ARG73 4.0 36.2 1.0
CD A:ARG73 4.1 27.4 1.0
CZ A:ARG73 4.1 35.1 1.0
CD2 A:LEU75 4.1 19.9 1.0
N A:LEU75 4.2 13.0 1.0
CB A:ASN74 4.3 13.9 1.0
CG A:ARG73 4.6 23.8 1.0
CA A:LEU75 4.6 14.6 1.0
CG A:LEU75 4.8 16.6 1.0
O A:HOH2163 4.9 36.2 1.0

Chlorine binding site 8 out of 8 in 3tmx

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Chlorine binding site 8 out of 8 in the X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=1.9MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1137

b:44.2
occ:1.00
 NH1 A:ARG68 2.8 22.3 1.0
CD A:ARG68 3.5 16.4 1.0
CZ A:ARG68 3.8 23.9 1.0
NE A:ARG68 4.1 20.1 1.0
CG A:ARG68 4.8 12.2 1.0
NH1 A:ARG45 4.8 35.2 1.0
CB A:ARG68 5.0 13.1 1.0
NH2 A:ARG68 5.0 13.5 1.0

Reference:

J.Kmetko, M.Warkentin, U.Englich, R.E.Thorne. Can Radiation Damage to Protein Crystals Be Reduced Using Small-Molecule Compounds? Acta Crystallogr.,Sect.D V. 67 881 2011.
ISSN: ISSN 0907-4449
PubMed: 21931220
DOI: 10.1107/S0907444911032835
Page generated: Sun Jul 21 05:23:36 2024

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