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Chlorine in PDB 3tmv: X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=0.12MGY)

Enzymatic activity of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=0.12MGY)

All present enzymatic activity of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=0.12MGY):
3.2.1.17;

Protein crystallography data

The structure of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=0.12MGY), PDB code: 3tmv 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) 35.72 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.876, 79.876, 38.736, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 21.9

Other elements in 3tmv:

The structure of X-Ray Radiation Damage to Hewl Crystals Soaked in 100MM Sodium Nitrate (Dose=0.12MGY) 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=0.12MGY) (pdb code 3tmv). 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=0.12MGY), PDB code: 3tmv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1130

b:26.3
occ:1.00
 OH A:TYR23 3.0 14.1 1.0
O A:HOH2031 3.5 21.7 1.0
CZ A:TYR23 3.8 10.9 1.0
CE2 A:TYR23 3.8 10.6 1.0
CA A:GLY104 4.2 15.6 1.0
O A:ARG21 4.8 20.1 1.0
N A:GLY104 4.8 14.8 1.0

Chlorine binding site 2 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1131

b:34.7
occ:1.00
 OG A:SER24 3.0 20.6 1.0
N A:GLY26 3.1 13.8 1.0
O A:HOH2151 3.3 50.1 1.0
CB A:SER24 3.5 18.3 1.0
CA A:GLY26 3.5 14.0 1.0
CA A:GLN121 3.9 25.4 1.0
CD1 A:ILE124 3.9 29.2 1.0
N A:LEU25 4.1 15.8 1.0
N A:GLN121 4.2 23.0 1.0
C A:SER24 4.2 18.4 1.0
C A:LEU25 4.3 15.5 1.0
CG1 A:ILE124 4.4 21.0 1.0
CB A:GLN121 4.4 27.1 1.0
CG2 A:VAL120 4.4 22.4 1.0
C A:VAL120 4.5 24.0 1.0
O A:VAL120 4.5 21.7 1.0
CA A:SER24 4.5 17.5 1.0
CA A:LEU25 4.6 15.9 1.0
C A:GLY26 4.6 13.9 1.0
CG A:GLN121 4.7 36.8 1.0
O A:SER24 4.7 16.8 1.0
N A:ASN27 4.8 11.9 1.0
CB A:LEU25 4.9 17.6 1.0

Chlorine binding site 3 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1132

b:44.3
occ:1.00
 O A:HOH2076 2.8 19.3 1.0
N A:THR69 3.2 20.8 1.0
O A:THR69 3.3 26.0 1.0
OD1 A:ASN65 3.4 28.3 1.0
O A:HOH2075 3.6 46.1 1.0
N A:ARG68 3.6 17.8 1.0
N A:GLY67 3.6 17.0 1.0
CA A:GLY67 3.7 18.5 1.0
C A:GLY67 3.7 20.8 1.0
C A:THR69 3.7 24.6 1.0
OG A:SER72 3.9 29.1 1.0
CA A:THR69 3.9 22.4 1.0
O A:HOH2081 4.1 27.4 1.0
OD1 A:ASP66 4.2 16.8 1.0
C A:ARG68 4.2 20.6 1.0
CB A:THR69 4.3 22.3 1.0
CA A:ARG68 4.4 19.7 1.0
O A:GLY67 4.5 22.1 1.0
N A:PRO70 4.5 28.0 1.0
N A:ASP66 4.6 14.5 1.0
CG A:ASN65 4.6 22.4 1.0
C A:ASP66 4.7 17.1 1.0
O A:HOH2077 4.7 43.4 1.0
OG1 A:THR69 4.8 20.3 1.0
NA A:NA1138 4.8 20.9 1.0
CA A:PRO70 4.9 29.5 1.0

Chlorine binding site 4 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1133

b:56.6
occ:1.00
 N A:ILE88 3.3 18.1 1.0
CG1 A:ILE88 3.7 19.9 1.0
O A:HOH2096 3.8 33.6 1.0
CA A:ASP87 3.9 21.9 1.0
OD1 A:ASP87 3.9 28.3 1.0
C A:ASP87 4.0 20.8 1.0
O A:SER86 4.2 24.5 1.0
CE1 A:HIS15 4.2 26.7 1.0
CB A:ILE88 4.4 15.8 1.0
CA A:ILE88 4.4 18.4 1.0
CG2 A:ILE88 4.5 16.4 1.0
CB A:ALA11 4.6 18.9 1.0
CD1 A:ILE88 4.6 19.5 1.0
CG A:ASP87 4.6 30.0 1.0
CZ A:PHE3 4.6 23.0 1.0
NH1 A:ARG14 4.7 45.8 1.0
CB A:ASP87 4.8 23.0 1.0
ND1 A:HIS15 4.9 29.9 1.0
N A:ASP87 4.9 21.7 1.0
N A:THR89 4.9 19.6 1.0

Chlorine binding site 5 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1134

b:58.1
occ:1.00
 O A:HOH2008 3.8 38.3 1.0
CE2 A:PHE38 3.9 18.6 1.0
CD A:ARG5 4.2 24.4 1.0
CZ3 A:TRP123 4.2 22.0 1.0
CB A:ARG5 4.4 21.4 1.0
NZ A:LYS33 4.4 33.9 1.0
CD A:LYS33 4.5 23.8 1.0
CZ A:PHE38 4.5 14.5 1.0
CE A:LYS33 4.6 32.1 1.0
CG A:ARG5 4.7 19.3 1.0
O A:HOH2154 4.8 49.9 1.0
NE A:ARG5 4.9 30.9 1.0
CD2 A:PHE38 4.9 15.1 1.0

Chlorine binding site 6 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1135

b:82.6
occ:1.00
 ND2 A:ASN65 3.0 35.6 1.0
CB A:PRO79 3.5 19.0 1.0
O A:HOH2084 3.7 43.6 1.0
O A:HOH2074 3.9 23.2 1.0
CA A:PRO79 4.0 17.2 1.0
O A:ASN65 4.1 14.8 1.0
CG A:ASN65 4.1 22.4 1.0
CB A:ASN65 4.4 15.2 1.0
CG A:PRO79 4.4 21.0 1.0
N A:PRO79 4.7 18.4 1.0
C A:ASN65 4.8 13.8 1.0

Chlorine binding site 7 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1136

b:72.9
occ:1.00
 N A:ASN74 3.3 23.2 1.0
CB A:ARG73 3.7 27.8 1.0
NE A:ARG73 3.9 56.6 1.0
CA A:ARG73 3.9 26.3 1.0
C A:ASN74 4.0 19.5 1.0
O A:ASN74 4.0 19.9 1.0
C A:ARG73 4.1 25.6 1.0
CA A:ASN74 4.2 21.5 1.0
N A:LEU75 4.4 21.3 1.0
CD2 A:LEU75 4.4 31.9 1.0
NH2 A:ARG73 4.4 62.3 1.0
CZ A:ARG73 4.5 61.9 1.0
CB A:ASN74 4.6 21.0 1.0
CD A:ARG73 4.6 48.3 1.0
CG A:ARG73 4.7 35.0 1.0
CA A:LEU75 4.8 22.1 1.0
CG A:LEU75 4.8 26.7 1.0
O A:HOH2148 4.9 49.6 1.0

Chlorine binding site 8 out of 8 in 3tmv

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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=0.12MGY)


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=0.12MGY) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1137

b:49.5
occ:1.00
 NH1 A:ARG68 3.1 29.8 1.0
CD A:ARG68 3.7 21.4 1.0
CZ A:ARG68 4.2 26.6 1.0
NE A:ARG68 4.4 27.9 1.0
CG A:ARG68 4.9 20.7 1.0
CB A:ARG68 4.9 18.8 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: Fri Jul 11 10:50:37 2025

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