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:
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
Go back to
Chlorine Binding Sites List in 3tmv
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
Go back to
Chlorine Binding Sites List in 3tmv
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
Go back to
Chlorine Binding Sites List in 3tmv
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
Go back to
Chlorine Binding Sites List in 3tmv
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 Sites List in 3tmv
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
Go back to
Chlorine Binding Sites List in 3tmv
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
Go back to
Chlorine Binding Sites List in 3tmv
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
Go back to
Chlorine Binding Sites List in 3tmv
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: Sun Jul 21 05:22:53 2024
|