Chlorine in PDB 8tkb: Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Protein crystallography data
The structure of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp, PDB code: 8tkb
was solved by
A.Jacewicz,
S.Dantuluri,
S.Shuman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.14 /
1.71
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.937,
43.665,
122.861,
90,
90,
90
|
R / Rfree (%)
|
18.5 /
20.9
|
Other elements in 8tkb:
The structure of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
(pdb code 8tkb). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp, PDB code: 8tkb:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 1 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl207
b:36.7
occ:0.52
|
OE2
|
A:GLU27
|
2.7
|
41.4
|
1.0
|
N
|
A:ARG83
|
2.8
|
42.8
|
1.0
|
O
|
A:ILE81
|
2.8
|
35.9
|
1.0
|
NH1
|
A:ARG71
|
2.8
|
31.0
|
1.0
|
CD
|
A:GLU27
|
3.3
|
44.2
|
1.0
|
CG
|
A:GLU27
|
3.3
|
30.9
|
1.0
|
CA
|
A:LEU82
|
3.4
|
38.9
|
1.0
|
CB
|
A:GLU27
|
3.5
|
30.3
|
1.0
|
C
|
A:LEU82
|
3.6
|
35.4
|
1.0
|
O
|
A:HOH302
|
3.6
|
46.7
|
1.0
|
C
|
A:ILE81
|
3.7
|
38.2
|
1.0
|
CB
|
A:ARG83
|
3.7
|
45.8
|
1.0
|
CA
|
A:ARG83
|
3.7
|
47.4
|
1.0
|
CZ
|
A:ARG71
|
3.8
|
28.4
|
1.0
|
NH2
|
A:ARG71
|
3.8
|
29.2
|
1.0
|
N
|
A:LEU82
|
3.9
|
32.5
|
1.0
|
CG
|
A:ARG83
|
4.0
|
56.2
|
1.0
|
CL
|
A:CL208
|
4.1
|
48.5
|
0.6
|
CA
|
A:GLU27
|
4.3
|
30.4
|
1.0
|
OE1
|
A:GLU27
|
4.3
|
44.3
|
1.0
|
C
|
A:ARG83
|
4.5
|
41.8
|
1.0
|
NH1
|
A:ARG83
|
4.5
|
71.8
|
1.0
|
O
|
A:GLU27
|
4.6
|
29.6
|
1.0
|
CD
|
A:ARG83
|
4.6
|
48.0
|
1.0
|
CB
|
A:LEU82
|
4.7
|
41.3
|
1.0
|
O
|
A:LEU82
|
4.8
|
41.0
|
1.0
|
O
|
A:ARG83
|
4.8
|
50.0
|
1.0
|
CG2
|
A:ILE81
|
4.8
|
40.6
|
1.0
|
CD2
|
A:LEU82
|
4.9
|
32.8
|
1.0
|
C
|
A:GLU27
|
5.0
|
28.2
|
1.0
|
CA
|
A:ILE81
|
5.0
|
33.1
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 2 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl208
b:48.5
occ:0.60
|
O
|
A:HOH302
|
2.7
|
46.7
|
1.0
|
OE2
|
A:GLU27
|
2.7
|
41.4
|
1.0
|
NH1
|
A:ARG66
|
2.8
|
43.6
|
1.0
|
CD
|
A:GLU27
|
3.6
|
44.2
|
1.0
|
OE1
|
A:GLU27
|
3.7
|
44.3
|
1.0
|
NH2
|
A:ARG66
|
3.7
|
48.8
|
1.0
|
CZ
|
A:ARG66
|
3.7
|
54.5
|
1.0
|
CL
|
A:CL207
|
4.1
|
36.7
|
0.5
|
CB
|
A:ARG83
|
4.2
|
45.8
|
1.0
|
O
|
A:ARG83
|
4.4
|
50.0
|
1.0
|
NH1
|
A:ARG83
|
4.6
|
71.8
|
1.0
|
CD
|
A:ARG83
|
4.7
|
48.0
|
1.0
|
CG
|
A:GLU27
|
4.9
|
30.9
|
1.0
|
CG
|
A:ARG83
|
5.0
|
56.2
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 3 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl209
b:41.3
occ:0.78
|
O
|
A:HOH376
|
2.4
|
49.4
|
1.0
|
N
|
A:GLY96
|
3.1
|
22.9
|
1.0
|
CA
|
A:ALA127
|
3.8
|
25.5
|
1.0
|
CA
|
A:HIS95
|
3.8
|
23.4
|
1.0
|
CB
|
A:ALA127
|
3.8
|
24.9
|
1.0
|
C
|
A:HIS95
|
3.9
|
24.8
|
1.0
|
O
|
A:TYR94
|
4.0
|
24.4
|
1.0
|
CA
|
A:GLY96
|
4.0
|
24.6
|
1.0
|
O
|
A:HIS119
|
4.1
|
27.4
|
1.0
|
CB
|
A:THR130
|
4.1
|
37.9
|
1.0
|
CG2
|
A:THR130
|
4.1
|
42.5
|
1.0
|
O
|
A:GLY96
|
4.2
|
26.4
|
1.0
|
O
|
A:ALA127
|
4.3
|
23.7
|
1.0
|
ND1
|
A:HIS95
|
4.5
|
25.4
|
1.0
|
N
|
A:SER121
|
4.5
|
23.9
|
1.0
|
C
|
A:LEU120
|
4.5
|
27.6
|
1.0
|
C
|
A:ALA127
|
4.5
|
24.8
|
1.0
|
O
|
A:HOH374
|
4.5
|
43.1
|
1.0
|
CA
|
A:LEU120
|
4.6
|
20.7
|
1.0
|
OG1
|
A:THR130
|
4.6
|
41.4
|
1.0
|
CB
|
A:SER121
|
4.6
|
31.5
|
1.0
|
C
|
A:TYR94
|
4.6
|
26.9
|
1.0
|
N
|
A:HIS95
|
4.6
|
21.8
|
1.0
|
C
|
A:GLY96
|
4.6
|
27.7
|
1.0
|
C
|
A:HIS119
|
4.7
|
28.2
|
1.0
|
N
|
A:ALA127
|
4.8
|
23.6
|
1.0
|
CG
|
A:HIS95
|
4.9
|
23.1
|
1.0
|
CB
|
A:HIS95
|
4.9
|
23.1
|
1.0
|
N
|
A:LEU120
|
4.9
|
23.1
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 4 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl210
b:43.8
occ:0.76
|
N
|
A:ILE65
|
3.0
|
27.2
|
1.0
|
NH2
|
A:ARG73
|
3.5
|
23.3
|
0.5
|
O
|
A:ILE65
|
3.6
|
28.8
|
1.0
|
CA
|
A:GLU64
|
3.7
|
25.2
|
1.0
|
C
|
A:GLU64
|
3.8
|
25.4
|
1.0
|
CA
|
A:ILE65
|
4.0
|
23.6
|
1.0
|
CG1
|
A:VAL55
|
4.1
|
26.4
|
1.0
|
CG
|
A:GLU64
|
4.2
|
27.8
|
1.0
|
CB
|
A:ILE65
|
4.2
|
24.4
|
1.0
|
C
|
A:ILE65
|
4.2
|
26.3
|
1.0
|
O
|
A:TYR63
|
4.3
|
25.0
|
1.0
|
CB
|
A:GLU64
|
4.4
|
25.8
|
1.0
|
CZ
|
A:ARG73
|
4.7
|
30.8
|
0.5
|
N
|
A:GLU64
|
4.7
|
24.8
|
1.0
|
CG1
|
A:ILE65
|
4.9
|
25.3
|
1.0
|
C
|
A:TYR63
|
4.9
|
26.1
|
1.0
|
O
|
A:HOH305
|
5.0
|
48.8
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 5 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl211
b:28.3
occ:0.51
|
OG
|
A:SER16
|
2.7
|
28.4
|
1.0
|
N
|
A:GLU19
|
3.1
|
31.1
|
1.0
|
CA
|
A:SER16
|
3.2
|
23.6
|
1.0
|
C
|
A:SER16
|
3.3
|
24.6
|
1.0
|
N
|
A:TRP18
|
3.4
|
29.0
|
1.0
|
CB
|
A:SER16
|
3.5
|
25.6
|
1.0
|
CB
|
A:TRP18
|
3.6
|
30.0
|
1.0
|
CE3
|
A:TRP18
|
3.6
|
33.3
|
1.0
|
O
|
A:SER16
|
3.7
|
27.0
|
1.0
|
CB
|
A:GLU19
|
3.7
|
36.9
|
1.0
|
CA
|
A:TRP18
|
3.8
|
28.7
|
1.0
|
C
|
A:TRP18
|
3.8
|
32.7
|
1.0
|
N
|
A:PRO17
|
3.8
|
24.8
|
1.0
|
CA
|
A:GLU19
|
3.9
|
27.7
|
1.0
|
C
|
A:PRO17
|
4.2
|
30.4
|
1.0
|
CD2
|
A:TRP18
|
4.4
|
31.3
|
1.0
|
CG
|
A:TRP18
|
4.4
|
31.6
|
1.0
|
O
|
A:HIS15
|
4.5
|
26.5
|
1.0
|
CD
|
A:PRO17
|
4.5
|
27.0
|
1.0
|
N
|
A:SER16
|
4.6
|
24.1
|
1.0
|
CZ3
|
A:TRP18
|
4.6
|
28.4
|
1.0
|
CA
|
A:PRO17
|
4.7
|
23.0
|
1.0
|
OE1
|
A:GLU19
|
4.9
|
35.5
|
1.0
|
O
|
A:TRP18
|
4.9
|
32.6
|
1.0
|
C
|
A:HIS15
|
5.0
|
27.5
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 6 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl212
b:39.2
occ:0.69
|
O
|
A:HOH375
|
2.1
|
41.8
|
1.0
|
NE2
|
A:HIS119
|
2.8
|
33.1
|
1.0
|
N
|
A:GLY75
|
3.0
|
27.3
|
1.0
|
CE1
|
A:HIS119
|
3.6
|
36.0
|
1.0
|
CA
|
A:TYR74
|
3.6
|
26.4
|
1.0
|
CB
|
A:TYR74
|
3.7
|
29.8
|
1.0
|
CD2
|
A:HIS119
|
3.8
|
33.0
|
1.0
|
C
|
A:TYR74
|
3.8
|
24.3
|
1.0
|
CA
|
A:GLY75
|
3.9
|
30.7
|
1.0
|
CD1
|
A:LEU82
|
4.0
|
38.1
|
1.0
|
CD2
|
A:TYR117
|
4.5
|
41.3
|
1.0
|
N
|
A:HIS76
|
4.5
|
26.1
|
1.0
|
CG2
|
A:ILE164
|
4.6
|
30.4
|
1.0
|
C
|
A:GLY75
|
4.7
|
31.6
|
1.0
|
CB
|
A:TYR117
|
4.7
|
30.0
|
1.0
|
ND1
|
A:HIS119
|
4.8
|
33.5
|
1.0
|
ND1
|
A:HIS76
|
4.8
|
24.7
|
1.0
|
CG
|
A:TYR74
|
4.9
|
29.3
|
1.0
|
CG
|
A:HIS119
|
4.9
|
26.3
|
1.0
|
CG
|
A:TYR117
|
4.9
|
35.0
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 8tkb
Go back to
Chlorine Binding Sites List in 8tkb
Chlorine binding site 7 out
of 7 in the Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl213
b:67.3
occ:1.00
|
NA
|
A:NA214
|
2.6
|
39.0
|
0.9
|
O4'
|
A:AMP202
|
3.4
|
41.1
|
0.8
|
NH1
|
A:ARG133
|
3.5
|
40.3
|
1.0
|
CD
|
A:ARG133
|
3.6
|
41.3
|
1.0
|
CG2
|
A:THR130
|
3.9
|
42.5
|
1.0
|
N3
|
A:AMP202
|
4.1
|
38.1
|
0.8
|
C1'
|
A:AMP202
|
4.1
|
44.0
|
0.8
|
O2P
|
A:AMP201
|
4.2
|
32.9
|
1.0
|
CZ
|
A:ARG133
|
4.4
|
51.6
|
1.0
|
NE2
|
A:HIS134
|
4.5
|
32.3
|
1.0
|
C4'
|
A:AMP202
|
4.5
|
44.9
|
0.8
|
NE
|
A:ARG133
|
4.5
|
39.6
|
1.0
|
C4
|
A:AMP202
|
4.5
|
35.8
|
0.8
|
CB
|
A:ARG133
|
4.6
|
32.3
|
1.0
|
N9
|
A:AMP202
|
4.6
|
44.6
|
0.8
|
O
|
A:THR130
|
4.6
|
28.0
|
1.0
|
CG
|
A:ARG133
|
4.7
|
36.5
|
1.0
|
C2
|
A:AMP202
|
4.8
|
38.5
|
0.8
|
C5'
|
A:AMP202
|
4.9
|
34.3
|
0.8
|
NH2
|
A:ARG115
|
4.9
|
42.2
|
1.0
|
CD2
|
A:HIS134
|
5.0
|
30.3
|
1.0
|
|
Reference:
A.Jacewicz,
S.Dantuluri,
S.Shuman.
Trna 2-Phosphotransferase (TPT1) From Pyrococcus Horikoshii in Complex with 5'-Amp To Be Published.
Page generated: Tue Jul 30 12:51:12 2024
|