Iodine in PDB 8syj: Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
Protein crystallography data
The structure of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form), PDB code: 8syj
was solved by
B.E.Eckenroth,
A.F.Gardner,
S.Doublie,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.49 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.554,
89.116,
128.043,
90,
90,
90
|
R / Rfree (%)
|
22.5 /
26
|
Iodine Binding Sites:
Iodine binding site 1 out
of 51 in 8syj
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Iodine Binding Sites List in 8syj
Iodine binding site 1 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I201
b:41.4
occ:0.50
|
I
|
A:IOD201
|
0.0
|
41.4
|
0.5
|
I
|
A:IOD201
|
2.2
|
43.0
|
0.5
|
OG1
|
A:THR104
|
3.3
|
44.7
|
1.0
|
N
|
A:ILE101
|
3.5
|
31.8
|
1.0
|
CG2
|
A:THR104
|
3.7
|
39.1
|
1.0
|
CG1
|
A:ILE101
|
3.8
|
31.3
|
1.0
|
N
|
A:THR104
|
4.1
|
35.1
|
1.0
|
O
|
A:ILE101
|
4.1
|
31.9
|
1.0
|
CA
|
A:VAL100
|
4.1
|
32.2
|
1.0
|
CB
|
A:THR104
|
4.1
|
35.8
|
1.0
|
CB
|
A:PHE103
|
4.2
|
45.0
|
1.0
|
CE
|
A:MET32
|
4.2
|
43.1
|
1.0
|
C
|
A:VAL100
|
4.3
|
32.1
|
1.0
|
CA
|
A:ILE101
|
4.3
|
30.0
|
1.0
|
C
|
A:ILE101
|
4.4
|
37.5
|
1.0
|
CB
|
A:VAL100
|
4.6
|
37.2
|
1.0
|
CB
|
A:ILE101
|
4.6
|
34.9
|
1.0
|
O
|
A:CYS99
|
4.7
|
34.2
|
1.0
|
CA
|
A:THR104
|
4.7
|
43.5
|
1.0
|
C
|
A:PHE103
|
4.8
|
43.7
|
1.0
|
CD1
|
A:ILE101
|
4.8
|
32.8
|
1.0
|
N
|
A:PHE103
|
4.8
|
32.6
|
1.0
|
CA
|
A:PHE103
|
4.8
|
41.1
|
1.0
|
|
Iodine binding site 2 out
of 51 in 8syj
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Iodine Binding Sites List in 8syj
Iodine binding site 2 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I201
b:43.0
occ:0.50
|
I
|
A:IOD201
|
0.0
|
43.0
|
0.5
|
I
|
A:IOD201
|
2.2
|
41.4
|
0.5
|
CE
|
A:MET32
|
3.6
|
43.1
|
1.0
|
CB
|
A:PHE103
|
4.3
|
45.0
|
1.0
|
CB
|
A:ALA21
|
4.4
|
36.0
|
1.0
|
CG1
|
A:ILE101
|
4.4
|
31.3
|
1.0
|
CB
|
A:MET32
|
4.5
|
37.8
|
1.0
|
CD2
|
A:PHE103
|
4.5
|
45.5
|
1.0
|
SD
|
A:MET23
|
4.5
|
59.6
|
1.0
|
CE
|
A:MET23
|
4.8
|
54.4
|
1.0
|
CD1
|
A:ILE101
|
4.8
|
32.8
|
1.0
|
SD
|
A:MET32
|
4.8
|
49.6
|
1.0
|
CG
|
A:PHE103
|
4.8
|
42.8
|
1.0
|
CG
|
A:MET32
|
4.8
|
46.0
|
1.0
|
CG2
|
A:THR104
|
4.9
|
39.1
|
1.0
|
|
Iodine binding site 3 out
of 51 in 8syj
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Iodine Binding Sites List in 8syj
Iodine binding site 3 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I202
b:52.2
occ:1.00
|
N
|
A:PRO16
|
3.7
|
39.5
|
1.0
|
C
|
A:LYS15
|
3.8
|
46.9
|
1.0
|
CA
|
A:LYS15
|
3.9
|
45.6
|
1.0
|
CD
|
A:PRO16
|
3.9
|
39.4
|
1.0
|
OG
|
A:SER3
|
4.0
|
59.2
|
1.0
|
N
|
A:LYS15
|
4.2
|
44.3
|
1.0
|
O
|
A:ASP14
|
4.2
|
48.6
|
1.0
|
C
|
A:ASP14
|
4.2
|
47.4
|
1.0
|
O
|
A:LYS15
|
4.2
|
43.9
|
1.0
|
CB
|
A:ASP14
|
4.3
|
47.8
|
1.0
|
CA
|
A:PRO16
|
4.3
|
43.3
|
1.0
|
CG
|
A:PRO16
|
4.6
|
42.9
|
1.0
|
CB
|
A:SER3
|
4.9
|
48.4
|
1.0
|
CA
|
A:ASP14
|
4.9
|
45.2
|
1.0
|
|
Iodine binding site 4 out
of 51 in 8syj
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Iodine Binding Sites List in 8syj
Iodine binding site 4 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I203
b:60.6
occ:1.00
|
OG
|
A:SER7
|
3.4
|
59.5
|
1.0
|
O
|
A:GLY10
|
3.6
|
58.5
|
1.0
|
C
|
A:GLY10
|
3.9
|
54.5
|
1.0
|
O
|
A:LYS5
|
3.9
|
54.2
|
1.0
|
O
|
A:HOH318
|
4.0
|
43.7
|
1.0
|
CD1
|
A:ILE12
|
4.0
|
43.6
|
1.0
|
N
|
A:SER7
|
4.1
|
61.5
|
1.0
|
CB
|
A:SER7
|
4.1
|
63.6
|
1.0
|
CG1
|
A:ILE12
|
4.1
|
46.6
|
1.0
|
CG
|
A:LYS5
|
4.2
|
63.7
|
1.0
|
CE
|
A:LYS5
|
4.3
|
66.4
|
1.0
|
N
|
A:TYR11
|
4.3
|
50.2
|
1.0
|
CD
|
A:LYS5
|
4.3
|
62.6
|
1.0
|
N
|
A:GLY10
|
4.4
|
57.9
|
1.0
|
C
|
A:LYS5
|
4.4
|
54.5
|
1.0
|
C
|
A:LYS6
|
4.4
|
60.5
|
1.0
|
CA
|
A:TYR11
|
4.5
|
50.9
|
1.0
|
C
|
A:TYR11
|
4.6
|
46.9
|
1.0
|
CA
|
A:GLY10
|
4.6
|
55.2
|
1.0
|
CA
|
A:LYS6
|
4.6
|
63.3
|
1.0
|
N
|
A:LYS6
|
4.6
|
60.2
|
1.0
|
CA
|
A:SER7
|
4.7
|
65.2
|
1.0
|
N
|
A:ILE12
|
4.7
|
42.2
|
1.0
|
CB
|
A:LYS5
|
4.9
|
51.4
|
1.0
|
CB
|
A:ILE12
|
4.9
|
47.7
|
1.0
|
CB
|
A:SER9
|
5.0
|
71.8
|
1.0
|
NZ
|
A:LYS5
|
5.0
|
62.2
|
1.0
|
O
|
A:TYR11
|
5.0
|
45.1
|
1.0
|
|
Iodine binding site 5 out
of 51 in 8syj
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Iodine Binding Sites List in 8syj
Iodine binding site 5 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I204
b:68.9
occ:0.50
|
C
|
A:SER7
|
3.8
|
65.2
|
1.0
|
CA
|
A:SER7
|
3.9
|
65.2
|
1.0
|
N
|
A:LYS8
|
4.0
|
56.5
|
1.0
|
CG
|
A:LYS6
|
4.1
|
60.3
|
1.0
|
O
|
A:SER7
|
4.2
|
66.2
|
1.0
|
N
|
A:SER7
|
4.3
|
61.5
|
1.0
|
C
|
A:LYS6
|
4.5
|
60.5
|
1.0
|
CD
|
A:LYS6
|
4.5
|
64.6
|
1.0
|
O
|
A:LYS6
|
4.6
|
68.8
|
1.0
|
CE
|
A:LYS6
|
4.6
|
72.1
|
1.0
|
CA
|
A:LYS8
|
4.7
|
61.9
|
1.0
|
|
Iodine binding site 6 out
of 51 in 8syj
Go back to
Iodine Binding Sites List in 8syj
Iodine binding site 6 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I205
b:98.7
occ:1.00
|
CG
|
A:LYS67
|
3.7
|
57.4
|
1.0
|
CD
|
A:LYS70
|
3.8
|
54.3
|
1.0
|
CG
|
A:PRO62
|
3.9
|
53.3
|
1.0
|
CD
|
A:PRO62
|
4.2
|
57.5
|
1.0
|
CB
|
A:LYS67
|
4.2
|
51.2
|
1.0
|
CE
|
A:LYS70
|
4.2
|
61.1
|
1.0
|
CA
|
A:LYS67
|
4.2
|
52.4
|
1.0
|
CD
|
A:LYS67
|
4.4
|
65.0
|
1.0
|
CE
|
A:LYS67
|
4.5
|
72.8
|
1.0
|
CB
|
A:PRO62
|
4.9
|
51.3
|
1.0
|
CB
|
A:LYS70
|
4.9
|
55.5
|
1.0
|
CG
|
A:LYS70
|
5.0
|
49.0
|
1.0
|
|
Iodine binding site 7 out
of 51 in 8syj
Go back to
Iodine Binding Sites List in 8syj
Iodine binding site 7 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I206
b:65.7
occ:1.00
|
O
|
A:HOH324
|
3.2
|
27.9
|
1.0
|
N
|
A:GLY89
|
3.8
|
40.0
|
1.0
|
CA
|
A:GLY89
|
4.0
|
43.4
|
1.0
|
CD2
|
A:LEU162
|
4.1
|
48.5
|
1.0
|
CD1
|
A:LEU162
|
4.1
|
53.6
|
1.0
|
NE
|
A:ARG158
|
4.3
|
88.0
|
1.0
|
CG
|
A:ARG158
|
4.3
|
66.5
|
1.0
|
CD
|
A:ARG158
|
4.3
|
69.6
|
1.0
|
CB
|
A:LYS88
|
4.4
|
49.7
|
1.0
|
CG
|
A:LYS88
|
4.4
|
55.9
|
1.0
|
CG
|
A:LEU162
|
4.5
|
54.3
|
1.0
|
C
|
A:LYS88
|
4.5
|
40.9
|
1.0
|
CD
|
A:LYS88
|
4.8
|
61.2
|
1.0
|
CA
|
A:LYS88
|
5.0
|
46.5
|
1.0
|
CZ
|
A:ARG158
|
5.0
|
93.1
|
1.0
|
|
Iodine binding site 8 out
of 51 in 8syj
Go back to
Iodine Binding Sites List in 8syj
Iodine binding site 8 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I207
b:87.1
occ:1.00
|
CG
|
A:GLU159
|
3.8
|
92.5
|
1.0
|
CD1
|
A:LEU162
|
4.0
|
53.6
|
1.0
|
CA
|
A:GLU159
|
4.1
|
65.1
|
1.0
|
CB
|
B:PRO154
|
4.2
|
65.1
|
1.0
|
CB
|
A:GLU159
|
4.3
|
76.9
|
1.0
|
N
|
A:GLU159
|
4.4
|
63.9
|
1.0
|
CD
|
A:GLU159
|
4.5
|
86.9
|
1.0
|
CA
|
B:PRO154
|
4.6
|
58.2
|
1.0
|
CG
|
A:ARG158
|
4.6
|
66.5
|
1.0
|
OE2
|
A:GLU159
|
4.8
|
93.2
|
1.0
|
CD
|
A:ARG158
|
4.9
|
69.6
|
1.0
|
C
|
A:ARG158
|
4.9
|
61.4
|
1.0
|
|
Iodine binding site 9 out
of 51 in 8syj
Go back to
Iodine Binding Sites List in 8syj
Iodine binding site 9 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I208
b:67.9
occ:0.50
|
I
|
A:IOD208
|
0.0
|
67.9
|
0.5
|
I
|
A:IOD208
|
2.0
|
57.4
|
0.5
|
CE1
|
A:PHE136
|
3.9
|
42.9
|
1.0
|
NZ
|
A:LYS148
|
4.4
|
58.2
|
1.0
|
CE
|
A:LYS148
|
4.4
|
58.6
|
1.0
|
CD
|
A:LYS148
|
4.4
|
56.8
|
1.0
|
CG1
|
A:VAL144
|
4.6
|
44.3
|
1.0
|
CD1
|
A:PHE136
|
4.6
|
42.0
|
1.0
|
CZ
|
A:PHE136
|
4.8
|
49.8
|
1.0
|
|
Iodine binding site 10 out
of 51 in 8syj
Go back to
Iodine Binding Sites List in 8syj
Iodine binding site 10 out
of 51 in the Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form)
 Mono view
 Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Structure of Apurinic/Apyrimidinic Dna Lyase TK0353 From Thermococcus Kodakarensis (Iodide Crystal Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I208
b:57.4
occ:0.50
|
I
|
A:IOD208
|
0.0
|
57.4
|
0.5
|
I
|
A:IOD208
|
2.0
|
67.9
|
0.5
|
CE1
|
A:PHE136
|
4.2
|
42.9
|
1.0
|
CG1
|
A:VAL144
|
4.3
|
44.3
|
1.0
|
CZ
|
A:PHE136
|
4.6
|
49.8
|
1.0
|
|
Reference:
P.J.Caffrey,
B.E.Eckenroth,
B.W.Burkhart,
K.M.Zatopek,
C.M.Mcclung,
T.J.Santangelo,
S.Doublie,
A.F.Gardner.
Thermococcus Kodakarensis TK0353 Is A Novel Ap Lyase with A New Fold. J.Biol.Chem. 05503 2023.
ISSN: ESSN 1083-351X
PubMed: 38013090
DOI: 10.1016/J.JBC.2023.105503
Page generated: Mon Aug 12 03:05:01 2024
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