Chlorine in PDB 5a0w: The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
Protein crystallography data
The structure of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn, PDB code: 5a0w
was solved by
R.Molina,
N.Besker,
J.Prieto,
G.Montoya,
M.D'abramo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.220 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.928,
69.770,
106.985,
90.00,
120.06,
90.00
|
R / Rfree (%)
|
17.06 /
20.79
|
Other elements in 5a0w:
The structure of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
(pdb code 5a0w). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn, PDB code: 5a0w:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 1 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1187
b:78.4
occ:1.00
|
N
|
A:LYS66
|
3.2
|
42.9
|
1.0
|
O
|
A:HOH2042
|
3.3
|
41.5
|
1.0
|
CA
|
A:VAL65
|
3.7
|
34.8
|
1.0
|
C
|
A:VAL65
|
4.0
|
41.3
|
1.0
|
CB
|
A:LYS66
|
4.0
|
75.5
|
1.0
|
CG1
|
A:VAL65
|
4.0
|
30.3
|
1.0
|
CA
|
A:LYS66
|
4.2
|
57.8
|
1.0
|
CB
|
A:LYS86
|
4.3
|
22.4
|
1.0
|
O
|
A:ASN64
|
4.3
|
42.4
|
1.0
|
CB
|
A:VAL65
|
4.3
|
32.8
|
1.0
|
OG
|
A:SER84
|
4.4
|
22.4
|
1.0
|
CD
|
A:LYS86
|
4.4
|
26.4
|
1.0
|
OP1
|
C:DC5
|
4.5
|
32.1
|
1.0
|
CG2
|
A:VAL65
|
4.6
|
27.9
|
1.0
|
N
|
A:SER67
|
4.8
|
39.8
|
1.0
|
CD
|
A:LYS66
|
4.8
|
94.7
|
1.0
|
N
|
A:VAL65
|
4.9
|
38.8
|
1.0
|
CG
|
A:LYS86
|
4.9
|
23.3
|
1.0
|
OG
|
A:SER67
|
5.0
|
32.8
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 2 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1300
b:86.9
occ:1.00
|
O
|
A:HOH2009
|
2.8
|
47.1
|
1.0
|
N
|
A:LEU24
|
3.9
|
23.5
|
1.0
|
CB
|
A:LEU24
|
4.1
|
22.3
|
1.0
|
O
|
A:HOH2021
|
4.2
|
50.8
|
1.0
|
CG
|
A:LEU24
|
4.3
|
26.5
|
1.0
|
CD1
|
A:LEU24
|
4.3
|
29.0
|
1.0
|
O
|
A:LEU24
|
4.5
|
23.3
|
1.0
|
CD2
|
A:LEU95
|
4.5
|
30.7
|
1.0
|
CA
|
A:LEU24
|
4.6
|
24.2
|
1.0
|
CD1
|
A:ILE19
|
4.6
|
31.8
|
1.0
|
CA
|
A:GLY23
|
4.8
|
20.6
|
1.0
|
C
|
A:GLY23
|
4.8
|
23.9
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 3 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl1196
b:72.3
occ:1.00
|
O
|
D:HOH2073
|
2.7
|
38.0
|
1.0
|
CD1
|
D:TYR114
|
3.5
|
27.1
|
1.0
|
CE1
|
D:TYR114
|
4.0
|
28.2
|
1.0
|
CG2
|
D:VAL115
|
4.1
|
35.8
|
1.0
|
CB
|
D:PRO186
|
4.2
|
46.4
|
1.0
|
CA
|
D:VAL115
|
4.4
|
30.0
|
1.0
|
OE1
|
D:GLU188
|
4.4
|
57.2
|
1.0
|
N
|
D:VAL115
|
4.5
|
28.1
|
1.0
|
CB
|
D:GLU188
|
4.5
|
52.2
|
0.9
|
CG
|
D:TYR114
|
4.6
|
28.1
|
1.0
|
CD
|
D:GLU188
|
4.7
|
59.2
|
0.5
|
CD2
|
D:LEU122
|
4.7
|
35.2
|
1.0
|
C
|
D:TYR114
|
4.8
|
29.4
|
1.0
|
CG
|
D:GLU188
|
4.8
|
55.7
|
0.8
|
CD1
|
D:LEU178
|
4.8
|
39.3
|
1.0
|
O
|
D:TYR114
|
4.8
|
28.6
|
1.0
|
CB
|
D:VAL115
|
4.8
|
36.4
|
1.0
|
CB
|
D:TYR114
|
4.9
|
26.2
|
1.0
|
CD2
|
D:LEU178
|
5.0
|
33.8
|
1.0
|
CG
|
D:PRO186
|
5.0
|
48.4
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 4 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl1026
b:78.2
occ:1.00
|
N3
|
F:DG4
|
3.2
|
29.5
|
1.0
|
O4'
|
F:DC5
|
3.5
|
26.7
|
1.0
|
N2
|
F:DG4
|
3.8
|
23.5
|
1.0
|
N2
|
E:DG23
|
3.9
|
38.8
|
1.0
|
C1'
|
F:DG4
|
3.9
|
29.9
|
1.0
|
C2
|
F:DG4
|
3.9
|
27.6
|
1.0
|
O5'
|
F:DC5
|
4.0
|
39.2
|
1.0
|
C4
|
F:DG4
|
4.2
|
26.5
|
1.0
|
N3
|
E:DG23
|
4.3
|
34.6
|
1.0
|
O4'
|
F:DG4
|
4.4
|
28.8
|
1.0
|
C4'
|
F:DC5
|
4.4
|
36.8
|
1.0
|
O3'
|
F:DG4
|
4.4
|
28.2
|
1.0
|
C2
|
E:DG23
|
4.4
|
30.8
|
1.0
|
O
|
E:HOH2018
|
4.5
|
48.2
|
1.0
|
N9
|
F:DG4
|
4.5
|
29.6
|
1.0
|
C1'
|
F:DC5
|
4.6
|
24.1
|
1.0
|
N1
|
F:DC5
|
4.8
|
34.0
|
1.0
|
C5'
|
F:DC5
|
4.8
|
38.3
|
1.0
|
C4'
|
F:DG4
|
4.9
|
29.4
|
1.0
|
C2'
|
F:DG4
|
4.9
|
31.1
|
1.0
|
C6
|
F:DC5
|
5.0
|
31.4
|
1.0
|
P
|
F:DC5
|
5.0
|
26.3
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 5 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1300
b:90.5
occ:1.00
|
N
|
G:LEU24
|
4.2
|
24.6
|
1.0
|
CD2
|
G:LEU95
|
4.4
|
29.3
|
1.0
|
CB
|
G:LEU24
|
4.4
|
25.6
|
1.0
|
CD1
|
G:ILE19
|
4.4
|
38.1
|
1.0
|
CG
|
G:LEU24
|
4.5
|
23.6
|
1.0
|
CD1
|
G:LEU24
|
4.6
|
27.9
|
1.0
|
O
|
G:LEU24
|
4.7
|
24.7
|
1.0
|
O
|
G:HOH2004
|
4.7
|
52.6
|
1.0
|
CA
|
G:GLY23
|
4.8
|
23.0
|
1.0
|
CA
|
G:LEU24
|
4.9
|
25.9
|
1.0
|
C
|
G:GLY23
|
4.9
|
20.1
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 6 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1301
b:90.0
occ:1.00
|
O
|
G:HOH2029
|
3.5
|
50.6
|
1.0
|
CG
|
G:ASP61
|
4.2
|
45.1
|
1.0
|
OD1
|
G:ASP61
|
4.2
|
49.2
|
1.0
|
O
|
G:HOH2030
|
4.2
|
59.6
|
1.0
|
CB
|
G:ASP61
|
4.5
|
33.9
|
1.0
|
OD2
|
G:ASP61
|
4.5
|
45.0
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 5a0w
Go back to
Chlorine Binding Sites List in 5a0w
Chlorine binding site 7 out
of 7 in the The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of The Crystal Structure of I-Dmoi E117A in Complex with Its Target Dna and in the Presence of 2MM Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl1026
b:86.4
occ:1.00
|
N3
|
H:DG6
|
3.5
|
45.3
|
1.0
|
O4'
|
H:DG6
|
3.8
|
38.4
|
1.0
|
C1'
|
H:DG6
|
3.8
|
40.9
|
1.0
|
C5'
|
H:DC7
|
4.1
|
42.7
|
1.0
|
O4'
|
H:DC7
|
4.2
|
47.2
|
1.0
|
C4
|
H:DG6
|
4.3
|
38.6
|
1.0
|
C2
|
H:DG6
|
4.3
|
44.4
|
1.0
|
N2
|
H:DG6
|
4.3
|
38.4
|
1.0
|
C4'
|
H:DC7
|
4.4
|
47.4
|
1.0
|
N9
|
H:DG6
|
4.4
|
44.7
|
1.0
|
C4'
|
H:DG6
|
4.7
|
33.3
|
1.0
|
O3'
|
H:DG6
|
4.7
|
43.3
|
1.0
|
|
Reference:
R.Molina,
N.Besker,
J.Prieto,
G.Montoya,
M.D'abramo.
Structural and Dynamical Characterization of the I- Dmo Catalytic Activity To Be Published.
Page generated: Fri Jul 26 04:54:09 2024
|