Manganese in PDB 1sx5: K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Enzymatic activity of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
All present enzymatic activity of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form:
3.1.21.4;
Protein crystallography data
The structure of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form, PDB code: 1sx5
was solved by
N.C.Horton,
J.J.Perona,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.708,
48.627,
63.544,
96.68,
108.94,
107.33
|
R / Rfree (%)
|
21.4 /
25.4
|
Manganese Binding Sites:
The binding sites of Manganese atom in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
(pdb code 1sx5). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the
K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form, PDB code: 1sx5:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Manganese binding site 1 out
of 9 in 1sx5
Go back to
Manganese Binding Sites List in 1sx5
Manganese binding site 1 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:24.5
occ:1.00
|
O
|
A:HOH503
|
2.0
|
31.1
|
1.0
|
OP2
|
D:DA7
|
2.1
|
22.8
|
1.0
|
OD1
|
A:ASP74
|
2.1
|
17.4
|
1.0
|
OE1
|
A:GLU45
|
2.3
|
23.0
|
1.0
|
O
|
A:HOH530
|
2.7
|
33.3
|
1.0
|
CG
|
A:ASP74
|
3.1
|
17.6
|
1.0
|
OP1
|
D:DA7
|
3.2
|
28.1
|
1.0
|
O
|
B:HOH507
|
3.2
|
39.3
|
1.0
|
P
|
D:DA7
|
3.2
|
24.8
|
1.0
|
CD
|
A:GLU45
|
3.3
|
21.6
|
1.0
|
OE2
|
A:GLU45
|
3.6
|
25.1
|
1.0
|
OD2
|
A:ASP74
|
3.6
|
14.9
|
1.0
|
MN
|
A:MN402
|
3.6
|
23.5
|
1.0
|
O
|
A:HOH495
|
3.8
|
40.1
|
1.0
|
OD2
|
B:ASP36
|
4.1
|
33.4
|
1.0
|
CG
|
B:ASP36
|
4.2
|
33.7
|
1.0
|
OP3
|
D:DA7
|
4.2
|
25.3
|
1.0
|
CB
|
A:ASP74
|
4.2
|
16.9
|
1.0
|
O
|
B:HOH504
|
4.3
|
30.7
|
1.0
|
O5'
|
D:DA7
|
4.3
|
25.8
|
1.0
|
O
|
A:HOH526
|
4.3
|
27.0
|
1.0
|
O
|
A:HOH531
|
4.4
|
26.7
|
1.0
|
CB
|
B:ASP36
|
4.5
|
31.0
|
1.0
|
O
|
D:HOH238
|
4.5
|
22.2
|
1.0
|
OD1
|
B:ASP36
|
4.7
|
34.8
|
1.0
|
CG
|
A:GLU45
|
4.7
|
22.3
|
1.0
|
CA
|
A:ASP74
|
4.7
|
17.2
|
1.0
|
O
|
B:HOH477
|
4.7
|
11.9
|
1.0
|
O
|
D:HOH237
|
4.9
|
37.4
|
1.0
|
|
Manganese binding site 2 out
of 9 in 1sx5
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Manganese Binding Sites List in 1sx5
Manganese binding site 2 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:23.5
occ:1.00
|
O
|
D:HOH238
|
1.9
|
22.2
|
1.0
|
OE2
|
A:GLU45
|
1.9
|
25.1
|
1.0
|
O
|
D:HOH237
|
2.1
|
37.4
|
1.0
|
OP2
|
D:DA7
|
2.2
|
22.8
|
1.0
|
O
|
A:ILE91
|
2.3
|
14.4
|
1.0
|
OD2
|
A:ASP74
|
2.3
|
14.9
|
1.0
|
CD
|
A:GLU45
|
2.9
|
21.6
|
1.0
|
CG
|
A:ASP74
|
3.2
|
17.6
|
1.0
|
OD1
|
A:ASP74
|
3.4
|
17.4
|
1.0
|
OE1
|
A:GLU45
|
3.4
|
23.0
|
1.0
|
C
|
A:ILE91
|
3.4
|
14.1
|
1.0
|
P
|
D:DA7
|
3.4
|
24.8
|
1.0
|
MN
|
A:MN401
|
3.6
|
24.5
|
1.0
|
OP3
|
D:DA7
|
3.7
|
25.3
|
1.0
|
O5'
|
D:DA7
|
3.7
|
25.8
|
1.0
|
N
|
A:ILE91
|
3.7
|
13.8
|
1.0
|
CA
|
A:ILE91
|
3.9
|
13.8
|
1.0
|
O
|
D:HOH104
|
3.9
|
24.2
|
1.0
|
CB
|
A:ILE91
|
4.1
|
15.1
|
1.0
|
CG
|
A:GLU45
|
4.2
|
22.3
|
1.0
|
OD1
|
A:ASP90
|
4.2
|
18.3
|
1.0
|
O
|
A:HOH530
|
4.2
|
33.3
|
1.0
|
N
|
A:LYS92
|
4.5
|
13.2
|
1.0
|
CD
|
A:LYS92
|
4.6
|
22.5
|
1.0
|
CB
|
A:ASP74
|
4.6
|
16.9
|
1.0
|
OP1
|
D:DA7
|
4.7
|
28.1
|
1.0
|
CG
|
A:ASP90
|
4.7
|
20.1
|
1.0
|
NZ
|
A:LYS92
|
4.7
|
23.5
|
1.0
|
C
|
A:ASP90
|
4.8
|
15.7
|
1.0
|
CA
|
A:LYS92
|
4.9
|
15.3
|
1.0
|
OP1
|
D:DT8
|
4.9
|
31.6
|
1.0
|
O3'
|
D:DA7
|
4.9
|
30.0
|
1.0
|
CE
|
A:LYS92
|
4.9
|
19.2
|
1.0
|
|
Manganese binding site 3 out
of 9 in 1sx5
Go back to
Manganese Binding Sites List in 1sx5
Manganese binding site 3 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn403
b:39.1
occ:1.00
|
O
|
A:HOH574
|
2.0
|
22.2
|
1.0
|
O
|
A:HOH575
|
2.0
|
34.5
|
1.0
|
NE2
|
A:HIS193
|
2.1
|
23.4
|
1.0
|
O
|
A:HOH474
|
2.4
|
43.7
|
1.0
|
CE1
|
A:HIS193
|
2.8
|
24.1
|
1.0
|
CD2
|
A:HIS193
|
3.3
|
23.8
|
1.0
|
ND1
|
A:HIS193
|
4.0
|
25.6
|
1.0
|
O
|
A:LYS102
|
4.1
|
21.5
|
1.0
|
CG
|
A:HIS193
|
4.2
|
22.4
|
1.0
|
CB
|
A:LYS102
|
4.7
|
26.3
|
1.0
|
O
|
A:HOH450
|
4.7
|
39.2
|
1.0
|
C
|
A:LYS102
|
4.7
|
22.7
|
1.0
|
|
Manganese binding site 4 out
of 9 in 1sx5
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Manganese Binding Sites List in 1sx5
Manganese binding site 4 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn404
b:35.3
occ:1.00
|
O
|
A:HOH420
|
2.1
|
27.2
|
1.0
|
ND1
|
A:HIS195
|
2.3
|
25.6
|
1.0
|
OD2
|
A:ASP198
|
2.3
|
23.0
|
1.0
|
CE1
|
A:HIS195
|
3.2
|
25.9
|
1.0
|
CG
|
A:ASP198
|
3.2
|
21.4
|
1.0
|
CG
|
A:HIS195
|
3.3
|
24.2
|
1.0
|
OD1
|
A:ASP198
|
3.5
|
24.3
|
1.0
|
CB
|
A:HIS195
|
3.6
|
22.3
|
1.0
|
N
|
A:HIS195
|
4.1
|
18.1
|
1.0
|
NE2
|
A:HIS195
|
4.4
|
26.5
|
1.0
|
CD2
|
A:HIS195
|
4.4
|
25.8
|
1.0
|
CA
|
A:HIS195
|
4.5
|
19.2
|
1.0
|
CB
|
A:ASP198
|
4.6
|
19.0
|
1.0
|
CB
|
A:ALA194
|
4.9
|
18.1
|
1.0
|
|
Manganese binding site 5 out
of 9 in 1sx5
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Manganese Binding Sites List in 1sx5
Manganese binding site 5 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn409
b:32.9
occ:1.00
|
O
|
A:HOH410
|
2.1
|
27.1
|
1.0
|
NE2
|
A:HIS71
|
2.3
|
25.6
|
1.0
|
O
|
A:HOH411
|
2.3
|
30.6
|
1.0
|
OP1
|
F:DT11
|
2.4
|
36.9
|
1.0
|
CE1
|
A:HIS71
|
3.1
|
28.5
|
1.0
|
CD2
|
A:HIS71
|
3.3
|
25.0
|
1.0
|
P
|
F:DT11
|
3.9
|
36.0
|
1.0
|
OE1
|
A:GLN68
|
3.9
|
40.5
|
1.0
|
ND1
|
A:HIS71
|
4.3
|
24.8
|
1.0
|
N
|
A:ASN120
|
4.3
|
21.4
|
1.0
|
C5'
|
F:DT11
|
4.4
|
43.9
|
1.0
|
CG
|
A:HIS71
|
4.4
|
25.4
|
1.0
|
O5'
|
F:DT11
|
4.5
|
40.3
|
1.0
|
O
|
A:THR118
|
4.6
|
25.2
|
1.0
|
O3'
|
F:DT10
|
4.6
|
34.0
|
1.0
|
CA
|
A:ASN120
|
4.7
|
22.2
|
1.0
|
OP2
|
F:DT11
|
4.9
|
37.3
|
1.0
|
CD
|
A:GLN68
|
4.9
|
38.6
|
1.0
|
|
Manganese binding site 6 out
of 9 in 1sx5
Go back to
Manganese Binding Sites List in 1sx5
Manganese binding site 6 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn405
b:23.5
occ:1.00
|
O
|
B:ILE91
|
2.2
|
13.8
|
1.0
|
OP1
|
F:DA7
|
2.2
|
34.9
|
1.0
|
OP3
|
F:DA7
|
2.2
|
28.8
|
1.0
|
OD2
|
B:ASP74
|
2.3
|
16.9
|
1.0
|
OD2
|
B:ASP90
|
2.4
|
22.7
|
1.0
|
P
|
F:DA7
|
2.7
|
31.6
|
1.0
|
C
|
B:ILE91
|
3.2
|
16.0
|
1.0
|
CG
|
B:ASP74
|
3.2
|
16.7
|
1.0
|
CG
|
B:ASP90
|
3.3
|
18.8
|
1.0
|
N
|
B:ILE91
|
3.5
|
16.2
|
1.0
|
OD1
|
B:ASP74
|
3.5
|
17.1
|
1.0
|
O5'
|
F:DA7
|
3.5
|
34.0
|
1.0
|
OE2
|
B:GLU45
|
3.7
|
30.9
|
1.0
|
OD1
|
B:ASP90
|
3.7
|
17.3
|
1.0
|
CA
|
B:ILE91
|
3.8
|
15.2
|
1.0
|
MN
|
B:MN408
|
3.8
|
36.9
|
1.0
|
OP2
|
F:DA7
|
4.0
|
32.6
|
1.0
|
O
|
B:HOH558
|
4.0
|
13.5
|
1.0
|
CB
|
B:ILE91
|
4.1
|
18.2
|
1.0
|
O
|
B:HOH512
|
4.1
|
31.9
|
1.0
|
CD
|
B:LYS92
|
4.2
|
19.8
|
1.0
|
NZ
|
B:LYS92
|
4.2
|
22.0
|
1.0
|
C
|
B:ASP90
|
4.3
|
16.6
|
1.0
|
N
|
B:LYS92
|
4.4
|
16.0
|
1.0
|
O
|
B:HOH561
|
4.4
|
50.2
|
1.0
|
CE
|
B:LYS92
|
4.5
|
21.4
|
1.0
|
CB
|
B:ASP90
|
4.5
|
18.1
|
1.0
|
CB
|
B:ASP74
|
4.6
|
16.2
|
1.0
|
O
|
B:HOH445
|
4.7
|
25.9
|
1.0
|
O
|
B:HOH413
|
4.7
|
35.7
|
1.0
|
C5'
|
F:DA7
|
4.7
|
33.1
|
1.0
|
CA
|
B:ASP90
|
4.7
|
16.3
|
1.0
|
CA
|
B:LYS92
|
4.8
|
17.7
|
1.0
|
C3'
|
F:DA7
|
4.9
|
31.6
|
1.0
|
CD
|
B:GLU45
|
4.9
|
31.9
|
1.0
|
C4'
|
F:DA7
|
4.9
|
32.7
|
1.0
|
CG1
|
B:ILE91
|
4.9
|
21.9
|
1.0
|
|
Manganese binding site 7 out
of 9 in 1sx5
Go back to
Manganese Binding Sites List in 1sx5
Manganese binding site 7 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn406
b:24.7
occ:1.00
|
O
|
D:HOH37
|
1.9
|
40.6
|
1.0
|
O
|
D:HOH163
|
2.2
|
24.3
|
1.0
|
NE2
|
B:HIS71
|
2.2
|
22.3
|
1.0
|
OP1
|
D:DT11
|
2.2
|
26.2
|
1.0
|
O
|
B:HOH476
|
2.3
|
24.4
|
1.0
|
O
|
B:HOH423
|
2.5
|
24.7
|
1.0
|
CE1
|
B:HIS71
|
3.1
|
25.8
|
1.0
|
CD2
|
B:HIS71
|
3.2
|
22.1
|
1.0
|
P
|
D:DT11
|
3.7
|
26.2
|
1.0
|
C5'
|
D:DT11
|
4.0
|
30.9
|
1.0
|
ND1
|
B:HIS71
|
4.3
|
23.5
|
1.0
|
O5'
|
D:DT11
|
4.3
|
25.8
|
1.0
|
O3'
|
D:DT10
|
4.3
|
23.6
|
1.0
|
CG
|
B:HIS71
|
4.3
|
23.4
|
1.0
|
O
|
B:THR118
|
4.4
|
24.6
|
1.0
|
N
|
B:ASN120
|
4.4
|
19.5
|
1.0
|
OP2
|
D:DT11
|
4.7
|
25.8
|
1.0
|
CA
|
B:ASN120
|
4.8
|
19.7
|
1.0
|
O
|
B:ILE121
|
4.9
|
18.2
|
1.0
|
|
Manganese binding site 8 out
of 9 in 1sx5
Go back to
Manganese Binding Sites List in 1sx5
Manganese binding site 8 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn407
b:60.5
occ:1.00
|
ND1
|
B:HIS195
|
2.4
|
35.9
|
1.0
|
OD2
|
B:ASP198
|
2.4
|
32.7
|
1.0
|
CG
|
B:ASP198
|
3.3
|
30.2
|
1.0
|
CE1
|
B:HIS195
|
3.3
|
35.6
|
1.0
|
CG
|
B:HIS195
|
3.4
|
34.3
|
1.0
|
OD1
|
B:ASP198
|
3.4
|
32.3
|
1.0
|
CB
|
B:HIS195
|
3.7
|
31.7
|
1.0
|
N
|
B:HIS195
|
4.0
|
28.2
|
1.0
|
CA
|
B:HIS195
|
4.4
|
28.9
|
1.0
|
NE2
|
B:HIS195
|
4.4
|
35.7
|
1.0
|
CD2
|
B:HIS195
|
4.5
|
34.1
|
1.0
|
CB
|
B:ASP198
|
4.7
|
26.2
|
1.0
|
|
Manganese binding site 9 out
of 9 in 1sx5
Go back to
Manganese Binding Sites List in 1sx5
Manganese binding site 9 out
of 9 in the K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of K38A Ecorv Bound to Cleaved Dna and MN2+: P1 Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn408
b:36.9
occ:1.00
|
OE2
|
B:GLU45
|
2.0
|
30.9
|
1.0
|
OD1
|
B:ASP74
|
2.3
|
17.1
|
1.0
|
O
|
B:HOH559
|
2.4
|
34.1
|
1.0
|
O
|
B:HOH558
|
2.4
|
13.5
|
1.0
|
CD
|
B:GLU45
|
2.6
|
31.9
|
1.0
|
OE1
|
B:GLU45
|
2.8
|
35.9
|
1.0
|
CG
|
B:ASP74
|
3.2
|
16.7
|
1.0
|
OP1
|
F:DA7
|
3.2
|
34.9
|
1.0
|
OD2
|
B:ASP74
|
3.6
|
16.9
|
1.0
|
O5'
|
F:DA7
|
3.6
|
34.0
|
1.0
|
MN
|
B:MN405
|
3.8
|
23.5
|
1.0
|
CG
|
B:GLU45
|
3.9
|
29.0
|
1.0
|
P
|
F:DA7
|
4.1
|
31.6
|
1.0
|
CB
|
B:ASP74
|
4.4
|
16.2
|
1.0
|
O
|
B:HOH560
|
4.4
|
49.6
|
1.0
|
O
|
A:HOH412
|
4.6
|
34.7
|
1.0
|
OD2
|
A:ASP36
|
4.6
|
42.5
|
1.0
|
O
|
B:HOH491
|
4.6
|
28.8
|
1.0
|
C5'
|
F:DA7
|
4.9
|
33.1
|
1.0
|
CB
|
B:GLU45
|
4.9
|
21.4
|
1.0
|
OP3
|
F:DA7
|
4.9
|
28.8
|
1.0
|
CA
|
B:ASP74
|
5.0
|
15.3
|
1.0
|
|
Reference:
N.C.Horton,
J.J.Perona.
Dna Cleavage By Ecorv Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites Biochemistry V. 43 6841 2004.
ISSN: ISSN 0006-2960
PubMed: 15170321
DOI: 10.1021/BI0499056
Page generated: Sat Oct 5 12:27:38 2024
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