Nickel in PDB 8rly: E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Enzymatic activity of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
All present enzymatic activity of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+:
3.1.21.2;
Protein crystallography data
The structure of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+, PDB code: 8rly
was solved by
M.A.Saper,
N.G.Paterson,
S.Kirillov,
A.Rouvinski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
97.12 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.78,
115.98,
177.7,
90,
90,
90
|
R / Rfree (%)
|
15.7 /
20.7
|
Other elements in 8rly:
The structure of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
(pdb code 8rly). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 7 binding sites of Nickel where determined in the
E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+, PDB code: 8rly:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
Nickel binding site 1 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 1 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni306
b:26.0
occ:1.00
|
O
|
A:HOH576
|
2.1
|
21.1
|
1.0
|
NE2
|
A:HIS60
|
2.1
|
24.2
|
1.0
|
CD2
|
A:HIS60
|
3.1
|
24.8
|
1.0
|
CE1
|
A:HIS60
|
3.2
|
24.5
|
1.0
|
HD2
|
A:HIS60
|
3.2
|
29.7
|
1.0
|
HE1
|
A:HIS60
|
3.4
|
29.5
|
1.0
|
O
|
A:LYS58
|
4.2
|
21.9
|
1.0
|
O
|
A:HOH484
|
4.2
|
21.2
|
1.0
|
CG
|
A:HIS60
|
4.2
|
23.7
|
1.0
|
ND1
|
A:HIS60
|
4.2
|
21.4
|
1.0
|
HA
|
A:TYR59
|
4.4
|
23.9
|
1.0
|
O
|
A:HOH581
|
4.4
|
14.8
|
0.4
|
O
|
A:HOH672
|
4.7
|
34.7
|
1.0
|
HD1
|
A:TYR59
|
4.8
|
29.5
|
1.0
|
|
Nickel binding site 2 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 2 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni305
b:47.0
occ:1.00
|
HE2
|
B:HIS60
|
1.5
|
45.0
|
1.0
|
O
|
B:HOH489
|
2.1
|
24.4
|
1.0
|
O
|
B:HOH487
|
2.1
|
33.3
|
1.0
|
O
|
B:HOH421
|
2.2
|
28.4
|
1.0
|
NE2
|
B:HIS60
|
2.3
|
37.5
|
1.0
|
OE1
|
E:GLU120
|
2.3
|
38.1
|
1.0
|
HE1
|
B:HIS60
|
2.9
|
38.7
|
1.0
|
CE1
|
B:HIS60
|
2.9
|
32.2
|
1.0
|
CD
|
E:GLU120
|
3.3
|
40.9
|
1.0
|
CD2
|
B:HIS60
|
3.5
|
28.6
|
1.0
|
OE2
|
E:GLU120
|
3.6
|
39.5
|
1.0
|
HD2
|
B:HIS60
|
3.9
|
34.4
|
1.0
|
O
|
B:LYS58
|
3.9
|
21.4
|
1.0
|
ND1
|
B:HIS60
|
4.2
|
31.7
|
1.0
|
HB3
|
E:GLU120
|
4.4
|
36.3
|
1.0
|
CG
|
B:HIS60
|
4.5
|
27.5
|
1.0
|
CG
|
E:GLU120
|
4.6
|
32.6
|
1.0
|
HB2
|
E:GLU120
|
4.8
|
36.3
|
1.0
|
CB
|
E:GLU120
|
4.9
|
30.2
|
1.0
|
HG
|
E:SER118
|
4.9
|
35.0
|
1.0
|
|
Nickel binding site 3 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 3 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni306
b:22.6
occ:1.00
|
NE2
|
B:HIS241
|
2.1
|
19.4
|
1.0
|
O
|
B:HOH501
|
2.1
|
17.8
|
1.0
|
O
|
B:HOH574
|
2.2
|
19.9
|
1.0
|
CE1
|
B:HIS241
|
2.9
|
24.2
|
1.0
|
HE1
|
B:HIS241
|
3.0
|
29.1
|
1.0
|
CD2
|
B:HIS241
|
3.2
|
21.9
|
1.0
|
HD2
|
B:HIS241
|
3.4
|
26.4
|
1.0
|
HA3
|
B:GLY235
|
3.8
|
26.8
|
1.0
|
ND1
|
B:HIS241
|
4.1
|
22.8
|
1.0
|
OE2
|
B:GLU236
|
4.2
|
25.8
|
1.0
|
CG
|
B:HIS241
|
4.2
|
21.4
|
1.0
|
O
|
B:HOH468
|
4.4
|
20.4
|
1.0
|
O
|
B:LEU234
|
4.5
|
17.9
|
1.0
|
CA
|
B:GLY235
|
4.8
|
22.3
|
1.0
|
HD1
|
B:HIS241
|
4.8
|
27.3
|
1.0
|
|
Nickel binding site 4 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 4 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni305
b:59.7
occ:1.00
|
NE2
|
C:HIS60
|
2.3
|
31.4
|
1.0
|
O
|
C:HOH473
|
2.6
|
30.1
|
1.0
|
CD2
|
C:HIS60
|
3.2
|
27.6
|
1.0
|
CE1
|
C:HIS60
|
3.3
|
27.0
|
1.0
|
HD2
|
C:HIS60
|
3.4
|
33.1
|
1.0
|
HE1
|
C:HIS60
|
3.5
|
32.5
|
1.0
|
ND1
|
C:HIS60
|
4.4
|
35.6
|
1.0
|
O
|
C:LYS58
|
4.4
|
22.6
|
1.0
|
CG
|
C:HIS60
|
4.4
|
28.1
|
1.0
|
O
|
C:GLU57
|
4.5
|
20.4
|
1.0
|
HA
|
C:LYS58
|
4.6
|
26.1
|
1.0
|
|
Nickel binding site 5 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 5 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni306
b:23.4
occ:1.00
|
O
|
C:HOH494
|
2.1
|
24.3
|
1.0
|
NE2
|
C:HIS241
|
2.1
|
17.6
|
1.0
|
O
|
C:HOH580
|
2.4
|
29.8
|
1.0
|
CE1
|
C:HIS241
|
2.9
|
29.2
|
1.0
|
HE1
|
C:HIS241
|
3.0
|
35.1
|
1.0
|
CD2
|
C:HIS241
|
3.2
|
19.9
|
1.0
|
HD2
|
C:HIS241
|
3.4
|
24.0
|
1.0
|
HA3
|
C:GLY235
|
3.9
|
21.7
|
1.0
|
ND1
|
C:HIS241
|
4.1
|
30.9
|
1.0
|
OE2
|
C:GLU236
|
4.1
|
31.7
|
1.0
|
CG
|
C:HIS241
|
4.2
|
22.0
|
1.0
|
O
|
C:LEU234
|
4.4
|
16.2
|
1.0
|
O
|
C:HOH460
|
4.5
|
16.6
|
1.0
|
CA
|
C:GLY235
|
4.8
|
18.0
|
1.0
|
HD1
|
C:HIS241
|
4.8
|
37.0
|
1.0
|
|
Nickel binding site 6 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 6 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni305
b:58.1
occ:1.00
|
NE2
|
D:HIS241
|
2.1
|
44.5
|
1.0
|
O
|
D:HOH554
|
2.2
|
41.5
|
1.0
|
O
|
D:HOH473
|
2.2
|
48.2
|
1.0
|
O
|
D:HOH468
|
2.3
|
41.1
|
1.0
|
CD2
|
D:HIS241
|
3.0
|
40.0
|
1.0
|
CE1
|
D:HIS241
|
3.1
|
43.0
|
1.0
|
HD2
|
D:HIS241
|
3.2
|
48.0
|
1.0
|
HE1
|
D:HIS241
|
3.3
|
51.6
|
1.0
|
HA3
|
D:GLY235
|
3.9
|
40.3
|
1.0
|
CG
|
D:HIS241
|
4.2
|
43.0
|
1.0
|
ND1
|
D:HIS241
|
4.2
|
43.6
|
1.0
|
O
|
D:LEU234
|
4.3
|
27.2
|
1.0
|
OE2
|
D:GLU236
|
4.7
|
42.1
|
1.0
|
O
|
D:HOH499
|
4.8
|
48.6
|
1.0
|
CA
|
D:GLY235
|
4.9
|
33.5
|
1.0
|
HE1
|
D:TRP274
|
4.9
|
48.4
|
1.0
|
NE1
|
D:TRP274
|
4.9
|
40.3
|
1.0
|
O
|
D:HOH481
|
5.0
|
30.7
|
1.0
|
HD1
|
D:HIS241
|
5.0
|
52.4
|
1.0
|
|
Nickel binding site 7 out
of 7 in 8rly
Go back to
Nickel Binding Sites List in 8rly
Nickel binding site 7 out
of 7 in the E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of E. Coli Endonuclease IV Complexed with Sulfate, Catalytic FE2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni305
b:30.7
occ:1.00
|
NE2
|
E:HIS60
|
2.0
|
33.2
|
1.0
|
O
|
E:HOH544
|
2.2
|
34.7
|
1.0
|
O
|
E:HOH462
|
2.2
|
26.7
|
1.0
|
HE1
|
E:HIS60
|
2.7
|
42.4
|
1.0
|
CE1
|
E:HIS60
|
2.7
|
35.3
|
1.0
|
CD2
|
E:HIS60
|
3.2
|
25.6
|
1.0
|
HD2
|
E:HIS60
|
3.6
|
30.8
|
1.0
|
ND1
|
E:HIS60
|
3.9
|
33.5
|
1.0
|
O
|
E:HOH572
|
4.1
|
40.5
|
1.0
|
O
|
E:LYS58
|
4.1
|
22.7
|
1.0
|
CG
|
E:HIS60
|
4.2
|
22.0
|
1.0
|
HD1
|
E:HIS60
|
4.6
|
40.2
|
1.0
|
|
Reference:
S.Kirillov,
M.Isupov,
N.G.Paterson,
R.Wiener,
S.Abeldenov,
M.A.Saper,
A.Rouvinski.
Octahedral Iron in Catalytic Sites of Endonuclease IV From Staphylococcus Aureus and Escherichia Coli Biochemistry 2024.
ISSN: ISSN 0006-2960
DOI: 10.1021/ACS.BIOCHEM.4C00447
Page generated: Sun Dec 15 11:47:00 2024
|