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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:

Iron (Fe) 5 atoms
Chlorine (Cl) 5 atoms
Zinc (Zn) 10 atoms

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

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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

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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

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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

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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

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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

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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

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