Calcium in PDB 8ezf: A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant

Enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant

All present enzymatic activity of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant:
5.1.2.1;

Protein crystallography data

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant, PDB code: 8ezf was solved by S.Gatreddi, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	37.97 / 2.15
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	42.84, 79.913, 121.788, 90, 90, 90
*R / R_free (%)*	18.6 / 24.3

Other elements in 8ezf:

The structure of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Chlorine	(Cl)	1 atom
Magnesium	(Mg)	2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant (pdb code 8ezf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant, PDB code: 8ezf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8ezf

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Calcium Binding Sites List in 8ezf

Calcium binding site 1 out of 2 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca501 b:20.0 occ:1.00	O1	B:EDO519	2.4	21.7	1.0
	O2	B:EDO519	2.5	18.5	1.0
	OE2	B:GLU400	2.5	22.6	1.0
	OE1	B:GLU400	2.6	21.1	1.0
	O	B:HOH719	2.7	32.8	1.0
	CD	B:GLU400	2.9	20.4	1.0
	C1	B:EDO519	3.2	26.2	1.0
	C2	B:EDO519	3.3	24.6	1.0
	CA	B:CA502	3.9	22.2	1.0
	OD2	B:ASP396	4.2	17.8	1.0
	CG	B:GLU400	4.4	15.2	1.0

Calcium binding site 2 out of 2 in 8ezf

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Calcium Binding Sites List in 8ezf

Calcium binding site 2 out of 2 in the A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Tethered Niacin-Derived Pincer Complex with A Nickel-Carbon or Sulfite-Carbon Bond in Lactate Racemase R98A/R100A Variant within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Ca502 b:22.2 occ:1.00	OE1	B:GLU400	2.3	21.1	1.0
	O	B:HOH629	2.6	17.3	1.0
	OD2	B:ASP396	2.6	17.8	1.0
	CG	B:ASP396	3.5	22.2	1.0
	CD	B:GLU400	3.5	20.4	1.0
	OD1	B:ASP396	3.6	19.2	1.0
	CA	B:CA501	3.9	20.0	1.0
	O2	B:EDO519	4.0	18.5	1.0
	CG	B:GLU400	4.3	15.2	1.0
	OE2	B:GLU400	4.4	22.6	1.0
	CB	B:ASP396	4.9	14.5	1.0
	C2	B:EDO519	4.9	24.6	1.0

Reference:

S.Gatreddi, D.Sui, R.P.Hausinger, J.Hu. Irreversible Inactivation of Lactate Racemase By Sodium Borohydride Reveals Reactivity of the Nickel-Pincer Nucleotide Cofactor Acs Catalysis 1441 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C05461

Page generated: Fri Jul 19 08:42:37 2024

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