Magnesium in PDB 1h17: Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate

Enzymatic activity of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate

All present enzymatic activity of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate:
2.3.1.54;

Protein crystallography data

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate, PDB code: 1h17 was solved by A.Becker, W.Kabsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	15 / 1.75
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	54.938, 153.169, 205.909, 90.00, 90.00, 90.00
*R / R_free (%)*	14.8 / 17.3

Other elements in 1h17:

The structure of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate (pdb code 1h17). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate, PDB code: 1h17:

Magnesium binding site 1 out of 1 in 1h17

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Magnesium Binding Sites List in 1h17

Magnesium binding site 1 out of 1 in the Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Formate-Lyase (E.Coli) in Complex with Coa and the Substrate Analog Oxamate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg9008 b:60.7 occ:1.00	O5B	A:COA1000	2.1	19.0	1.0
	O5A	A:COA1000	2.2	24.5	1.0
	O	A:HOH3246	2.7	41.1	1.0
	O	A:HOH2491	2.8	42.2	1.0
	C5B	A:COA1000	2.8	16.7	1.0
	P1A	A:COA1000	3.0	22.0	1.0
	P2A	A:COA1000	3.1	22.9	1.0
	O3A	A:COA1000	3.1	22.1	1.0
	O1A	A:COA1000	3.2	23.4	1.0
	C3B	A:COA1000	3.6	17.8	1.0
	C4B	A:COA1000	3.6	16.9	1.0
	O6A	A:COA1000	3.8	20.9	1.0
	O	A:HOH3239	3.9	56.3	1.0
	C2B	A:COA1000	4.0	16.8	1.0
	NZ	A:LYS161	4.4	23.7	1.0
	O4A	A:COA1000	4.4	25.3	1.0
	O2A	A:COA1000	4.4	22.4	1.0
	O7A	A:COA1000	4.6	24.1	1.0
	O2B	A:COA1000	4.8	17.4	1.0
	O4B	A:COA1000	4.8	15.5	1.0
	O3B	A:COA1000	4.8	19.9	1.0
	N3A	A:COA1000	4.8	13.6	1.0

Reference:

A.Becker, W.Kabsch. X-Ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and Coa.How the Enzyme Uses the Cys-418 Thiyl Radical For Pyruvate Cleavage J.Biol.Chem. V. 277 40036 2002.
ISSN: ISSN 0021-9258
PubMed: 12163496
DOI: 10.1074/JBC.M205821200

Page generated: Tue Aug 13 03:52:23 2024

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