Magnesium in PDB 5jvn: C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism

Enzymatic activity of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism

All present enzymatic activity of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism:
2.7.9.1;

Protein crystallography data

The structure of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism, PDB code: 5jvn was solved by A.Minges, A.Hoeppner, G.Groth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.54 / 2.90
*Space group*	P 6 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	249.430, 249.430, 84.060, 90.00, 90.00, 120.00
*R / R_free (%)*	19.8 / 23.5

Other elements in 5jvn:

The structure of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism also contains other interesting chemical elements:

Bromine

(Br)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism (pdb code 5jvn). 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 C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism, PDB code: 5jvn:

Magnesium binding site 1 out of 1 in 5jvn

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Magnesium Binding Sites List in 5jvn

Magnesium binding site 1 out of 1 in the C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C3-Type Pyruvate Phosphate Dikinase: Intermediate State of the Central Domain in the Swiveling Mechanism within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg903 b:61.5 occ:1.00	OE1	A:GLU748	2.0	72.0	1.0
	OD2	A:ASP772	2.2	81.0	1.0
	O2	A:PEP902	2.3	94.3	1.0
	O2'	A:PEP902	2.7	65.1	1.0
	CD	A:GLU748	2.8	70.4	1.0
	O3P	A:PEP902	3.0	0.1	1.0
	C2	A:PEP902	3.0	88.0	1.0
	OE2	A:GLU748	3.0	69.1	1.0
	P	A:PEP902	3.1	95.2	1.0
	NH2	A:ARG669	3.3	81.7	1.0
	C1	A:PEP902	3.3	78.6	1.0
	CG	A:ASP772	3.4	78.3	1.0
	OD2	A:ASP622	3.6	86.5	1.0
	NH1	A:ARG619	3.6	75.2	1.0
	O2P	A:PEP902	3.8	82.4	1.0
	C3	A:PEP902	4.0	81.6	1.0
	CG	A:GLU748	4.2	70.0	1.0
	CB	A:ASP772	4.2	76.8	1.0
	OD1	A:ASP772	4.3	77.0	1.0
	O1P	A:PEP902	4.4	85.0	1.0
	CZ	A:ARG619	4.5	77.5	1.0
	CZ	A:ARG669	4.5	76.2	1.0
	O1	A:PEP902	4.6	64.2	1.0
	NH2	A:ARG619	4.7	82.7	1.0
	CG	A:ASP622	4.7	90.2	1.0
	CB	A:GLU748	4.7	69.5	1.0
	CD1	A:LEU710	5.0	72.5	1.0

Reference:

A.Minges, D.Ciupka, C.Winkler, A.Hoppner, H.Gohlke, G.Groth. Structural Intermediates and Directionality of the Swiveling Motion of Pyruvate Phosphate Dikinase. Sci Rep V. 7 45389 2017.
ISSN: ESSN 2045-2322
PubMed: 28358005
DOI: 10.1038/SREP45389

Page generated: Sun Sep 29 17:58:33 2024

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