Manganese in PDB 5ekw: A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348

Enzymatic activity of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348

All present enzymatic activity of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348:
4.2.1.19;

Protein crystallography data

The structure of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348, PDB code: 5ekw was solved by C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.C.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.70 / 1.10
*Space group*	P 4 3 2
*Cell size a, b, c (Å), α, β, γ (°)*	112.905, 112.905, 112.905, 90.00, 90.00, 90.00
*R / R_free (%)*	12.3 / 13.3

Other elements in 5ekw:

The structure of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348 (pdb code 5ekw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348, PDB code: 5ekw:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5ekw

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Manganese Binding Sites List in 5ekw

Manganese binding site 1 out of 3 in the A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn401 b:6.8 occ:0.70	MN	A:MN401	0.0	6.8	0.7
	MN	A:MN401	0.7	9.7	0.3
	O13	A:5LD404	2.2	17.4	0.3
	N1	A:5DL403	2.2	9.1	0.7
	N1	A:5LD404	2.3	6.9	0.3
	O13	A:5DL403	2.4	11.7	0.7
	C5	A:5LD404	3.2	4.4	0.3
	N2	A:5DL403	3.3	10.0	0.7
	C5	A:5DL403	3.3	9.2	0.7
	C7	A:5LD404	3.3	15.1	0.3
	N2	A:5LD404	3.4	7.6	0.3
	C7	A:5DL403	3.5	10.9	0.7
	C6	A:5LD404	3.6	10.1	0.3
	C6	A:5DL403	3.6	9.9	0.7
	N4	A:5LD404	4.4	9.6	0.3
	C3	A:5DL403	4.4	8.7	0.7
	N4	A:5DL403	4.4	7.4	0.7
	C3	A:5LD404	4.5	8.3	0.3
	C8	A:5LD404	4.6	7.9	0.3
	C8	A:5DL403	4.6	11.7	0.7

Manganese binding site 2 out of 3 in 5ekw

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Manganese Binding Sites List in 5ekw

Manganese binding site 2 out of 3 in the A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn401 b:9.7 occ:0.30	MN	A:MN401	0.0	9.7	0.3
	MN	A:MN401	0.7	6.8	0.7
	N1	A:5DL403	2.6	9.1	0.7
	N1	A:5LD404	2.7	6.9	0.3
	O13	A:5LD404	2.8	17.4	0.3
	O13	A:5DL403	2.9	11.7	0.7
	C5	A:5LD404	3.4	4.4	0.3
	C5	A:5DL403	3.5	9.2	0.7
	N2	A:5DL403	3.8	10.0	0.7
	N2	A:5LD404	3.8	7.6	0.3
	C7	A:5LD404	3.9	15.1	0.3
	C7	A:5DL403	4.1	10.9	0.7
	C6	A:5LD404	4.1	10.1	0.3
	C6	A:5DL403	4.3	9.9	0.7
	N4	A:5LD404	4.7	9.6	0.3
	N4	A:5DL403	4.7	7.4	0.7
	C3	A:5DL403	4.9	8.7	0.7
	C3	A:5LD404	4.9	8.3	0.3

Manganese binding site 3 out of 3 in 5ekw

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Manganese Binding Sites List in 5ekw

Manganese binding site 3 out of 3 in the A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of A. Thaliana IGPD2 in Complex with the Racemate of the Triazole- Phosphonate Inhibitor, C348 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn402 b:7.0 occ:1.00	N4	A:5DL403	2.2	7.4	0.7
	N4	A:5LD404	2.3	9.6	0.3
	C3	A:5LD404	3.2	8.3	0.3
	C3	A:5DL403	3.2	8.7	0.7
	C5	A:5DL403	3.2	9.2	0.7
	C5	A:5LD404	3.4	4.4	0.3
	N2	A:5DL403	4.3	10.0	0.7
	N2	A:5LD404	4.3	7.6	0.3
	N1	A:5DL403	4.4	9.1	0.7
	N1	A:5LD404	4.5	6.9	0.3

Reference:

C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.C.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice. Mirror-Image Packing Provides A Molecular Basis For the Nanomolar Equipotency of Enantiomers of An Experimental Herbicide. Angew.Chem.Int.Ed.Engl. V. 55 13485 2016.
ISSN: ESSN 1521-3773
PubMed: 27717128
DOI: 10.1002/ANIE.201607185

Page generated: Sun Oct 6 00:09:18 2024

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