Magnesium in PDB 5kgn: 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)

Enzymatic activity of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)

All present enzymatic activity of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D):
5.4.2.12;

Protein crystallography data

The structure of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D), PDB code: 5kgn was solved by S.Lovell, N.Mehzabeen, K.P.Battaile, H.Yu, P.Dranchak, R.Macarthur, Z.Li, T.Carlow, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.49 / 1.95
*Space group*	P 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	73.782, 75.832, 101.420, 90.00, 95.66, 90.00
*R / R_free (%)*	15.4 / 20.4

Other elements in 5kgn:

The structure of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) (pdb code 5kgn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D), PDB code: 5kgn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5kgn

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Magnesium Binding Sites List in 5kgn

Magnesium binding site 1 out of 2 in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg603 b:18.0 occ:1.00	O	A:HOH944	2.3	15.1	1.0
	O	A:ILE50	2.3	13.2	1.0
	O	A:ALA53	2.3	13.8	1.0
	OG1	A:THR55	2.4	16.2	1.0
	O	A:HOH808	2.6	14.7	1.0
	O	A:LEU51	2.7	22.7	1.0
	C	A:LEU51	3.2	15.6	1.0
	C	A:ILE50	3.4	14.0	1.0
	CB	A:THR55	3.4	17.9	1.0
	C	A:ALA53	3.5	12.0	1.0
	CG2	A:THR55	3.5	15.0	1.0
	CA	A:LEU51	3.6	18.6	1.0
	N	A:THR55	3.7	13.2	1.0
	N	A:ALA53	4.0	15.8	1.0
	N	A:LEU51	4.0	14.4	1.0
	CA	A:THR55	4.1	18.4	1.0
	N	A:ASN52	4.1	17.6	1.0
	CA	A:ALA53	4.2	15.1	1.0
	OD1	A:ASP59	4.2	18.5	1.0
	C	A:ASN52	4.3	20.9	1.0
	OD2	A:ASP59	4.4	20.0	1.0
	C	A:GLN54	4.4	14.0	1.0
	N	A:GLN54	4.5	15.6	1.0
	CB	A:ALA53	4.6	15.0	1.0
	CA	A:GLN54	4.7	13.2	1.0
	O	A:HOH1050	4.7	36.7	1.0
	CA	A:ILE50	4.7	13.9	1.0
	CA	A:ASN52	4.7	14.1	1.0
	CG	A:ASP59	4.8	22.2	1.0
	C	A:THR55	4.8	14.3	1.0
	O	A:ASN52	4.9	14.5	1.0
	O	A:THR55	4.9	13.3	1.0
	CD1	A:LEU51	5.0	30.5	1.0
	CG2	A:ILE50	5.0	16.6	1.0

Magnesium binding site 2 out of 2 in 5kgn

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Magnesium Binding Sites List in 5kgn

Magnesium binding site 2 out of 2 in the 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D)

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 1.95A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (2D) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg603 b:16.9 occ:1.00	OG1	B:THR55	2.3	13.4	1.0
	O	B:ALA53	2.3	13.4	1.0
	O	B:HOH807	2.4	19.0	1.0
	O	B:ILE50	2.4	16.8	1.0
	O	B:HOH735	2.5	17.9	1.0
	O	B:LEU51	2.8	18.0	1.0
	C	B:LEU51	3.3	13.7	1.0
	CB	B:THR55	3.4	15.2	1.0
	C	B:ALA53	3.4	12.6	1.0
	CG2	B:THR55	3.5	17.4	1.0
	C	B:ILE50	3.5	19.4	1.0
	N	B:THR55	3.6	13.2	1.0
	CA	B:LEU51	3.6	17.6	1.0
	N	B:ALA53	4.0	15.6	1.0
	CA	B:THR55	4.0	19.5	1.0
	N	B:LEU51	4.1	16.6	1.0
	OD1	B:ASP59	4.2	18.5	1.0
	CA	B:ALA53	4.2	10.7	1.0
	N	B:ASN52	4.2	18.8	1.0
	OD2	B:ASP59	4.3	18.8	1.0
	O	B:HOH1029	4.4	34.7	1.0
	C	B:GLN54	4.4	12.5	1.0
	C	B:ASN52	4.4	13.4	1.0
	N	B:GLN54	4.4	11.6	1.0
	CB	B:ALA53	4.5	12.3	1.0
	CA	B:GLN54	4.6	14.6	1.0
	CG	B:ASP59	4.7	19.5	1.0
	C	B:THR55	4.8	11.0	1.0
	CA	B:ASN52	4.8	16.7	1.0
	CA	B:ILE50	4.8	13.7	1.0
	O	B:THR55	4.8	13.0	1.0
	CG2	B:ILE50	5.0	21.3	1.0

Reference:

H.Yu, P.Dranchak, Z.Li, R.Macarthur, M.S.Munson, N.Mehzabeen, N.J.Baird, K.P.Battalie, D.Ross, S.Lovell, C.K.Carlow, H.Suga, J.Inglese. Macrocycle Peptides Delineate Locked-Open Inhibition Mechanism For Microorganism Phosphoglycerate Mutases. Nat Commun V. 8 14932 2017.
ISSN: ESSN 2041-1723
PubMed: 28368002
DOI: 10.1038/NCOMMS14932

Page generated: Sun Sep 29 19:07:25 2024

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