Magnesium in PDB 3kbw: Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors

Enzymatic activity of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors

All present enzymatic activity of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors:
5.3.1.5;

Protein crystallography data

The structure of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors, PDB code: 3kbw was solved by A.Y.Kovalevsky, L.Hanson, P.Langan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	10.00 / 1.60
*Space group*	I 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	93.972, 99.701, 102.855, 90.00, 90.00, 90.00
*R / R_free (%)*	11.9 / 16.7

Other elements in 3kbw:

The structure of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors (pdb code 3kbw). 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 Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors, PDB code: 3kbw:

Magnesium binding site 1 out of 1 in 3kbw

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Magnesium Binding Sites List in 3kbw

Magnesium binding site 1 out of 1 in the Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Room Temperature X-Ray Mixed-Metal Structure of D-Xylose Isomerase in Complex with Ni(2+) and Mg(2+) Co-Factors within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg392 b:15.1 occ:1.00	OD2	A:ASP287	2.3	21.6	1.0
	OE2	A:GLU181	2.3	35.9	1.0
	OE1	A:GLU217	2.4	16.6	1.0
	OD2	A:ASP245	2.5	21.1	1.0
	CD	A:GLU181	3.0	22.7	1.0
	OE1	A:GLU181	3.1	24.5	1.0
	CG	A:ASP287	3.3	14.1	1.0
	O	A:HOH1116	3.4	34.2	1.0
	CG	A:ASP245	3.5	15.3	1.0
	O	A:HOH1097	3.6	25.6	1.0
	O	A:HOH1115	3.6	37.2	1.0
	CD	A:GLU217	3.6	9.2	1.0
	CB	A:ASP287	3.6	13.7	1.0
	O	A:HOH1142	3.7	37.5	1.0
	O	A:HOH1001	3.9	18.1	1.0
	CB	A:ASP245	4.0	12.6	1.0
	CB	A:GLU217	4.1	11.3	1.0
	CG	A:GLU217	4.2	11.7	1.0
	CE1	A:HIS220	4.3	12.2	1.0
	CG	A:GLU181	4.3	17.0	1.0
	OD1	A:ASP287	4.4	16.5	1.0
	OD1	A:ASP245	4.6	20.8	1.0
	OE2	A:GLU217	4.6	15.4	1.0
	ND2	A:ASN215	4.7	17.0	1.0
	ND1	A:HIS220	4.9	9.9	1.0
	NE2	A:HIS220	5.0	12.7	1.0

Reference:

A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, P.Langan. Metal Ion Roles and the Movement of Hydrogen During Reaction Catalyzed By D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study. Structure V. 18 688 2010.
ISSN: ISSN 0969-2126
PubMed: 20541506
DOI: 10.1016/J.STR.2010.03.011

Page generated: Wed Aug 14 18:01:48 2024

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