Manganese in PDB 4eeo: Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

Enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

All present enzymatic activity of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl:
2.4.1.22; 2.4.1.38; 2.4.1.90;

Protein crystallography data

The structure of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl, PDB code: 4eeo was solved by B.Ramakrishnan, P.K.Qasba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.80 / 2.30
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	107.804, 198.217, 143.732, 90.00, 90.00, 90.00
*R / R_free (%)*	20.3 / 25.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl (pdb code 4eeo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl, PDB code: 4eeo:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4eeo

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Manganese Binding Sites List in 4eeo

Manganese binding site 1 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn404 b:48.2 occ:1.00	O3B	A:UDP403	2.0	71.0	1.0
	OD2	A:ASP250	2.2	38.6	1.0
	NE2	A:HIS343	2.2	47.9	1.0
	O1A	A:UDP403	2.2	63.5	1.0
	NE2	A:HIS340	2.5	34.4	1.0
	O	A:HOH550	2.8	45.7	1.0
	CE1	A:HIS343	3.1	50.7	1.0
	CG	A:ASP250	3.1	37.8	1.0
	PB	A:UDP403	3.2	77.3	1.0
	CD2	A:HIS343	3.3	51.2	1.0
	PA	A:UDP403	3.3	67.0	1.0
	CE1	A:HIS340	3.4	36.6	1.0
	O3A	A:UDP403	3.4	71.4	1.0
	CD2	A:HIS340	3.5	38.1	1.0
	OD1	A:ASP250	3.6	39.8	1.0
	O2B	A:UDP403	3.9	75.3	1.0
	O2A	A:UDP403	4.1	64.4	1.0
	NH2	A:ARG187	4.2	43.5	1.0
	ND1	A:HIS343	4.2	52.3	1.0
	CB	A:ASP250	4.3	37.5	1.0
	O3'	A:UDP403	4.3	44.9	1.0
	CG	A:HIS343	4.3	50.4	1.0
	O1B	A:UDP403	4.4	74.6	1.0
	NH1	A:ARG187	4.4	39.7	1.0
	ND1	A:HIS340	4.5	41.3	1.0
	CG	A:HIS340	4.6	38.9	1.0
	O5'	A:UDP403	4.6	57.6	1.0
	C3'	A:UDP403	4.8	40.1	1.0
	CZ	A:ARG187	4.8	43.4	1.0
	NZ	A:LYS275	4.9	53.2	1.0
	C5'	A:UDP403	4.9	48.1	1.0
	O	A:ILE341	5.0	43.2	1.0

Manganese binding site 2 out of 3 in 4eeo

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Manganese Binding Sites List in 4eeo

Manganese binding site 2 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn404 b:42.0 occ:1.00	O1A	B:UDP403	2.1	63.1	1.0
	NE2	B:HIS343	2.2	37.5	1.0
	NE2	B:HIS340	2.2	37.8	1.0
	OD2	B:ASP250	2.3	30.1	1.0
	O3B	B:UDP403	2.3	79.9	1.0
	CE1	B:HIS340	3.0	37.7	1.0
	CE1	B:HIS343	3.1	39.4	1.0
	O	B:HOH533	3.1	53.2	1.0
	CG	B:ASP250	3.2	26.9	1.0
	CD2	B:HIS343	3.3	40.9	1.0
	PA	B:UDP403	3.3	67.6	1.0
	PB	B:UDP403	3.3	82.5	1.0
	CD2	B:HIS340	3.4	34.8	1.0
	O3A	B:UDP403	3.5	74.3	1.0
	OD1	B:ASP250	3.7	25.8	1.0
	O2B	B:UDP403	3.9	78.8	1.0
	O2A	B:UDP403	3.9	69.8	1.0
	NH2	B:ARG187	4.1	30.8	1.0
	ND1	B:HIS340	4.2	34.3	1.0
	ND1	B:HIS343	4.2	41.2	1.0
	NZ	B:LYS275	4.3	42.0	1.0
	O3'	B:UDP403	4.3	30.1	1.0
	CB	B:ASP250	4.3	24.9	1.0
	CG	B:HIS343	4.4	40.8	1.0
	CG	B:HIS340	4.4	38.1	1.0
	NH1	B:ARG187	4.4	29.1	1.0
	O1B	B:UDP403	4.6	79.8	1.0
	O5'	B:UDP403	4.7	56.3	1.0
	CZ	B:ARG187	4.8	34.1	1.0
	C3'	B:UDP403	4.9	31.3	1.0

Manganese binding site 3 out of 3 in 4eeo

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Manganese Binding Sites List in 4eeo

Manganese binding site 3 out of 3 in the Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-1 (M340H-B4GAL-T1) in Complex with Glcnac-BETA1,6-Glcnac-Alpha-Benzyl within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mn404 b:60.4 occ:1.00	O3B	C:UDP403	2.1	89.2	1.0
	OD2	C:ASP250	2.1	49.7	1.0
	NE2	C:HIS343	2.1	56.8	1.0
	NE2	C:HIS340	2.4	61.5	1.0
	O	C:HOH513	2.5	57.6	1.0
	O1A	C:UDP403	2.6	85.9	1.0
	CE1	C:HIS343	3.0	59.6	1.0
	CG	C:ASP250	3.1	45.9	1.0
	PB	C:UDP403	3.1	93.1	1.0
	CD2	C:HIS343	3.3	60.8	1.0
	O3A	C:UDP403	3.3	89.7	1.0
	CD2	C:HIS340	3.3	60.3	1.0
	CE1	C:HIS340	3.4	63.7	1.0
	PA	C:UDP403	3.5	86.0	1.0
	OD1	C:ASP250	3.5	43.8	1.0
	O2B	C:UDP403	3.7	91.2	1.0
	NH2	C:ARG187	4.1	47.9	1.0
	ND1	C:HIS343	4.2	58.2	1.0
	O3'	C:UDP403	4.3	54.3	1.0
	CG	C:HIS343	4.3	60.6	1.0
	NZ	C:LYS275	4.4	68.3	1.0
	CB	C:ASP250	4.4	43.6	1.0
	O2A	C:UDP403	4.4	88.9	1.0
	O1B	C:UDP403	4.4	90.1	1.0
	CG	C:HIS340	4.5	58.9	1.0
	ND1	C:HIS340	4.5	62.7	1.0
	NH1	C:ARG187	4.7	56.2	1.0
	O5'	C:UDP403	4.7	78.9	1.0
	C3'	C:UDP403	4.9	55.2	1.0
	CZ	C:ARG187	4.9	52.7	1.0
	C5'	C:UDP403	5.0	66.9	1.0

Reference:

B.Ramakrishnan, E.Boeggeman, P.K.Qasba. Binding of N-Acetylglucosamine (Glcnac) Beta 1-6-Branched Oligosaccharide Acceptors to Beta 4-Galactosyltransferase I Reveals A New Ligand Binding Mode. J.Biol.Chem. V. 287 28666 2012.
ISSN: ISSN 0021-9258
PubMed: 22740701
DOI: 10.1074/JBC.M112.373514

Page generated: Sat Oct 5 19:18:57 2024

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