Manganese in PDB 6pxu: Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

Enzymatic activity of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

All present enzymatic activity of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp:
2.4.1.41;

Protein crystallography data

The structure of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp, PDB code: 6pxu was solved by N.L.Samara, A.J.Fernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.03 / 2.01
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	72.820, 73.123, 74.441, 113.08, 100.50, 108.23
*R / R_free (%)*	17.1 / 21.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp (pdb code 6pxu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp, PDB code: 6pxu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6pxu

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Manganese Binding Sites List in 6pxu

Manganese binding site 1 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

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 Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn610 b:32.1 occ:1.00	O2A	A:UDP601	2.1	28.4	1.0
	NE2	A:HIS363	2.2	29.8	1.0
	O3B	A:UDP601	2.2	32.8	1.0
	NE2	A:HIS230	2.3	31.3	1.0
	OD2	A:ASP228	2.3	36.6	1.0
	O	A:HOH726	2.4	32.2	1.0
	CE1	A:HIS363	3.0	34.0	1.0
	PB	A:UDP601	3.2	34.5	1.0
	CE1	A:HIS230	3.2	34.0	1.0
	CD2	A:HIS230	3.2	22.9	1.0
	CG	A:ASP228	3.3	32.7	1.0
	CD2	A:HIS363	3.3	27.5	1.0
	PA	A:UDP601	3.3	29.3	1.0
	O2B	A:UDP601	3.5	32.5	1.0
	O3A	A:UDP601	3.7	31.9	1.0
	O5'	A:UDP601	3.7	41.1	1.0
	CB	A:ASP228	3.8	29.5	1.0
	ND1	A:HIS363	4.1	35.8	1.0
	CG	A:HIS363	4.3	30.2	1.0
	ND1	A:HIS230	4.3	31.7	1.0
	OD1	A:ASP228	4.3	39.0	1.0
	CG	A:HIS230	4.4	29.3	1.0
	O1A	A:UDP601	4.5	28.1	1.0
	O1B	A:UDP601	4.5	31.0	1.0
	O	A:HOH826	4.6	44.8	1.0
	C3'	A:UDP601	4.9	28.3	1.0

Manganese binding site 2 out of 4 in 6pxu

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Manganese Binding Sites List in 6pxu

Manganese binding site 2 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

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 Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn611 b:31.1 occ:0.80	O	A:HOH775	2.3	25.9	1.0
	O	A:VAL197	2.4	22.4	1.0
	O	A:HOH750	2.5	21.4	1.0
	C	A:VAL197	3.6	24.1	1.0
	O	A:HOH920	4.0	33.9	1.0
	O	A:LEU194	4.2	21.1	1.0
	N	A:VAL197	4.3	23.3	1.0
	CA	A:VAL197	4.5	22.3	1.0
	N	A:ARG198	4.5	18.1	1.0
	CA	A:ARG198	4.6	21.1	1.0
	O	A:SER192	4.7	27.1	1.0
	CG	A:ARG198	4.8	20.6	1.0
	CB	A:VAL197	4.9	23.1	1.0
	O	A:HOH923	4.9	20.6	1.0

Manganese binding site 3 out of 4 in 6pxu

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Manganese Binding Sites List in 6pxu

Manganese binding site 3 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

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 Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn601 b:30.6 occ:1.00	O1A	B:UDP602	2.2	28.1	1.0
	OD2	B:ASP228	2.3	41.1	1.0
	O1B	B:UDP602	2.3	31.4	1.0
	NE2	B:HIS363	2.3	28.5	1.0
	NE2	B:HIS230	2.3	34.5	1.0
	O	B:HOH815	2.4	41.0	1.0
	CE1	B:HIS363	3.1	34.5	1.0
	PB	B:UDP602	3.2	31.4	1.0
	CE1	B:HIS230	3.3	35.6	1.0
	CG	B:ASP228	3.3	35.4	1.0
	CD2	B:HIS230	3.3	30.7	1.0
	CD2	B:HIS363	3.4	31.8	1.0
	PA	B:UDP602	3.4	29.3	1.0
	O2B	B:UDP602	3.5	33.0	1.0
	O3A	B:UDP602	3.7	30.5	1.0
	CB	B:ASP228	3.8	26.9	1.0
	C5'	B:UDP602	4.2	26.0	1.0
	O5'	B:UDP602	4.3	25.6	1.0
	OD1	B:ASP228	4.3	33.5	1.0
	ND1	B:HIS363	4.3	35.4	1.0
	O	B:HOH890	4.3	37.3	1.0
	ND1	B:HIS230	4.4	31.0	1.0
	CG	B:HIS230	4.4	32.4	1.0
	CG	B:HIS363	4.5	29.3	1.0
	O2A	B:UDP602	4.5	32.0	1.0
	O3B	B:UDP602	4.6	29.2	1.0
	C3'	B:UDP602	4.6	32.2	1.0
	C4'	B:UDP602	5.0	29.4	1.0

Manganese binding site 4 out of 4 in 6pxu

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Manganese Binding Sites List in 6pxu

Manganese binding site 4 out of 4 in the Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Galnac-T12 Bound to A Diglycosylated Peptide, MN2+, and Udp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn615 b:82.2 occ:0.50	OH	B:TYR145	2.2	44.7	1.0
	OD2	B:ASP179	2.2	65.6	1.0
	O	B:HOH823	2.6	46.2	1.0
	CZ	B:TYR145	3.1	37.3	1.0
	CE1	B:TYR145	3.3	32.8	1.0
	CG	B:ASP179	3.4	57.7	1.0
	O	B:HOH846	3.5	51.1	1.0
	ND2	B:ASN146	3.6	38.9	1.0
	CB	B:ASP179	4.2	44.4	1.0
	CE2	B:TYR145	4.3	35.2	1.0
	OD1	B:ASP179	4.3	69.9	1.0
	CG	B:ASN146	4.5	33.1	1.0
	N	B:ASP179	4.6	30.0	1.0
	O	B:TYR177	4.6	30.5	1.0
	CD1	B:TYR145	4.6	24.0	1.0
	OD1	B:ASN146	4.6	29.7	1.0
	NH1	B:ARG205	4.7	49.5	1.0

Reference:

A.J.Fernandez, E.J.P.Daniel, S.P.Mahajan, J.J.Gray, T.A.Gerken, L.A.Tabak, N.L.Samara. The Structure of the Colorectal Cancer-Associated Enzyme Galnac-T12 Reveals How Nonconserved Residues Dictate Its Function. Proc.Natl.Acad.Sci.Usa V. 116 20404 2019.
ISSN: ESSN 1091-6490
PubMed: 31548401
DOI: 10.1073/PNAS.1902211116

Page generated: Sun Oct 6 05:52:42 2024

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