Manganese in PDB 4ccm: 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1)

Enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1)

All present enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1):
1.14.11.27;

Protein crystallography data

The structure of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1), PDB code: 4ccm was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.07 / 2.51
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	154.770, 83.500, 96.870, 90.00, 100.20, 90.00
*R / R_free (%)*	22.8 / 23.6

Manganese Binding Sites:

The binding sites of Manganese atom in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1) (pdb code 4ccm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1), PDB code: 4ccm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4ccm

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Manganese Binding Sites List in 4ccm

Manganese binding site 1 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn901 b:39.0 occ:1.00	O	A:HOH2075	2.3	55.2	1.0
	O2'	A:OGA902	2.3	42.4	1.0
	O2	A:OGA902	2.4	41.4	1.0
	OD2	A:ASP342	2.4	51.1	1.0
	NE2	A:HIS405	2.5	43.4	1.0
	NE2	A:HIS340	2.5	36.8	1.0
	C2	A:OGA902	3.1	43.2	1.0
	C1	A:OGA902	3.1	42.6	1.0
	CE1	A:HIS340	3.2	34.8	1.0
	CG	A:ASP342	3.2	49.3	1.0
	CE1	A:HIS405	3.3	43.7	1.0
	OD1	A:ASP342	3.3	53.3	1.0
	CD2	A:HIS405	3.6	41.3	1.0
	CD2	A:HIS340	3.7	33.8	1.0
	CB	C:HIS216	4.1	88.1	1.0
	O1	A:OGA902	4.3	44.1	1.0
	ND1	A:HIS340	4.4	36.6	1.0
	N1	A:OGA902	4.4	43.7	1.0
	ND1	A:HIS405	4.5	43.4	1.0
	OH	A:TYR328	4.5	31.3	1.0
	CG	A:HIS405	4.6	41.3	1.0
	CB	A:ASP342	4.7	45.2	1.0
	N	C:HIS216	4.7	87.2	1.0
	CG	A:HIS340	4.7	35.2	1.0
	CB	C:ASN215	4.8	81.8	1.0
	CG	C:HIS216	5.0	87.5	1.0

Manganese binding site 2 out of 2 in 4ccm

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Manganese Binding Sites List in 4ccm

Manganese binding site 2 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G220C) Peptide Fragment (Complex-1) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn901 b:39.8 occ:1.00	O2'	B:OGA902	2.2	41.2	1.0
	O	B:HOH2068	2.3	61.5	1.0
	NE2	B:HIS405	2.3	40.5	1.0
	OD2	B:ASP342	2.4	51.8	1.0
	O2	B:OGA902	2.5	37.5	1.0
	NE2	B:HIS340	2.6	38.7	1.0
	C2	B:OGA902	3.0	42.2	1.0
	CE1	B:HIS405	3.0	40.4	1.0
	C1	B:OGA902	3.1	41.1	1.0
	CG	B:ASP342	3.2	48.8	1.0
	CE1	B:HIS340	3.2	39.0	1.0
	OD1	B:ASP342	3.2	50.5	1.0
	CD2	B:HIS405	3.6	38.2	1.0
	CD2	B:HIS340	3.7	40.6	1.0
	CB	D:HIS216	4.2	82.4	1.0
	ND1	B:HIS405	4.3	40.4	1.0
	N1	B:OGA902	4.3	43.4	1.0
	O1	B:OGA902	4.3	40.1	1.0
	ND1	B:HIS340	4.4	40.5	1.0
	CG	B:HIS405	4.5	37.1	1.0
	OH	B:TYR328	4.6	35.7	1.0
	CB	B:ASP342	4.6	46.1	1.0
	N	D:HIS216	4.6	81.6	1.0
	CG	B:HIS340	4.7	40.1	1.0
	CB	D:ASN215	4.9	76.1	1.0
	C4	B:OGA902	5.0	47.6	1.0

Reference:

R.Chowdhury, R.Sekirnik, N.C.Brissett, T.Krojer, C.-H.Ho, S.S.Ng, I.J.Clifton, W.Ge, N.J.Kershaw, G.C.Fox, J.R.C.Muniz, M.Vollmar, C.Phillips, E.S.Pilka, K.L.Kavanagh, F. Von Deflt, U.Oppermann, M.A.Mcdonough, A.J.Doherty, C.J.Schofield. Ribosomal Oxygenases Are Structurally Conserved From Prokaryotes to Humans. Nature V. 510 422 2014.
ISSN: ISSN 0028-0836
PubMed: 24814345
DOI: 10.1038/NATURE13263

Page generated: Sat Oct 5 18:54:03 2024

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