Manganese in PDB 4cco: 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)

Enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)

All present enzymatic activity of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3):
1.14.11.27;

Protein crystallography data

The structure of 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3), PDB code: 4cco 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)*	43.70 / 2.30
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	155.390, 84.944, 97.300, 90.00, 100.30, 90.00
*R / R_free (%)*	21 / 22.5

Manganese Binding Sites:

The binding sites of Manganese atom in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3) (pdb code 4cco). 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 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3), PDB code: 4cco:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4cco

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Manganese Binding Sites List in 4cco

Manganese binding site 1 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)

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 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn901 b:24.7 occ:1.00	OD2	A:ASP342	2.0	34.0	1.0
	O2	A:OGA902	2.2	28.7	1.0
	O	A:HOH2122	2.3	62.7	1.0
	O2'	A:OGA902	2.3	27.0	1.0
	NE2	A:HIS340	2.3	24.1	1.0
	NE2	A:HIS405	2.4	26.9	1.0
	CG	A:ASP342	3.0	32.7	1.0
	C1	A:OGA902	3.0	29.7	1.0
	C2	A:OGA902	3.0	30.1	1.0
	CE1	A:HIS340	3.2	23.7	1.0
	CE1	A:HIS405	3.3	26.0	1.0
	OD1	A:ASP342	3.3	36.2	1.0
	CD2	A:HIS405	3.4	26.4	1.0
	CD2	A:HIS340	3.4	23.1	1.0
	O1	A:OGA902	4.1	28.1	1.0
	CB	C:HIS216	4.2	56.7	1.0
	CB	A:ASP342	4.3	30.7	1.0
	N1	A:OGA902	4.3	31.7	1.0
	ND1	A:HIS340	4.3	25.2	1.0
	ND1	A:HIS405	4.4	25.9	1.0
	CG	A:HIS340	4.5	24.7	1.0
	CG	A:HIS405	4.5	27.3	1.0
	OH	A:TYR328	4.6	23.6	1.0
	CB	C:ASN215	4.8	54.1	1.0
	N	C:HIS216	4.8	56.6	1.0
	C4	A:OGA902	5.0	34.8	1.0

Manganese binding site 2 out of 2 in 4cco

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Manganese Binding Sites List in 4cco

Manganese binding site 2 out of 2 in the 60S Ribosomal Protein L8 Histidine Hydroxylase (NO66 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3)

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 S373C) in Complex with Mn(II), N-Oxalylglycine (Nog) and 60S Ribosomal Protein L8 (RPL8 G214C) Peptide Fragment (Complex-3) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn901 b:27.6 occ:1.00	OD2	B:ASP342	2.2	24.8	1.0
	NE2	B:HIS405	2.2	25.7	1.0
	O2'	B:OGA902	2.2	25.2	1.0
	O	B:HOH2123	2.3	48.8	1.0
	O2	B:OGA902	2.3	28.2	1.0
	NE2	B:HIS340	2.4	22.5	1.0
	C2	B:OGA902	2.9	28.8	1.0
	C1	B:OGA902	2.9	29.5	1.0
	CE1	B:HIS340	3.1	22.0	1.0
	CE1	B:HIS405	3.1	26.2	1.0
	CG	B:ASP342	3.1	24.2	1.0
	CD2	B:HIS405	3.2	25.3	1.0
	OD1	B:ASP342	3.5	29.1	1.0
	CD2	B:HIS340	3.5	20.8	1.0
	O1	B:OGA902	4.1	29.8	1.0
	N1	B:OGA902	4.2	27.9	1.0
	ND1	B:HIS405	4.2	26.3	1.0
	ND1	B:HIS340	4.3	23.1	1.0
	CG	B:HIS405	4.3	26.4	1.0
	CB	D:HIS216	4.4	57.5	1.0
	CB	B:ASP342	4.5	23.5	1.0
	CG	B:HIS340	4.5	20.7	1.0
	OD1	D:ASN215	4.5	60.7	1.0
	OH	B:TYR328	4.7	23.4	1.0
	CB	D:ASN215	4.7	59.3	1.0
	C4	B:OGA902	4.9	29.8	1.0
	N	D:HIS216	4.9	60.1	1.0
	CG	D:ASN215	4.9	60.1	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 18:54:16 2024

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