Sodium in PDB 4blw: Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp)

Enzymatic activity of Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp)

All present enzymatic activity of Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp):
2.1.1.266;

Protein crystallography data

The structure of Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp), PDB code: 4blw was solved by A.S.Punekar, J.Liljeruhm, T.R.Shepherd, A.C.Forster, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	45.951 / 1.95
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	46.590, 77.060, 84.370, 90.00, 99.50, 90.00
*R / R_free (%)*	16.7 / 19.91

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp) (pdb code 4blw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp), PDB code: 4blw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4blw

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Sodium Binding Sites List in 4blw

Sodium binding site 1 out of 2 in the Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1294 b:30.7 occ:1.00	O	A:HOH2126	2.5	16.6	1.0
	O	A:HOH2128	2.5	17.6	1.0
	OH	A:TYR4	2.9	15.8	1.0
	O	A:HOH2019	2.9	15.0	1.0
	CZ3	A:TRP195	3.4	9.1	1.0
	CZ	A:TYR4	3.4	12.2	1.0
	N6	A:AMP1281	3.5	19.9	1.0
	CA	A:PRO166	3.5	10.7	1.0
	O	A:PRO165	3.6	13.7	1.0
	CH2	A:TRP195	3.7	11.1	1.0
	CE2	A:TYR4	3.9	11.3	1.0
	CE3	A:TRP195	4.2	11.2	1.0
	CE1	A:TYR4	4.2	10.1	1.0
	CB	A:PRO166	4.2	10.9	1.0
	O	A:PRO166	4.3	11.2	1.0
	N	A:PRO166	4.3	11.5	1.0
	C	A:PRO165	4.3	13.1	1.0
	N7	A:AMP1281	4.3	20.8	1.0
	C	A:PRO166	4.4	12.5	1.0
	ND1	A:HIS6	4.4	11.2	1.0
	SD	A:SAH1282	4.4	13.4	1.0
	CE1	A:HIS6	4.5	10.5	1.0
	C6	A:AMP1281	4.5	19.2	1.0
	OD1	A:ASP164	4.6	11.2	1.0
	CZ2	A:TRP195	4.6	9.4	1.0
	C5	A:AMP1281	4.7	21.3	1.0
	C5'	A:SAH1282	4.9	11.5	1.0
	CD2	A:TYR4	5.0	12.8	1.0

Sodium binding site 2 out of 2 in 4blw

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Sodium Binding Sites List in 4blw

Sodium binding site 2 out of 2 in the Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Escherichia Coli 23S Rrna (A2030-N6)- Methyltransferase Rlmj in Complex with S- Adenosylhomocysteine (Adohcy) and Adenosine Monophosphate ( Amp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na1287 b:32.6 occ:1.00	O	B:HOH2077	2.3	20.8	1.0
	O	B:HOH2078	2.6	22.6	1.0
	OH	B:TYR4	2.8	20.3	1.0
	O	B:HOH2013	2.8	21.7	1.0
	N6	B:AMP1280	3.3	26.4	1.0
	CZ	B:TYR4	3.4	19.1	1.0
	CZ3	B:TRP195	3.5	19.7	1.0
	CA	B:PRO166	3.7	17.9	1.0
	O	B:PRO165	3.7	15.7	1.0
	CH2	B:TRP195	3.7	18.8	1.0
	CE2	B:TYR4	4.0	22.8	1.0
	SD	B:SAH1281	4.1	18.0	1.0
	CE1	B:TYR4	4.2	16.6	1.0
	CE3	B:TRP195	4.2	16.1	1.0
	N7	B:AMP1280	4.2	32.9	1.0
	ND1	B:HIS6	4.3	13.4	1.0
	C	B:PRO165	4.3	15.6	1.0
	C6	B:AMP1280	4.4	27.4	1.0
	N	B:PRO166	4.4	14.7	1.0
	CB	B:PRO166	4.4	19.9	1.0
	O	B:PRO166	4.4	18.8	1.0
	CE1	B:HIS6	4.5	17.7	1.0
	C	B:PRO166	4.5	19.7	1.0
	OD1	B:ASP164	4.5	18.8	1.0
	C5	B:AMP1280	4.6	34.4	1.0
	CZ2	B:TRP195	4.7	17.6	1.0
	C5'	B:SAH1281	4.8	13.2	1.0
	O	B:ASP164	4.8	19.0	1.0

Reference:

A.S.Punekar, J.Liljeruhm, T.R.Shepherd, A.C.Forster, M.Selmer. Structural and Functional Insights Into the Molecular Mechanism of Rrna M6A Methyltransferase Rlmj. Nucleic Acids Res. V. 41 9537 2013.
ISSN: ISSN 0305-1048
PubMed: 23945937
DOI: 10.1093/NAR/GKT719

Page generated: Mon Oct 7 14:33:09 2024

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