Atomistry » Sodium » PDB 4blw-4c44 » 4blw
Atomistry »
  Sodium »
    PDB 4blw-4c44 »
      4blw »

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 / Rfree (%) 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

Go back to 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

Go back to 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: Tue Dec 15 06:34:39 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy