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Sodium in PDB 4n49: Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam

Enzymatic activity of Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam

All present enzymatic activity of Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam:
2.1.1.57;

Protein crystallography data

The structure of Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam, PDB code: 4n49 was solved by M.Smietanski, M.Werener, E.Purta, K.H.Kaminska, J.Stepinski, E.Darzynkiewicz, M.Nowotny, J.M.Bujnicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.80 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.834, 87.619, 57.310, 90.00, 112.89, 90.00
R / Rfree (%) 15.4 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam (pdb code 4n49). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam, PDB code: 4n49:

Sodium binding site 1 out of 1 in 4n49

Go back to Sodium Binding Sites List in 4n49
Sodium binding site 1 out of 1 in the Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cap-Specific Mrna (Nucleoside-2'-O-)-Methyltransferase 1 Protein in Complex with M7GPPPG and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:3.2
occ:1.00
 O A:HOH1035 3.0 18.9 1.0
NH1 A:ARG235 3.2 5.8 1.0
N A:ARG436 3.2 4.6 1.0
NZ A:LYS239 3.3 3.7 1.0
ND2 A:ASN439 3.4 4.5 1.0
OE1 A:GLU441 3.5 5.8 1.0
CE A:LYS239 3.8 7.5 1.0
CA A:SER435 3.8 2.0 1.0
CG A:ARG436 3.9 4.6 1.0
O A:HOH1012 4.0 13.4 1.0
C A:SER435 4.0 7.5 1.0
CB A:ARG436 4.0 6.1 1.0
CD A:GLU441 4.2 11.7 1.0
OG A:SER435 4.2 2.9 1.0
CA A:ARG436 4.2 4.7 1.0
CZ A:ARG235 4.3 11.4 1.0
OE2 A:GLU441 4.3 7.7 1.0
O A:THR434 4.4 4.5 1.0
CB A:SER435 4.6 5.5 1.0
CG A:ASN439 4.6 5.9 1.0
O A:HOH1242 4.6 29.6 1.0
NH2 A:ARG235 4.6 7.5 1.0
O A:HOH1005 4.7 27.1 1.0
O2B A:MGT602 4.7 16.6 1.0
NH1 A:ARG436 4.9 8.3 1.0
OD1 A:ASN439 4.9 6.1 1.0
CD A:ARG436 4.9 4.0 1.0
N A:SER435 5.0 5.3 1.0

Reference:

M.Smietanski, M.Werner, E.Purta, K.H.Kaminska, J.Stepinski, E.Darzynkiewicz, M.Nowotny, J.M.Bujnicki. Structural Analysis of Human 2'-O-Ribose Methyltransferases Involved in Mrna Cap Structure Formation. Nat Commun V. 5 3004 2014.
ISSN: ESSN 2041-1723
PubMed: 24402442
DOI: 10.1038/NCOMMS4004
Page generated: Sun Aug 17 20:44:14 2025

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