Atomistry » Sodium » PDB 5npp-5o7v » 5o4h
Atomistry »
  Sodium »
    PDB 5npp-5o7v »
      5o4h »

Sodium in PDB 5o4h: Hcgc From Methanococcus Maripaludis Cocrystallized with Sam and Pyridinol

Protein crystallography data

The structure of Hcgc From Methanococcus Maripaludis Cocrystallized with Sam and Pyridinol, PDB code: 5o4h was solved by T.Wagner, L.Bai, T.Xu, X.Hu, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.85 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.168, 77.736, 100.991, 90.00, 110.87, 90.00
R / Rfree (%) 16.8 / 19.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Hcgc From Methanococcus Maripaludis Cocrystallized with Sam and Pyridinol (pdb code 5o4h). 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 Hcgc From Methanococcus Maripaludis Cocrystallized with Sam and Pyridinol, PDB code: 5o4h:

Sodium binding site 1 out of 1 in 5o4h

Go back to Sodium Binding Sites List in 5o4h
Sodium binding site 1 out of 1 in the Hcgc From Methanococcus Maripaludis Cocrystallized with Sam and Pyridinol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hcgc From Methanococcus Maripaludis Cocrystallized with Sam and Pyridinol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:32.2
occ:1.00
O D:ASP148 2.6 27.6 1.0
O D:SER145 2.8 28.5 1.0
O D:LYS146 3.0 40.5 1.0
C D:LYS146 3.5 38.5 1.0
O D:HOH510 3.6 45.6 1.0
C D:ASP148 3.7 27.7 1.0
CA D:LYS146 3.9 32.8 1.0
C D:SER145 3.9 31.6 1.0
N D:ASP148 4.1 27.7 1.0
O D:HOH512 4.3 54.0 1.0
N D:LYS146 4.3 30.6 1.0
CA D:ASP148 4.4 26.4 1.0
N D:ILE147 4.5 35.1 1.0
O D:HOH564 4.5 35.5 1.0
C D:ILE147 4.6 34.0 1.0
CB D:ASP148 4.7 27.0 1.0
N D:ASN149 4.8 24.7 1.0
CA D:ILE147 5.0 34.8 1.0

Reference:

L.Bai, T.Wagner, T.Xu, X.Hu, U.Ermler, S.Shima. A Water-Bridged H-Bonding Network Contributes to the Catalysis of the Sam-Dependent C-Methyltransferase Hcgc. Angew. Chem. Int. Ed. Engl. V. 56 10806 2017.
ISSN: ESSN 1521-3773
PubMed: 28682478
DOI: 10.1002/ANIE.201705605
Page generated: Mon Oct 7 23:05:49 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy