Sodium in PDB 2ygj: Methanobactin MB4

The structure of Methanobactin MB4, PDB code: 2ygj was solved by A.Ghazouani, A.Basle, S.J.Firbank, J.Gray, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 0.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	9.060, 13.320, 42.650, 90.00, 90.00, 90.00
R / Rfree (%)	8.6 / 10.9

The structure of Methanobactin MB4 also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Sodium atom in the Methanobactin MB4 (pdb code 2ygj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Methanobactin MB4, PDB code: 2ygj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Methanobactin MB4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Methanobactin MB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:5.7 occ:1.00 O A:MET6 2.3 5.7 1.0 O A:HOH2011 2.4 4.8 1.0 C A:MET6 3.4 4.8 1.0 CA A:MET6 3.8 4.7 1.0 OXT A:MET6 4.5 5.4 1.0 O A:ALA5 4.6 5.1 1.0 CB A:MET6 4.7 5.1 1.0 N A:MET6 4.9 4.4 1.0 O A:HOH2012 5.0 16.5 1.0

Sodium binding site 2 out of 2 in the Methanobactin MB4


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Methanobactin MB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:10.2 occ:1.00 O A:HOH2010 2.4 10.5 1.0 O A:HOH2013 2.7 5.2 0.3 OBZ A:HM84 2.7 9.8 1.0 SBV A:HM84 3.7 6.2 1.0 OBW A:HM84 3.8 5.1 1.0 O A:HOH2005 3.8 6.2 1.0 OBY A:HM84 4.0 6.5 1.0 O A:HOH2007 4.0 19.3 1.0 O A:HOH2009 4.6 14.1 1.0 CAW A:HM84 5.0 4.7 1.0 CAV A:HM84 5.0 4.3 1.0 OBX A:HM84 5.0 7.7 1.0

A.El Ghazouani, A.Basle, J.Gray, D.W.Graham, S.J.Firbank, C.Dennison. Variations in Methanobactin Structure Influences Copper Utilization By Methane-Oxidizing Bacteria. Proc.Natl.Acad.Sci.Usa V. 109 8400 2012.
ISSN: ISSN 0027-8424
PubMed: 22582172
DOI: 10.1073/PNAS.1112921109