Copper 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:

Sodium

(Na)

2 atoms

The binding sites of Copper atom in the Methanobactin MB4 (pdb code 2ygj). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the Methanobactin MB4, PDB code: 2ygj:

Copper binding site 1 out of 1 in the Methanobactin MB4


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Methanobactin MB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1007 b:4.0 occ:1.00 NAB A:HM91 2.0 3.9 1.0 NBA A:HM84 2.0 4.2 1.0 SAE A:HM91 2.3 4.2 1.0 SBG A:HM84 2.3 3.9 1.0 CAB A:HM84 2.9 4.4 1.0 CAC A:HM91 2.9 4.2 1.0 CAA A:HM91 3.0 3.8 1.0 C A:HM91 3.0 4.2 1.0 C A:HM84 3.0 4.0 1.0 CAZ A:HM84 3.1 4.1 1.0 CBW A:HM91 3.2 4.0 1.0 CAV A:HM84 3.8 4.3 1.0 CAA A:HM84 3.8 4.4 1.0 CBX A:HM91 3.8 4.1 1.0 N A:HM84 3.9 4.0 1.0 CBC A:HM84 4.2 4.8 1.0 OBB A:HM84 4.2 4.8 1.0 CAF A:HM91 4.2 4.2 1.0 CAW A:HM84 4.3 4.7 1.0 CAI A:HM91 4.3 4.2 1.0 N A:ALA2 4.3 4.4 1.0 N A:ALA5 4.3 5.2 1.0 CBY A:HM91 4.6 4.4 1.0 NAH A:HM91 4.7 4.2 1.0 NCC A:HM91 5.0 5.3 1.0 OBW A:HM84 5.0 5.1 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