Copper in PDB 2ygi: Methanobactin HM1

The structure of Methanobactin HM1, PDB code: 2ygi 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)	30.00 / 0.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	9.072, 22.535, 23.572, 64.79, 86.06, 91.77
R / Rfree (%)	6.5 / 8.9

The binding sites of Copper atom in the Methanobactin HM1 (pdb code 2ygi). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Methanobactin HM1, PDB code: 2ygi:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Methanobactin HM1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Methanobactin HM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu7 b:1.7 occ:1.00 NBA A:HM84 2.1 1.5 1.0 NAB A:HM71 2.1 1.5 1.0 SAE A:HM71 2.2 2.0 1.0 SBG A:HM84 2.3 1.9 1.0 CAB A:HM84 2.9 1.4 1.0 CA A:HM71 2.9 1.6 1.0 C A:HM71 3.0 2.0 1.0 C A:HM84 3.0 1.5 1.0 CAA A:HM71 3.0 1.4 1.0 CAZ A:HM84 3.2 1.6 1.0 CBR A:HM71 3.2 1.8 1.0 N A:HM84 3.8 1.6 1.0 CAA A:HM84 3.8 1.5 1.0 CBS A:HM71 3.9 2.4 1.0 CAV A:HM84 4.1 1.8 1.0 O B:HOH2006 4.2 5.6 1.0 CBC A:HM84 4.2 1.7 1.0 N A:ALA2 4.3 2.2 1.0 OBB A:HM84 4.3 1.8 1.0 N A:ALA5 4.3 1.7 1.0 CAF A:HM71 4.3 1.5 1.0 CAI A:HM71 4.4 1.8 1.0 SBT A:HM71 4.7 2.1 0.6 CAW A:HM84 4.7 2.2 1.0 O A:HOH2004 4.8 9.1 1.0 NAH A:HM71 4.8 1.8 1.0 CB B:ALA6 4.8 6.1 1.0 N A:SER3 4.9 2.2 1.0

Copper binding site 2 out of 4 in the Methanobactin HM1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Methanobactin HM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu7 b:2.0 occ:1.00 NBA B:HM84 2.1 2.0 1.0 NAB B:HM71 2.1 2.0 1.0 SAE B:HM71 2.3 2.4 1.0 SBG B:HM84 2.3 1.8 1.0 CAB B:HM84 2.9 1.9 1.0 CA B:HM71 3.0 2.2 1.0 C B:HM71 3.0 2.0 1.0 CAA B:HM71 3.0 2.4 1.0 C B:HM84 3.0 1.6 1.0 CAZ B:HM84 3.2 1.6 1.0 CBR B:HM71 3.2 2.6 1.0 N B:HM84 3.7 2.0 1.0 CAA B:HM84 3.8 2.0 1.0 CBS B:HM71 3.8 2.6 1.0 CAV B:HM84 4.0 2.6 1.0 O D:HOH2002 4.1 6.0 1.0 CBC B:HM84 4.2 1.5 1.0 OBB B:HM84 4.3 1.9 1.0 N B:ALA2 4.3 2.9 1.0 CAF B:HM71 4.3 2.2 1.0 N B:ALA5 4.3 1.9 1.0 CAI B:HM71 4.4 2.6 1.0 O B:HOH2002 4.6 6.6 1.0 CAW B:HM84 4.6 3.5 1.0 CB D:ALA6 4.7 6.9 1.0 SBT B:HM71 4.8 2.7 1.0 NAH B:HM71 4.8 2.4 1.0 N B:SER3 4.9 2.5 1.0 C B:SER3 5.0 2.1 1.0

Copper binding site 3 out of 4 in the Methanobactin HM1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Methanobactin HM1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu7 b:2.5 occ:1.00 NBA C:HM84 2.1 2.0 1.0 NAB C:HM71 2.1 2.7 1.0 SAE C:HM71 2.3 3.1 1.0 SBG C:HM84 2.3 2.5 1.0 CAB C:HM84 2.9 2.2 1.0 CA C:HM71 3.0 2.8 1.0 C C:HM71 3.0 3.1 1.0 C C:HM84 3.0 2.2 1.0 CAA C:HM71 3.0 3.2 1.0 CAZ C:HM84 3.2 5.0 1.0 CBR C:HM71 3.2 3.5 1.0 N C:HM84 3.7 2.7 1.0 CAA C:HM84 3.8 2.8 1.0 CBS C:HM71 3.8 4.0 1.0 CAV C:HM84 3.9 3.7 1.0 CB A:ALA6 4.0 2.0 0.2 CBC C:HM84 4.2 2.6 1.0 OBB C:HM84 4.3 2.8 1.0 N C:ALA2 4.3 3.6 1.0 N C:ALA5 4.3 2.4 1.0 CAF C:HM71 4.3 3.0 1.0 CAI C:HM71 4.4 3.0 1.0 O A:HOH2009 4.4 6.2 1.0 CAW C:HM84 4.6 4.2 1.0 CB A:ALA6 4.6 12.3 0.8 O A:HOH2010 4.7 6.2 1.0 SBT C:HM71 4.7 3.3 1.0 NAH C:HM71 4.8 3.0 1.0 N C:SER3 4.9 3.0 1.0 C C:SER3 4.9 3.3 1.0 C C:ALA2 5.0 3.2 1.0

Copper binding site 4 out of 4 in the Methanobactin HM1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Methanobactin HM1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu7 b:1.7 occ:1.00 NBA D:HM84 2.1 1.7 1.0 NAB D:HM71 2.1 1.9 1.0 SAE D:HM71 2.2 2.2 1.0 SBG D:HM84 2.3 1.6 1.0 CAB D:HM84 2.9 1.5 1.0 CA D:HM71 2.9 1.8 1.0 C D:HM71 3.0 2.1 1.0 C D:HM84 3.0 1.3 1.0 CAA D:HM71 3.0 1.6 1.0 CAZ D:HM84 3.2 2.3 1.0 CBR D:HM71 3.2 1.6 1.0 N D:HM84 3.8 2.2 1.0 CBS D:HM71 3.8 1.8 1.0 CAA D:HM84 3.8 2.1 1.0 CAV D:HM84 4.0 2.1 1.0 CBC D:HM84 4.2 1.7 1.0 OBB D:HM84 4.3 2.4 1.0 N D:ALA2 4.3 3.1 1.0 N D:ALA5 4.3 1.5 1.0 CAF D:HM71 4.3 1.8 1.0 CAI D:HM71 4.4 1.7 1.0 CAW D:HM84 4.7 2.8 1.0 SBT D:HM71 4.8 2.5 1.0 NAH D:HM71 4.8 1.9 1.0 N D:SER3 4.9 3.1 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