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Copper in PDB 2ygi: Methanobactin HM1

Protein crystallography data

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

Copper Binding Sites:

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 2ygi

Go back to Copper Binding Sites List in 2ygi
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 2ygi

Go back to Copper Binding Sites List in 2ygi
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 2ygi

Go back to Copper Binding Sites List in 2ygi
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 2ygi

Go back to Copper Binding Sites List in 2ygi
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

Reference:

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
Page generated: Wed Oct 28 14:22:39 2020
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