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Copper in PDB 1yew: Crystal Structure of Particulate Methane Monooxygenase

Protein crystallography data

The structure of Crystal Structure of Particulate Methane Monooxygenase, PDB code: 1yew was solved by R.L.Lieberman, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 264.140, 264.140, 150.005, 90.00, 90.00, 90.00
R / Rfree (%) 27.2 / 30.2

Other elements in 1yew:

The structure of Crystal Structure of Particulate Methane Monooxygenase also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Particulate Methane Monooxygenase (pdb code 1yew). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of Particulate Methane Monooxygenase, PDB code: 1yew:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 1yew

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Copper binding site 1 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu4

b:61.6
occ:1.00
ND1 A:HIS48 1.9 70.3 1.0
ND1 A:HIS72 1.9 70.6 1.0
CE1 A:HIS48 2.8 70.8 1.0
CE1 A:HIS72 2.9 70.4 1.0
OE1 A:GLN404 3.0 75.2 1.0
CG A:HIS48 3.0 69.6 1.0
CG A:HIS72 3.0 69.5 1.0
CB A:HIS72 3.4 67.6 1.0
CB A:HIS48 3.4 68.8 1.0
CD A:GLN404 3.8 76.1 1.0
O A:HIS72 3.9 68.1 1.0
NE2 A:HIS48 3.9 71.6 1.0
CD2 A:LEU390 3.9 65.9 1.0
NE2 A:HIS72 4.0 71.8 1.0
CD2 A:HIS48 4.0 71.2 1.0
CD2 A:HIS72 4.1 71.8 1.0
C A:HIS72 4.2 67.9 1.0
CA A:PHE74 4.2 67.9 1.0
CA A:HIS72 4.4 67.8 1.0
N A:PHE74 4.4 67.9 1.0
CB A:PHE74 4.5 67.9 1.0
NE2 A:GLN404 4.5 77.8 1.0
N A:HIS48 4.5 69.3 1.0
CA A:HIS48 4.6 69.2 1.0
CD2 A:PHE74 4.6 68.7 1.0
CG A:LEU390 4.7 67.4 1.0
CD1 A:LEU390 4.7 65.2 1.0
CG A:GLN404 4.7 72.3 1.0
OE1 A:GLU75 4.8 74.7 1.0
C A:VAL73 4.8 67.7 1.0
N A:VAL73 5.0 67.5 1.0

Copper binding site 2 out of 9 in 1yew

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Copper binding site 2 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3

b:74.5
occ:1.00
CU1 A:CUA3 0.0 74.5 1.0
ND1 A:HIS33 1.9 71.3 1.0
N A:HIS33 2.2 71.9 1.0
NE2 A:HIS139 2.4 71.5 1.0
CU2 A:CUA3 2.6 82.9 1.0
CG A:HIS33 2.6 72.0 1.0
CB A:HIS33 2.8 72.1 1.0
CA A:HIS33 3.0 72.0 1.0
CE1 A:HIS33 3.0 72.5 1.0
CD2 A:HIS139 3.1 71.2 1.0
ND1 A:HIS137 3.4 75.8 1.0
CE1 A:HIS139 3.5 72.5 1.0
CD2 A:HIS33 3.8 72.5 1.0
CB A:HIS137 3.9 69.3 1.0
O A:HIS33 3.9 71.2 1.0
C A:HIS33 3.9 71.7 1.0
NE2 A:HIS33 4.0 73.7 1.0
O A:HIS137 4.0 68.9 1.0
CG A:HIS137 4.1 71.8 1.0
CG A:HIS139 4.4 69.7 1.0
ND1 A:HIS139 4.5 70.1 1.0
CE1 A:HIS137 4.5 75.1 1.0
C A:HIS137 4.7 68.8 1.0
OE2 A:GLU35 4.8 78.0 1.0
CA A:HIS137 4.9 69.1 1.0

Copper binding site 3 out of 9 in 1yew

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Copper binding site 3 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu3

b:82.9
occ:1.00
CU2 A:CUA3 0.0 82.9 1.0
ND1 A:HIS137 1.8 75.8 1.0
NE2 A:HIS139 2.2 71.5 1.0
CE1 A:HIS137 2.3 75.1 1.0
CE1 A:HIS139 2.5 72.5 1.0
CU1 A:CUA3 2.6 74.5 1.0
CG A:HIS137 2.9 71.8 1.0
ND1 A:HIS33 3.2 71.3 1.0
N A:HIS33 3.2 71.9 1.0
CD2 A:HIS139 3.4 71.2 1.0
NE2 A:HIS137 3.4 73.9 1.0
ND1 A:HIS139 3.6 70.1 1.0
CE1 A:HIS33 3.7 72.5 1.0
CB A:HIS137 3.7 69.3 1.0
CA A:GLY154 3.7 69.2 1.0
CD2 A:HIS137 3.7 73.6 1.0
CG A:HIS139 4.1 69.7 1.0
OE1 A:GLU35 4.2 78.2 1.0
C A:GLY154 4.3 69.3 1.0
N A:GLY154 4.3 69.0 1.0
CG A:HIS33 4.4 72.0 1.0
O A:HIS137 4.5 68.9 1.0
O A:GLY154 4.6 69.8 1.0
CA A:HIS33 4.6 72.0 1.0
C A:HIS137 4.6 68.8 1.0
CA A:HIS137 4.7 69.1 1.0
OE2 A:GLU35 4.9 78.0 1.0
CB A:HIS33 4.9 72.1 1.0
NE2 A:HIS33 5.0 73.7 1.0
OH A:TYR374 5.0 71.8 1.0
CD A:GLU35 5.0 77.5 1.0

Copper binding site 4 out of 9 in 1yew

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Copper binding site 4 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:61.6
occ:1.00
ND1 E:HIS72 1.8 70.2 1.0
ND1 E:HIS48 1.9 70.2 1.0
CG E:HIS72 2.8 69.4 1.0
CE1 E:HIS72 2.8 70.2 1.0
CE1 E:HIS48 2.8 71.0 1.0
OE1 E:GLN404 2.9 75.1 1.0
CG E:HIS48 3.1 69.5 1.0
CB E:HIS72 3.2 68.0 1.0
CB E:HIS48 3.5 69.1 1.0
O E:HIS72 3.8 68.2 1.0
CD E:GLN404 3.8 76.0 1.0
CD2 E:LEU390 3.9 65.8 1.0
NE2 E:HIS72 3.9 71.2 1.0
CD2 E:HIS72 3.9 71.8 1.0
NE2 E:HIS48 4.0 72.0 1.0
C E:HIS72 4.1 68.0 1.0
CD2 E:HIS48 4.1 71.0 1.0
CA E:HIS72 4.3 68.0 1.0
CA E:PHE74 4.3 68.1 1.0
N E:PHE74 4.5 68.0 1.0
NE2 E:GLN404 4.5 77.7 1.0
N E:HIS48 4.6 69.4 1.0
CB E:PHE74 4.6 68.1 1.0
CA E:HIS48 4.7 69.5 1.0
CG E:GLN404 4.7 72.2 1.0
CG E:LEU390 4.7 67.2 1.0
C E:VAL73 4.8 67.5 1.0
CD2 E:PHE74 4.8 68.6 1.0
OE1 E:GLU75 4.8 74.8 1.0
N E:VAL73 4.9 67.3 1.0
CD1 E:LEU390 4.9 65.3 1.0
CB E:GLN404 4.9 70.3 1.0

Copper binding site 5 out of 9 in 1yew

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Copper binding site 5 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu500

b:75.0
occ:1.00
CU1 E:CUA500 0.0 75.0 1.0
ND1 E:HIS33 1.8 71.5 1.0
N E:HIS33 2.1 72.0 1.0
NE2 E:HIS139 2.3 71.5 1.0
CU2 E:CUA500 2.6 83.0 1.0
CG E:HIS33 2.7 72.1 1.0
CE1 E:HIS33 2.9 72.4 1.0
CB E:HIS33 3.0 72.2 1.0
CA E:HIS33 3.0 72.1 1.0
CD2 E:HIS139 3.2 70.9 1.0
ND1 E:HIS137 3.2 75.4 1.0
CE1 E:HIS139 3.4 72.5 1.0
CB E:HIS137 3.7 69.1 1.0
CD2 E:HIS33 3.8 72.8 1.0
NE2 E:HIS33 3.9 73.9 1.0
CG E:HIS137 3.9 71.5 1.0
O E:HIS33 4.0 71.0 1.0
C E:HIS33 4.0 71.5 1.0
O E:HIS137 4.1 68.7 1.0
CE1 E:HIS137 4.3 75.3 1.0
CG E:HIS139 4.4 69.5 1.0
ND1 E:HIS139 4.5 70.0 1.0
OE2 E:GLU35 4.7 78.2 1.0
C E:HIS137 4.8 68.5 1.0
CA E:HIS137 4.9 69.0 1.0

Copper binding site 6 out of 9 in 1yew

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Copper binding site 6 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu500

b:83.0
occ:1.00
CU2 E:CUA500 0.0 83.0 1.0
ND1 E:HIS137 1.8 75.4 1.0
NE2 E:HIS139 2.1 71.5 1.0
CE1 E:HIS137 2.3 75.3 1.0
CE1 E:HIS139 2.5 72.5 1.0
CU1 E:CUA500 2.6 75.0 1.0
CG E:HIS137 2.7 71.5 1.0
CD2 E:HIS139 3.1 70.9 1.0
NE2 E:HIS137 3.3 73.8 1.0
CA E:GLY154 3.4 69.2 1.0
CD2 E:HIS137 3.5 73.5 1.0
CB E:HIS137 3.5 69.1 1.0
ND1 E:HIS33 3.5 71.5 1.0
ND1 E:HIS139 3.5 70.0 1.0
N E:HIS33 3.5 72.0 1.0
CG E:HIS139 3.8 69.5 1.0
CE1 E:HIS33 3.9 72.4 1.0
C E:GLY154 4.0 69.5 1.0
N E:GLY154 4.2 68.8 1.0
O E:GLY154 4.3 70.0 1.0
O E:HIS137 4.4 68.7 1.0
OE1 E:GLU35 4.4 78.2 1.0
C E:HIS137 4.4 68.5 1.0
CA E:HIS137 4.5 69.0 1.0
CG E:HIS33 4.8 72.1 1.0
N E:LYS155 4.8 69.3 1.0
CA E:HIS33 4.9 72.1 1.0
N E:VAL138 5.0 67.9 1.0

Copper binding site 7 out of 9 in 1yew

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Copper binding site 7 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu601

b:61.4
occ:1.00
ND1 I:HIS48 1.9 70.2 1.0
ND1 I:HIS72 2.1 70.5 1.0
CE1 I:HIS48 2.7 70.9 1.0
OE1 I:GLN404 2.9 75.5 1.0
CE1 I:HIS72 3.0 70.3 1.0
CG I:HIS48 3.0 69.6 1.0
CG I:HIS72 3.1 69.6 1.0
CB I:HIS72 3.4 68.2 1.0
CB I:HIS48 3.5 69.1 1.0
CD2 I:LEU390 3.7 65.6 1.0
CD I:GLN404 3.8 76.2 1.0
NE2 I:HIS48 3.9 71.8 1.0
CD2 I:HIS48 4.1 71.1 1.0
NE2 I:HIS72 4.1 71.5 1.0
O I:HIS72 4.1 67.8 1.0
CD2 I:HIS72 4.2 71.5 1.0
CA I:PHE74 4.3 68.1 1.0
C I:HIS72 4.3 68.0 1.0
CA I:HIS72 4.5 68.1 1.0
N I:HIS48 4.5 69.3 1.0
CB I:PHE74 4.6 67.9 1.0
N I:PHE74 4.6 67.9 1.0
CG I:GLN404 4.6 72.4 1.0
NE2 I:GLN404 4.6 77.9 1.0
CD2 I:PHE74 4.6 68.7 1.0
CA I:HIS48 4.6 69.4 1.0
CG I:LEU390 4.6 67.0 1.0
OE1 I:GLU75 4.8 74.7 1.0
CD1 I:LEU390 4.8 65.5 1.0
C I:VAL73 4.9 67.6 1.0
CB I:GLN404 4.9 70.4 1.0

Copper binding site 8 out of 9 in 1yew

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Copper binding site 8 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu600

b:76.1
occ:1.00
CU1 I:CUA600 0.0 76.1 1.0
ND1 I:HIS33 1.8 71.4 1.0
N I:HIS33 2.1 72.0 1.0
NE2 I:HIS139 2.5 71.6 1.0
CG I:HIS33 2.6 72.2 1.0
CU2 I:CUA600 2.6 82.2 1.0
CB I:HIS33 2.8 72.1 1.0
CA I:HIS33 2.9 72.2 1.0
CE1 I:HIS33 2.9 72.2 1.0
CD2 I:HIS139 3.3 71.0 1.0
ND1 I:HIS137 3.3 75.4 1.0
CE1 I:HIS139 3.6 72.4 1.0
CD2 I:HIS33 3.8 72.5 1.0
NE2 I:HIS33 3.9 73.5 1.0
C I:HIS33 3.9 71.9 1.0
O I:HIS33 3.9 71.5 1.0
CB I:HIS137 3.9 69.2 1.0
CG I:HIS137 4.0 72.0 1.0
O I:HIS137 4.2 68.8 1.0
CE1 I:HIS137 4.4 75.0 1.0
CG I:HIS139 4.5 69.4 1.0
ND1 I:HIS139 4.6 69.8 1.0
OE2 I:GLU35 4.6 78.2 1.0
C I:HIS137 4.9 68.7 1.0

Copper binding site 9 out of 9 in 1yew

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Copper binding site 9 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu600

b:82.2
occ:1.00
CU2 I:CUA600 0.0 82.2 1.0
ND1 I:HIS137 1.8 75.4 1.0
NE2 I:HIS139 2.1 71.6 1.0
CE1 I:HIS137 2.4 75.0 1.0
CE1 I:HIS139 2.5 72.4 1.0
CU1 I:CUA600 2.6 76.1 1.0
CG I:HIS137 2.8 72.0 1.0
CD2 I:HIS139 3.1 71.0 1.0
NE2 I:HIS137 3.3 74.0 1.0
ND1 I:HIS33 3.4 71.4 1.0
CD2 I:HIS137 3.5 74.0 1.0
N I:HIS33 3.5 72.0 1.0
CB I:HIS137 3.5 69.2 1.0
ND1 I:HIS139 3.6 69.8 1.0
CA I:GLY154 3.6 69.2 1.0
CE1 I:HIS33 3.9 72.2 1.0
CG I:HIS139 3.9 69.4 1.0
C I:GLY154 4.2 69.2 1.0
N I:GLY154 4.3 69.3 1.0
O I:HIS137 4.3 68.8 1.0
OE1 I:GLU35 4.3 78.2 1.0
C I:HIS137 4.4 68.7 1.0
CA I:HIS137 4.5 68.9 1.0
O I:GLY154 4.5 69.7 1.0
CG I:HIS33 4.7 72.2 1.0
CA I:HIS33 4.9 72.2 1.0
N I:LYS155 4.9 69.2 1.0
N I:VAL138 5.0 68.1 1.0

Reference:

R.L.Lieberman, A.C.Rosenzweig. Crystal Structure of A Membrane-Bound Metalloenzyme That Catalyses the Biological Oxidation of Methane. Nature V. 434 177 2005.
ISSN: ISSN 0028-0836
PubMed: 15674245
DOI: 10.1038/NATURE03311
Page generated: Sun Dec 13 11:03:07 2020

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