Atomistry » Copper » PDB 1x9r-2ahl » 1yew
Atomistry »
  Copper »
    PDB 1x9r-2ahl »
      1yew »

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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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

Go back to Copper Binding Sites List in 1yew
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: Tue Jul 30 23:03:54 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy