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Copper in PDB 8oyi: Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound

Enzymatic activity of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound

All present enzymatic activity of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound:
1.14.18.3;

Other elements in 8oyi:

The structure of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Copper Binding Sites:

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

Copper binding site 1 out of 9 in 8oyi

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Copper binding site 1 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:53.6
occ:1.00
 ND1 A:HIS33 2.0 49.3 1.0
NE2 A:HIS139 2.1 37.0 1.0
ND1 A:HIS137 2.3 37.0 1.0
N A:HIS33 2.5 49.3 1.0
CG A:HIS33 2.9 49.3 1.0
CD2 A:HIS139 2.9 37.0 1.0
CE1 A:HIS33 3.0 49.3 1.0
CA A:HIS33 3.0 49.3 1.0
CB A:HIS33 3.1 49.3 1.0
CE1 A:HIS139 3.2 37.0 1.0
CG A:HIS137 3.2 37.0 1.0
CE1 A:HIS137 3.4 37.0 1.0
CB A:HIS137 3.4 37.0 1.0
O A:HOH649 3.6 38.4 1.0
O A:HOH638 3.8 38.4 1.0
CD2 A:HIS33 4.0 49.3 1.0
NE2 A:HIS33 4.0 49.3 1.0
CG A:HIS139 4.1 37.0 1.0
O A:HIS137 4.1 37.0 1.0
ND1 A:HIS139 4.2 37.0 1.0
CD2 A:HIS137 4.4 37.0 1.0
NE2 A:HIS137 4.4 37.0 1.0
C A:HIS33 4.5 49.3 1.0
C A:HIS137 4.6 37.0 1.0
CA A:HIS137 4.6 37.0 1.0
N A:GLY34 4.9 43.1 1.0
OE1 A:GLU35 4.9 43.7 1.0

Copper binding site 2 out of 9 in 8oyi

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Copper binding site 2 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:56.2
occ:1.00
 ND1 A:HIS72 2.1 37.0 1.0
ND1 A:HIS48 2.1 37.4 1.0
OE1 A:GLN404 2.4 43.9 1.0
CE1 A:HIS48 2.8 37.4 1.0
CG A:HIS48 3.0 37.4 1.0
CE1 A:HIS72 3.0 37.0 1.0
CG A:HIS72 3.1 37.0 1.0
O A:HIS72 3.4 37.0 1.0
CB A:HIS72 3.4 37.0 1.0
CB A:HIS48 3.5 37.4 1.0
CD A:GLN404 3.6 43.9 1.0
C A:HIS72 3.9 37.0 1.0
NE2 A:HIS48 3.9 37.4 1.0
CD2 A:HIS48 4.0 37.4 1.0
CA A:PHE74 4.0 38.1 1.0
CD2 A:LEU390 4.1 40.9 1.0
N A:PHE74 4.1 38.1 1.0
NE2 A:HIS72 4.1 37.0 1.0
CD2 A:HIS72 4.2 37.0 1.0
CB A:PHE74 4.2 38.1 1.0
N A:HIS48 4.2 37.4 1.0
CA A:HIS72 4.2 37.0 1.0
NE2 A:GLN404 4.3 43.9 1.0
CD1 A:PHE74 4.4 38.1 1.0
C A:VAL73 4.4 37.2 1.0
CA A:HIS48 4.5 37.4 1.0
N A:VAL73 4.6 37.2 1.0
O A:VAL73 4.6 37.2 1.0
CG A:GLN404 4.7 43.9 1.0
CG A:LEU390 4.7 40.9 1.0
CG A:PHE74 4.8 38.1 1.0
CD1 A:LEU390 5.0 40.9 1.0
N A:HIS72 5.0 37.0 1.0

Copper binding site 3 out of 9 in 8oyi

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Copper binding site 3 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu301

b:91.1
occ:1.00
 NE2 C:HIS245 2.0 36.6 1.0
NE2 C:HIS231 2.0 38.8 1.0
HO C:ETF310 2.0 0.5 1.0
O C:ETF310 2.3 0.5 1.0
OD1 C:ASN227 2.3 37.5 1.0
CD2 C:HIS231 2.9 38.8 1.0
CE1 C:HIS231 2.9 38.8 1.0
CE1 C:HIS245 3.0 36.6 1.0
CD2 C:HIS245 3.0 36.6 1.0
O C:HOH401 3.0 30.0 1.0
CG C:ASN227 3.2 37.5 1.0
ND2 C:ASN227 3.5 37.5 1.0
C2 C:ETF310 3.6 0.5 1.0
CD1 C:LEU244 3.8 38.1 1.0
ND1 C:HIS231 4.0 38.8 1.0
H22 C:ETF310 4.0 0.5 1.0
CG C:HIS231 4.0 38.8 1.0
ND1 C:HIS245 4.0 36.6 1.0
CG C:HIS245 4.1 36.6 1.0
H21 C:ETF310 4.2 0.5 1.0
NH2 C:ARG165 4.2 41.7 1.0
F2 C:ETF310 4.3 0.5 1.0
C1 C:ETF310 4.4 0.5 1.0
CG C:LEU244 4.5 38.1 1.0
F3 C:ETF310 4.5 0.5 1.0
CB C:ASN227 4.6 37.5 1.0
CD2 C:LEU244 4.7 38.1 1.0
CZ C:ARG165 5.0 41.7 1.0

Copper binding site 4 out of 9 in 8oyi

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Copper binding site 4 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:53.6
occ:1.00
 ND1 E:HIS33 2.0 49.3 1.0
NE2 E:HIS139 2.1 37.0 1.0
ND1 E:HIS137 2.3 37.0 1.0
N E:HIS33 2.5 49.3 1.0
CG E:HIS33 2.9 49.3 1.0
CD2 E:HIS139 2.9 37.0 1.0
CE1 E:HIS33 3.0 49.3 1.0
CA E:HIS33 3.0 49.3 1.0
CB E:HIS33 3.1 49.3 1.0
CE1 E:HIS139 3.2 37.0 1.0
CG E:HIS137 3.2 37.0 1.0
CE1 E:HIS137 3.3 37.0 1.0
CB E:HIS137 3.4 37.0 1.0
O E:HOH638 3.6 38.4 1.0
O E:HOH639 3.8 38.4 1.0
CD2 E:HIS33 4.0 49.3 1.0
NE2 E:HIS33 4.0 49.3 1.0
CG E:HIS139 4.1 37.0 1.0
O E:HIS137 4.1 37.0 1.0
ND1 E:HIS139 4.2 37.0 1.0
CD2 E:HIS137 4.4 37.0 1.0
NE2 E:HIS137 4.4 37.0 1.0
C E:HIS33 4.5 49.3 1.0
O E:HOH669 4.5 38.4 1.0
C E:HIS137 4.6 37.0 1.0
CA E:HIS137 4.6 37.0 1.0
N E:GLY34 4.9 43.1 1.0
OE1 E:GLU35 4.9 43.7 1.0

Copper binding site 5 out of 9 in 8oyi

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Copper binding site 5 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu503

b:56.2
occ:1.00
 ND1 E:HIS72 2.1 37.0 1.0
ND1 E:HIS48 2.1 37.4 1.0
OE1 E:GLN404 2.4 43.9 1.0
CE1 E:HIS48 2.8 37.4 1.0
CG E:HIS48 3.0 37.4 1.0
CE1 E:HIS72 3.0 37.0 1.0
CG E:HIS72 3.1 37.0 1.0
O E:HIS72 3.4 37.0 1.0
CB E:HIS72 3.4 37.0 1.0
CB E:HIS48 3.5 37.4 1.0
CD E:GLN404 3.6 43.9 1.0
C E:HIS72 3.9 37.0 1.0
NE2 E:HIS48 3.9 37.4 1.0
CD2 E:HIS48 4.0 37.4 1.0
CA E:PHE74 4.0 38.1 1.0
CD2 E:LEU390 4.1 40.9 1.0
N E:PHE74 4.1 38.1 1.0
NE2 E:HIS72 4.1 37.0 1.0
CD2 E:HIS72 4.2 37.0 1.0
CB E:PHE74 4.2 38.1 1.0
N E:HIS48 4.2 37.4 1.0
CA E:HIS72 4.2 37.0 1.0
NE2 E:GLN404 4.3 43.9 1.0
CD1 E:PHE74 4.4 38.1 1.0
C E:VAL73 4.4 37.2 1.0
CA E:HIS48 4.5 37.4 1.0
N E:VAL73 4.6 37.2 1.0
O E:VAL73 4.6 37.2 1.0
CG E:GLN404 4.7 43.9 1.0
CG E:LEU390 4.7 40.9 1.0
CG E:PHE74 4.8 38.1 1.0
CD1 E:LEU390 5.0 40.9 1.0
N E:HIS72 5.0 37.0 1.0

Copper binding site 6 out of 9 in 8oyi

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Copper binding site 6 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu502

b:53.6
occ:1.00
 ND1 I:HIS33 2.0 49.3 1.0
NE2 I:HIS139 2.1 37.0 1.0
ND1 I:HIS137 2.3 37.0 1.0
N I:HIS33 2.5 49.3 1.0
CG I:HIS33 2.9 49.3 1.0
CD2 I:HIS139 2.9 37.0 1.0
CE1 I:HIS33 3.0 49.3 1.0
CA I:HIS33 3.0 49.3 1.0
CB I:HIS33 3.1 49.3 1.0
CE1 I:HIS139 3.2 37.0 1.0
CG I:HIS137 3.2 37.0 1.0
CE1 I:HIS137 3.4 37.0 1.0
CB I:HIS137 3.4 37.0 1.0
O I:HOH640 3.5 38.4 1.0
O I:HOH639 3.8 38.4 1.0
CD2 I:HIS33 4.0 49.3 1.0
NE2 I:HIS33 4.0 49.3 1.0
CG I:HIS139 4.1 37.0 1.0
O I:HIS137 4.1 37.0 1.0
ND1 I:HIS139 4.2 37.0 1.0
CD2 I:HIS137 4.4 37.0 1.0
NE2 I:HIS137 4.4 37.0 1.0
C I:HIS33 4.5 49.3 1.0
C I:HIS137 4.6 37.0 1.0
CA I:HIS137 4.6 37.0 1.0
N I:GLY34 4.9 43.1 1.0
OE1 I:GLU35 4.9 43.7 1.0

Copper binding site 7 out of 9 in 8oyi

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Copper binding site 7 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu503

b:56.2
occ:1.00
 ND1 I:HIS72 2.1 37.0 1.0
ND1 I:HIS48 2.1 37.4 1.0
OE1 I:GLN404 2.4 43.9 1.0
CE1 I:HIS48 2.8 37.4 1.0
CG I:HIS48 3.0 37.4 1.0
CE1 I:HIS72 3.0 37.0 1.0
CG I:HIS72 3.1 37.0 1.0
O I:HIS72 3.4 37.0 1.0
CB I:HIS72 3.4 37.0 1.0
CB I:HIS48 3.5 37.4 1.0
CD I:GLN404 3.6 43.9 1.0
C I:HIS72 3.9 37.0 1.0
NE2 I:HIS48 3.9 37.4 1.0
CD2 I:HIS48 4.0 37.4 1.0
CA I:PHE74 4.0 38.1 1.0
CD2 I:LEU390 4.1 40.9 1.0
N I:PHE74 4.1 38.1 1.0
NE2 I:HIS72 4.1 37.0 1.0
CD2 I:HIS72 4.2 37.0 1.0
CB I:PHE74 4.2 38.1 1.0
N I:HIS48 4.2 37.4 1.0
CA I:HIS72 4.2 37.0 1.0
NE2 I:GLN404 4.3 43.9 1.0
CD1 I:PHE74 4.4 38.1 1.0
C I:VAL73 4.4 37.2 1.0
CA I:HIS48 4.5 37.4 1.0
N I:VAL73 4.6 37.2 1.0
O I:VAL73 4.6 37.2 1.0
CG I:GLN404 4.7 43.9 1.0
CG I:LEU390 4.7 40.9 1.0
CG I:PHE74 4.8 38.1 1.0
CD1 I:LEU390 5.0 40.9 1.0
N I:HIS72 5.0 37.0 1.0

Copper binding site 8 out of 9 in 8oyi

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Copper binding site 8 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu301

b:91.1
occ:1.00
 NE2 G:HIS245 2.0 36.6 1.0
NE2 G:HIS231 2.0 38.8 1.0
HO G:ETF310 2.0 0.5 1.0
O G:ETF310 2.3 0.5 1.0
OD1 G:ASN227 2.3 37.5 1.0
CD2 G:HIS231 2.9 38.8 1.0
CE1 G:HIS231 2.9 38.8 1.0
CE1 G:HIS245 3.0 36.6 1.0
CD2 G:HIS245 3.0 36.6 1.0
O G:HOH401 3.0 30.0 1.0
CG G:ASN227 3.2 37.5 1.0
ND2 G:ASN227 3.5 37.5 1.0
C2 G:ETF310 3.6 0.5 1.0
CD1 G:LEU244 3.8 38.1 1.0
ND1 G:HIS231 4.0 38.8 1.0
H22 G:ETF310 4.0 0.5 1.0
CG G:HIS231 4.0 38.8 1.0
ND1 G:HIS245 4.0 36.6 1.0
CG G:HIS245 4.1 36.6 1.0
H21 G:ETF310 4.2 0.5 1.0
NH2 G:ARG165 4.2 41.7 1.0
F2 G:ETF310 4.3 0.5 1.0
C1 G:ETF310 4.4 0.5 1.0
CG G:LEU244 4.5 38.1 1.0
F3 G:ETF310 4.5 0.5 1.0
CB G:ASN227 4.6 37.5 1.0
CD2 G:LEU244 4.7 38.1 1.0
CZ G:ARG165 5.0 41.7 1.0

Copper binding site 9 out of 9 in 8oyi

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Copper binding site 9 out of 9 in the Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Particulate Methane Monooxygenase with 2,2,2-Trifluoroethanol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu301

b:91.1
occ:1.00
 NE2 K:HIS245 2.0 36.6 1.0
NE2 K:HIS231 2.0 38.8 1.0
HO K:ETF310 2.0 0.5 1.0
O K:ETF310 2.3 0.5 1.0
OD1 K:ASN227 2.3 37.5 1.0
CD2 K:HIS231 2.9 38.8 1.0
CE1 K:HIS231 2.9 38.8 1.0
CE1 K:HIS245 3.0 36.6 1.0
CD2 K:HIS245 3.0 36.6 1.0
O K:HOH401 3.0 30.0 1.0
CG K:ASN227 3.2 37.5 1.0
ND2 K:ASN227 3.5 37.5 1.0
C2 K:ETF310 3.6 0.5 1.0
CD1 K:LEU244 3.8 38.1 1.0
ND1 K:HIS231 4.0 38.8 1.0
H22 K:ETF310 4.0 0.5 1.0
CG K:HIS231 4.0 38.8 1.0
ND1 K:HIS245 4.0 36.6 1.0
CG K:HIS245 4.1 36.6 1.0
H21 K:ETF310 4.2 0.5 1.0
NH2 K:ARG165 4.2 41.7 1.0
F2 K:ETF310 4.3 0.5 1.0
C1 K:ETF310 4.4 0.5 1.0
CG K:LEU244 4.5 38.1 1.0
F3 K:ETF310 4.5 0.5 1.0
CB K:ASN227 4.6 37.5 1.0
CD2 K:LEU244 4.7 38.1 1.0
CZ K:ARG165 5.0 41.7 1.0

Reference:

F.J.Tucci, A.C.Rosenzweig. Product Analogue Binding Identifies the Copper Active Site of Particulate Methane Monooxygenase Nat Catal 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-01051-X
Page generated: Wed Jul 31 09:54:04 2024

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