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Copper in PDB 7s4j: Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution

Enzymatic activity of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution

All present enzymatic activity of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution:
1.14.13.25; 1.14.18.3;

Copper Binding Sites:

The binding sites of Copper atom in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution (pdb code 7s4j). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution, PDB code: 7s4j:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 7s4j

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Copper binding site 1 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:59.6
occ:1.00
 NE2 A:HIS139 2.0 44.0 1.0
ND1 A:HIS33 2.1 52.8 1.0
ND1 A:HIS137 2.1 44.0 1.0
N A:HIS33 2.7 52.8 1.0
CD2 A:HIS139 2.9 44.0 1.0
CE1 A:HIS33 3.0 52.8 1.0
CG A:HIS137 3.1 44.0 1.0
CE1 A:HIS137 3.1 44.0 1.0
CE1 A:HIS139 3.1 44.0 1.0
CA A:HIS33 3.1 52.8 1.0
CG A:HIS33 3.2 52.8 1.0
CB A:HIS137 3.4 44.0 1.0
O A:HOH616 3.5 45.0 1.0
CB A:HIS33 3.5 52.8 1.0
CG A:HIS139 4.1 44.0 1.0
NE2 A:HIS33 4.1 52.8 1.0
ND1 A:HIS139 4.2 44.0 1.0
O A:HIS137 4.2 44.0 1.0
NE2 A:HIS137 4.2 44.0 1.0
CD2 A:HIS137 4.2 44.0 1.0
CD2 A:HIS33 4.2 52.8 1.0
OE2 A:GLU35 4.4 53.4 1.0
C A:HIS137 4.6 44.0 1.0
CA A:HIS137 4.6 44.0 1.0
OE1 A:GLU35 4.6 53.4 1.0
C A:HIS33 4.6 52.8 1.0
O A:HOH665 4.7 45.0 1.0
CD A:GLU35 4.9 53.4 1.0

Copper binding site 2 out of 9 in 7s4j

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Copper binding site 2 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:56.7
occ:1.00
 ND1 A:HIS48 1.9 44.0 1.0
ND1 A:HIS72 2.0 44.0 1.0
OE1 A:GLN404 2.4 45.8 1.0
CE1 A:HIS48 2.7 44.0 1.0
CE1 A:HIS72 2.9 44.0 1.0
CG A:HIS48 2.9 44.0 1.0
CG A:HIS72 3.0 44.0 1.0
CB A:HIS72 3.3 44.0 1.0
CB A:HIS48 3.5 44.0 1.0
O A:HIS72 3.5 44.0 1.0
CD A:GLN404 3.6 45.8 1.0
NE2 A:HIS48 3.8 44.0 1.0
CD2 A:HIS48 3.9 44.0 1.0
C A:HIS72 3.9 44.0 1.0
CD2 A:LEU390 4.0 44.0 1.0
NE2 A:HIS72 4.0 44.0 1.0
CD2 A:HIS72 4.1 44.0 1.0
CA A:PHE74 4.1 44.0 1.0
CA A:HIS72 4.2 44.0 1.0
N A:PHE74 4.3 44.0 1.0
N A:HIS48 4.3 44.0 1.0
NE2 A:GLN404 4.3 45.8 1.0
CD1 A:PHE74 4.3 44.0 1.0
CB A:PHE74 4.4 44.0 1.0
C A:VAL73 4.5 44.0 1.0
CA A:HIS48 4.5 44.0 1.0
CG A:GLN404 4.6 45.8 1.0
CG A:LEU390 4.7 44.0 1.0
O A:VAL73 4.7 44.0 1.0
N A:VAL73 4.7 44.0 1.0
CG A:PHE74 4.8 44.0 1.0
CD1 A:LEU390 4.9 44.0 1.0
N A:HIS72 5.0 44.0 1.0

Copper binding site 3 out of 9 in 7s4j

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Copper binding site 3 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu301

b:30.0
occ:1.00
 NE2 C:HIS160 2.0 47.9 1.0
NE2 C:HIS173 2.2 50.3 1.0
OD2 C:ASP156 2.4 44.0 1.0
CE1 C:HIS160 2.4 47.9 1.0
OD1 C:ASP156 2.5 44.0 1.0
CG C:ASP156 2.7 44.0 1.0
CE1 C:HIS173 3.0 50.3 1.0
CD2 C:HIS173 3.2 50.3 1.0
CD2 C:HIS160 3.3 47.9 1.0
NH1 C:ARG165 3.4 61.2 1.0
ND1 C:HIS160 3.6 47.9 1.0
NH2 C:ARG165 3.8 61.2 1.0
CZ C:ARG165 4.0 61.2 1.0
CG C:HIS160 4.1 47.9 1.0
ND1 C:HIS173 4.2 50.3 1.0
CB C:ASP156 4.2 44.0 1.0
CG C:HIS173 4.2 50.3 1.0
O C:ASP156 4.7 44.0 1.0
CG2 C:THR170 4.7 54.4 1.0
OE1 C:GLU176 4.9 46.4 1.0
CE2 C:PHE177 5.0 50.6 1.0

Copper binding site 4 out of 9 in 7s4j

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Copper binding site 4 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:59.6
occ:1.00
 NE2 E:HIS139 2.0 44.0 1.0
ND1 E:HIS33 2.1 52.8 1.0
ND1 E:HIS137 2.1 44.0 1.0
N E:HIS33 2.7 52.8 1.0
CD2 E:HIS139 2.9 44.0 1.0
CE1 E:HIS33 3.0 52.8 1.0
CG E:HIS137 3.1 44.0 1.0
CE1 E:HIS137 3.1 44.0 1.0
CE1 E:HIS139 3.1 44.0 1.0
CA E:HIS33 3.1 52.8 1.0
CG E:HIS33 3.2 52.8 1.0
CB E:HIS137 3.4 44.0 1.0
O E:HOH610 3.5 45.0 1.0
CB E:HIS33 3.5 52.8 1.0
CG E:HIS139 4.1 44.0 1.0
NE2 E:HIS33 4.1 52.8 1.0
ND1 E:HIS139 4.2 44.0 1.0
O E:HIS137 4.2 44.0 1.0
NE2 E:HIS137 4.2 44.0 1.0
CD2 E:HIS137 4.2 44.0 1.0
CD2 E:HIS33 4.2 52.8 1.0
OE2 E:GLU35 4.4 53.4 1.0
C E:HIS137 4.6 44.0 1.0
CA E:HIS137 4.6 44.0 1.0
OE1 E:GLU35 4.6 53.4 1.0
C E:HIS33 4.6 52.8 1.0
O E:HOH659 4.6 45.0 1.0
CD E:GLU35 4.9 53.4 1.0

Copper binding site 5 out of 9 in 7s4j

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Copper binding site 5 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:56.7
occ:1.00
 ND1 E:HIS48 1.9 44.0 1.0
ND1 E:HIS72 2.0 44.0 1.0
OE1 E:GLN404 2.4 45.8 1.0
CE1 E:HIS48 2.7 44.0 1.0
CE1 E:HIS72 2.9 44.0 1.0
CG E:HIS48 2.9 44.0 1.0
CG E:HIS72 3.0 44.0 1.0
CB E:HIS72 3.3 44.0 1.0
CB E:HIS48 3.5 44.0 1.0
O E:HIS72 3.5 44.0 1.0
CD E:GLN404 3.6 45.8 1.0
NE2 E:HIS48 3.8 44.0 1.0
CD2 E:HIS48 3.9 44.0 1.0
C E:HIS72 3.9 44.0 1.0
CD2 E:LEU390 4.0 44.0 1.0
NE2 E:HIS72 4.0 44.0 1.0
CD2 E:HIS72 4.1 44.0 1.0
CA E:PHE74 4.1 44.0 1.0
CA E:HIS72 4.2 44.0 1.0
N E:PHE74 4.3 44.0 1.0
N E:HIS48 4.3 44.0 1.0
NE2 E:GLN404 4.3 45.8 1.0
CD1 E:PHE74 4.3 44.0 1.0
CB E:PHE74 4.4 44.0 1.0
C E:VAL73 4.5 44.0 1.0
CA E:HIS48 4.5 44.0 1.0
CG E:GLN404 4.6 45.8 1.0
CG E:LEU390 4.7 44.0 1.0
O E:VAL73 4.7 44.0 1.0
N E:VAL73 4.7 44.0 1.0
CG E:PHE74 4.8 44.0 1.0
CD1 E:LEU390 4.9 44.0 1.0
N E:HIS72 5.0 44.0 1.0

Copper binding site 6 out of 9 in 7s4j

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Copper binding site 6 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu501

b:59.6
occ:1.00
 NE2 I:HIS139 2.0 44.0 1.0
ND1 I:HIS33 2.1 52.8 1.0
ND1 I:HIS137 2.1 44.0 1.0
N I:HIS33 2.7 52.8 1.0
CD2 I:HIS139 2.9 44.0 1.0
CE1 I:HIS33 3.0 52.8 1.0
CG I:HIS137 3.1 44.0 1.0
CE1 I:HIS137 3.1 44.0 1.0
CE1 I:HIS139 3.1 44.0 1.0
CA I:HIS33 3.1 52.8 1.0
CG I:HIS33 3.2 52.8 1.0
CB I:HIS137 3.4 44.0 1.0
CB I:HIS33 3.5 52.8 1.0
CG I:HIS139 4.1 44.0 1.0
NE2 I:HIS33 4.1 52.8 1.0
ND1 I:HIS139 4.2 44.0 1.0
O I:HIS137 4.2 44.0 1.0
NE2 I:HIS137 4.2 44.0 1.0
CD2 I:HIS137 4.2 44.0 1.0
CD2 I:HIS33 4.2 52.8 1.0
OE2 I:GLU35 4.4 53.4 1.0
C I:HIS137 4.6 44.0 1.0
CA I:HIS137 4.6 44.0 1.0
OE1 I:GLU35 4.6 53.4 1.0
C I:HIS33 4.6 52.8 1.0
O I:HOH663 4.7 45.0 1.0
CD I:GLU35 4.9 53.4 1.0

Copper binding site 7 out of 9 in 7s4j

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Copper binding site 7 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu502

b:56.7
occ:1.00
 ND1 I:HIS48 1.9 44.0 1.0
ND1 I:HIS72 2.0 44.0 1.0
OE1 I:GLN404 2.4 45.8 1.0
CE1 I:HIS48 2.7 44.0 1.0
CE1 I:HIS72 2.9 44.0 1.0
CG I:HIS48 2.9 44.0 1.0
CG I:HIS72 3.0 44.0 1.0
CB I:HIS72 3.3 44.0 1.0
CB I:HIS48 3.5 44.0 1.0
O I:HIS72 3.5 44.0 1.0
CD I:GLN404 3.6 45.8 1.0
NE2 I:HIS48 3.8 44.0 1.0
CD2 I:HIS48 3.9 44.0 1.0
C I:HIS72 3.9 44.0 1.0
CD2 I:LEU390 4.0 44.0 1.0
NE2 I:HIS72 4.0 44.0 1.0
CD2 I:HIS72 4.1 44.0 1.0
CA I:PHE74 4.1 44.0 1.0
CA I:HIS72 4.2 44.0 1.0
N I:PHE74 4.3 44.0 1.0
N I:HIS48 4.3 44.0 1.0
NE2 I:GLN404 4.3 45.8 1.0
CD1 I:PHE74 4.3 44.0 1.0
CB I:PHE74 4.4 44.0 1.0
C I:VAL73 4.5 44.0 1.0
CA I:HIS48 4.5 44.0 1.0
CG I:GLN404 4.6 45.8 1.0
CG I:LEU390 4.7 44.0 1.0
O I:VAL73 4.7 44.0 1.0
N I:VAL73 4.7 44.0 1.0
CG I:PHE74 4.8 44.0 1.0
CD1 I:LEU390 4.9 44.0 1.0
N I:HIS72 5.0 44.0 1.0

Copper binding site 8 out of 9 in 7s4j

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Copper binding site 8 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu302

b:30.0
occ:1.00
 NE2 G:HIS160 2.0 47.9 1.0
NE2 G:HIS173 2.2 50.3 1.0
OD2 G:ASP156 2.4 44.0 1.0
CE1 G:HIS160 2.4 47.9 1.0
OD1 G:ASP156 2.5 44.0 1.0
CG G:ASP156 2.7 44.0 1.0
CE1 G:HIS173 3.0 50.3 1.0
CD2 G:HIS173 3.2 50.3 1.0
CD2 G:HIS160 3.3 47.9 1.0
NH1 G:ARG165 3.4 61.2 1.0
ND1 G:HIS160 3.6 47.9 1.0
NH2 G:ARG165 3.8 61.2 1.0
CZ G:ARG165 4.0 61.2 1.0
CG G:HIS160 4.1 47.9 1.0
ND1 G:HIS173 4.2 50.3 1.0
CB G:ASP156 4.2 44.0 1.0
CG G:HIS173 4.2 50.3 1.0
O G:ASP156 4.7 44.0 1.0
CG2 G:THR170 4.7 54.4 1.0
OE1 G:GLU176 4.9 46.4 1.0
CE2 G:PHE177 5.0 50.6 1.0

Copper binding site 9 out of 9 in 7s4j

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Copper binding site 9 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu302

b:30.0
occ:1.00
 NE2 K:HIS160 2.0 47.9 1.0
NE2 K:HIS173 2.2 50.3 1.0
OD2 K:ASP156 2.4 44.0 1.0
CE1 K:HIS160 2.4 47.9 1.0
OD1 K:ASP156 2.5 44.0 1.0
CG K:ASP156 2.7 44.0 1.0
CE1 K:HIS173 3.0 50.3 1.0
CD2 K:HIS173 3.2 50.3 1.0
CD2 K:HIS160 3.3 47.9 1.0
NH1 K:ARG165 3.4 61.2 1.0
ND1 K:HIS160 3.6 47.9 1.0
NH2 K:ARG165 3.8 61.2 1.0
CZ K:ARG165 4.0 61.2 1.0
CG K:HIS160 4.1 47.9 1.0
ND1 K:HIS173 4.2 50.3 1.0
CB K:ASP156 4.2 44.0 1.0
CG K:HIS173 4.2 50.3 1.0
O K:ASP156 4.7 44.0 1.0
CG2 K:THR170 4.7 54.4 1.0
OE1 K:GLU176 4.9 46.4 1.0
CE2 K:PHE177 5.0 50.6 1.0

Reference:

C.W.Koo, F.J.Tucci, Y.He, A.C.Rosenzweig. Recovery of Particulate Methane Monooxygenase Structure and Activity in A Lipid Bilayer. Science V. 375 1287 2022.
ISSN: ESSN 1095-9203
PubMed: 35298269
DOI: 10.1126/SCIENCE.ABM3282
Page generated: Wed Jul 31 09:11:00 2024

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