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Copper in PDB 7s4l: Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution

Enzymatic activity of Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution

All present enzymatic activity of Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution:
1.14.13.25;

Copper Binding Sites:

The binding sites of Copper atom in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution (pdb code 7s4l). 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution, PDB code: 7s4l:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 7s4l

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Copper binding site 1 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:107.4
occ:1.00
 NE2 A:HIS139 1.9 86.9 1.0
ND1 A:HIS33 2.0 93.1 1.0
ND1 A:HIS137 2.7 86.9 1.0
CE1 A:HIS139 2.8 86.9 1.0
CG A:HIS33 2.9 93.1 1.0
N A:HIS33 2.9 93.1 1.0
CA A:HIS33 2.9 93.1 1.0
CD2 A:HIS139 3.0 86.9 1.0
CE1 A:HIS33 3.1 93.1 1.0
CB A:HIS33 3.1 93.1 1.0
CG A:HIS137 3.3 86.9 1.0
CB A:HIS137 3.4 86.9 1.0
O A:HOH601 3.6 30.0 1.0
CE1 A:HIS137 3.7 86.9 1.0
ND1 A:HIS139 3.9 86.9 1.0
CG A:HIS139 4.0 86.9 1.0
CD2 A:HIS33 4.0 93.1 1.0
NE2 A:HIS33 4.1 93.1 1.0
C A:HIS33 4.4 93.1 1.0
OE1 A:GLU35 4.4 93.7 1.0
O A:HIS137 4.4 86.9 1.0
CD2 A:HIS137 4.5 86.9 1.0
NE2 A:HIS137 4.6 86.9 1.0
CA A:HIS137 4.7 86.9 1.0
C A:HIS137 4.8 86.9 1.0
OE2 A:GLU35 4.9 93.7 1.0

Copper binding site 2 out of 9 in 7s4l

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Copper binding site 2 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:117.3
occ:1.00
 ND1 A:HIS48 1.7 86.9 1.0
ND1 A:HIS72 2.0 86.9 1.0
CE1 A:HIS48 2.4 86.9 1.0
CE1 A:HIS72 2.6 86.9 1.0
CG A:HIS48 2.9 86.9 1.0
SD A:MET404 3.1 97.6 1.0
CG A:HIS72 3.2 86.9 1.0
O A:HIS72 3.4 86.9 1.0
CB A:HIS48 3.6 86.9 1.0
NE2 A:HIS48 3.6 86.9 1.0
CE A:MET404 3.6 97.6 1.0
CB A:HIS72 3.8 86.9 1.0
NE2 A:HIS72 3.8 86.9 1.0
CD2 A:HIS48 3.8 86.9 1.0
C A:HIS72 4.1 86.9 1.0
CD2 A:HIS72 4.1 86.9 1.0
CB A:PHE74 4.2 86.9 1.0
CD2 A:LEU390 4.2 88.4 1.0
CA A:PHE74 4.3 86.9 1.0
N A:PHE74 4.4 86.9 1.0
N A:HIS48 4.4 86.9 1.0
CG A:LEU390 4.5 88.4 1.0
CA A:HIS72 4.5 86.9 1.0
C A:VAL73 4.6 86.9 1.0
CA A:HIS48 4.7 86.9 1.0
CD1 A:PHE74 4.7 86.9 1.0
CG A:MET404 4.7 97.6 1.0
CG A:PHE74 4.8 86.9 1.0
O A:VAL73 4.8 86.9 1.0
CD1 A:LEU390 4.8 88.4 1.0
N A:VAL73 5.0 86.9 1.0

Copper binding site 3 out of 9 in 7s4l

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Copper binding site 3 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu301

b:130.9
occ:1.00
 NE2 C:HIS145 2.3 101.6 1.0
NE2 C:HIS132 2.4 94.9 1.0
CE1 C:HIS132 2.4 94.9 1.0
OD2 C:ASP128 2.6 91.1 1.0
OD1 C:ASP128 3.0 91.1 1.0
CD2 C:HIS145 3.1 101.6 1.0
CG C:ASP128 3.1 91.1 1.0
OD1 C:ASP138 3.2 117.2 1.0
CE1 C:HIS145 3.4 101.6 1.0
ND1 C:HIS132 3.6 94.9 1.0
CD2 C:HIS132 3.7 94.9 1.0
CG C:ASP138 3.9 117.2 1.0
OD2 C:ASP138 4.2 117.2 1.0
CG C:HIS132 4.3 94.9 1.0
CG C:HIS145 4.3 101.6 1.0
OG1 C:THR142 4.3 109.7 1.0
ND1 C:HIS145 4.4 101.6 1.0
CB C:ASP128 4.6 91.1 1.0
CB C:THR142 4.6 109.7 1.0
CE2 C:PHE149 4.7 97.6 1.0
O C:ASP128 4.7 91.1 1.0
CG2 C:THR142 4.9 109.7 1.0
CB C:ASP138 4.9 117.2 1.0

Copper binding site 4 out of 9 in 7s4l

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Copper binding site 4 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu302

b:130.9
occ:1.00
 ND1 H:HIS145 2.0 101.6 1.0
CE1 H:HIS132 2.2 94.9 1.0
NE2 H:HIS132 2.3 94.9 1.0
CE1 H:HIS145 2.5 101.6 1.0
OD2 H:ASP128 2.5 91.1 1.0
OD1 H:ASP128 3.2 91.1 1.0
CG H:ASP128 3.2 91.1 1.0
CG H:HIS145 3.3 101.6 1.0
ND1 H:HIS132 3.5 94.9 1.0
OD1 H:ASP138 3.7 117.2 1.0
CD2 H:HIS132 3.7 94.9 1.0
NE2 H:HIS145 3.7 101.6 1.0
CB H:HIS145 4.0 101.6 1.0
CD2 H:HIS145 4.1 101.6 1.0
CG H:HIS132 4.2 94.9 1.0
OG1 H:THR142 4.3 109.7 1.0
CG H:ASP138 4.3 117.2 1.0
CE2 H:PHE149 4.4 97.6 1.0
CB H:THR142 4.4 109.7 1.0
CB H:ASP128 4.7 91.1 1.0
OD2 H:ASP138 4.7 117.2 1.0
CG2 H:THR142 4.8 109.7 1.0
OE1 H:GLU148 4.8 94.4 1.0
CZ H:PHE149 4.9 97.6 1.0

Copper binding site 5 out of 9 in 7s4l

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Copper binding site 5 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu301

b:130.9
occ:1.00
 ND1 I:HIS145 2.0 101.6 1.0
CE1 I:HIS132 2.2 94.9 1.0
NE2 I:HIS132 2.3 94.9 1.0
CE1 I:HIS145 2.5 101.6 1.0
OD2 I:ASP128 2.5 91.1 1.0
OD1 I:ASP128 3.2 91.1 1.0
CG I:ASP128 3.2 91.1 1.0
CG I:HIS145 3.3 101.6 1.0
ND1 I:HIS132 3.5 94.9 1.0
OD1 I:ASP138 3.7 117.2 1.0
CD2 I:HIS132 3.7 94.9 1.0
NE2 I:HIS145 3.7 101.6 1.0
CB I:HIS145 4.0 101.6 1.0
CD2 I:HIS145 4.1 101.6 1.0
CG I:HIS132 4.2 94.9 1.0
OG1 I:THR142 4.3 109.7 1.0
CG I:ASP138 4.3 117.2 1.0
CE2 I:PHE149 4.4 97.6 1.0
CB I:THR142 4.4 109.7 1.0
CB I:ASP128 4.7 91.1 1.0
OD2 I:ASP138 4.7 117.2 1.0
CG2 I:THR142 4.8 109.7 1.0
OE1 I:GLU148 4.8 94.4 1.0
CZ I:PHE149 4.8 97.6 1.0

Copper binding site 6 out of 9 in 7s4l

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Copper binding site 6 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu501

b:107.4
occ:1.00
 NE2 D:HIS139 1.9 86.9 1.0
ND1 D:HIS33 2.0 93.1 1.0
ND1 D:HIS137 2.7 86.9 1.0
CE1 D:HIS139 2.8 86.9 1.0
CG D:HIS33 2.9 93.1 1.0
N D:HIS33 2.9 93.1 1.0
CA D:HIS33 2.9 93.1 1.0
CD2 D:HIS139 3.0 86.9 1.0
CE1 D:HIS33 3.1 93.1 1.0
CB D:HIS33 3.1 93.1 1.0
CG D:HIS137 3.3 86.9 1.0
CB D:HIS137 3.4 86.9 1.0
O D:HOH601 3.6 30.0 1.0
CE1 D:HIS137 3.7 86.9 1.0
ND1 D:HIS139 3.9 86.9 1.0
CG D:HIS139 4.0 86.9 1.0
CD2 D:HIS33 4.0 93.1 1.0
NE2 D:HIS33 4.1 93.1 1.0
C D:HIS33 4.4 93.1 1.0
OE1 D:GLU35 4.4 93.7 1.0
O D:HIS137 4.4 86.9 1.0
CD2 D:HIS137 4.5 86.9 1.0
NE2 D:HIS137 4.6 86.9 1.0
CA D:HIS137 4.7 86.9 1.0
C D:HIS137 4.8 86.9 1.0
OE2 D:GLU35 4.9 93.7 1.0

Copper binding site 7 out of 9 in 7s4l

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Copper binding site 7 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:117.3
occ:1.00
 ND1 D:HIS48 1.7 86.9 1.0
ND1 D:HIS72 2.0 86.9 1.0
CE1 D:HIS48 2.4 86.9 1.0
CE1 D:HIS72 2.6 86.9 1.0
CG D:HIS48 2.9 86.9 1.0
SD D:MET404 3.1 97.6 1.0
CG D:HIS72 3.2 86.9 1.0
O D:HIS72 3.4 86.9 1.0
CB D:HIS48 3.6 86.9 1.0
NE2 D:HIS48 3.6 86.9 1.0
CE D:MET404 3.6 97.6 1.0
CB D:HIS72 3.8 86.9 1.0
NE2 D:HIS72 3.8 86.9 1.0
CD2 D:HIS48 3.8 86.9 1.0
C D:HIS72 4.1 86.9 1.0
CD2 D:HIS72 4.1 86.9 1.0
CB D:PHE74 4.2 86.9 1.0
CD2 D:LEU390 4.2 88.4 1.0
CA D:PHE74 4.3 86.9 1.0
N D:PHE74 4.4 86.9 1.0
N D:HIS48 4.4 86.9 1.0
CG D:LEU390 4.5 88.4 1.0
CA D:HIS72 4.5 86.9 1.0
C D:VAL73 4.6 86.9 1.0
CA D:HIS48 4.7 86.9 1.0
CD1 D:PHE74 4.7 86.9 1.0
CG D:MET404 4.7 97.6 1.0
CG D:PHE74 4.8 86.9 1.0
O D:VAL73 4.8 86.9 1.0
CD1 D:LEU390 4.8 88.4 1.0
N D:VAL73 5.0 86.9 1.0

Copper binding site 8 out of 9 in 7s4l

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Copper binding site 8 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:107.4
occ:1.00
 NE2 E:HIS139 1.9 86.9 1.0
ND1 E:HIS33 2.0 93.1 1.0
ND1 E:HIS137 2.7 86.9 1.0
CE1 E:HIS139 2.8 86.9 1.0
CG E:HIS33 2.9 93.1 1.0
N E:HIS33 2.9 93.1 1.0
CA E:HIS33 2.9 93.1 1.0
CD2 E:HIS139 3.0 86.9 1.0
CE1 E:HIS33 3.1 93.1 1.0
CB E:HIS33 3.1 93.1 1.0
CG E:HIS137 3.3 86.9 1.0
CB E:HIS137 3.4 86.9 1.0
O E:HOH601 3.6 30.0 1.0
CE1 E:HIS137 3.7 86.9 1.0
ND1 E:HIS139 3.9 86.9 1.0
CG E:HIS139 4.0 86.9 1.0
CD2 E:HIS33 4.0 93.1 1.0
NE2 E:HIS33 4.1 93.1 1.0
C E:HIS33 4.4 93.1 1.0
OE1 E:GLU35 4.4 93.7 1.0
O E:HIS137 4.4 86.9 1.0
CD2 E:HIS137 4.5 86.9 1.0
NE2 E:HIS137 4.6 86.9 1.0
CA E:HIS137 4.7 86.9 1.0
C E:HIS137 4.8 86.9 1.0
OE2 E:GLU35 4.9 93.7 1.0

Copper binding site 9 out of 9 in 7s4l

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Copper binding site 9 out of 9 in the Cryoem Structure of Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 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 Methylotuvimicrobium Alcaliphilum 20Z Pmmo in A Popc Nanodisc at 2.46 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:117.3
occ:1.00
 ND1 E:HIS48 1.7 86.9 1.0
ND1 E:HIS72 2.0 86.9 1.0
CE1 E:HIS48 2.4 86.9 1.0
CE1 E:HIS72 2.6 86.9 1.0
CG E:HIS48 2.9 86.9 1.0
SD E:MET404 3.1 97.6 1.0
CG E:HIS72 3.2 86.9 1.0
O E:HIS72 3.4 86.9 1.0
CB E:HIS48 3.6 86.9 1.0
NE2 E:HIS48 3.6 86.9 1.0
CE E:MET404 3.6 97.6 1.0
CB E:HIS72 3.8 86.9 1.0
NE2 E:HIS72 3.8 86.9 1.0
CD2 E:HIS48 3.8 86.9 1.0
C E:HIS72 4.1 86.9 1.0
CD2 E:HIS72 4.1 86.9 1.0
CB E:PHE74 4.2 86.9 1.0
CD2 E:LEU390 4.2 88.4 1.0
CA E:PHE74 4.3 86.9 1.0
N E:PHE74 4.4 86.9 1.0
N E:HIS48 4.4 86.9 1.0
CG E:LEU390 4.5 88.4 1.0
CA E:HIS72 4.5 86.9 1.0
C E:VAL73 4.6 86.9 1.0
CD1 E:PHE74 4.7 86.9 1.0
CA E:HIS48 4.7 86.9 1.0
CG E:MET404 4.7 97.6 1.0
CG E:PHE74 4.8 86.9 1.0
O E:VAL73 4.8 86.9 1.0
CD1 E:LEU390 4.8 88.4 1.0
N E:VAL73 5.0 86.9 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 09:10:59 2024

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