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Copper in PDB 7s4h: Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.14 Angstrom Resolution

Enzymatic activity of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.14 Angstrom Resolution

All present enzymatic activity of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo in A Native Lipid Nanodisc at 2.14 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 2.14 Angstrom Resolution (pdb code 7s4h). 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 2.14 Angstrom Resolution, PDB code: 7s4h:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:55.7
occ:1.00
 ND1 A:HIS33 2.1 49.3 1.0
NE2 A:HIS139 2.1 39.0 1.0
ND1 A:HIS137 2.3 39.0 1.0
N A:HIS33 2.5 49.3 1.0
CD2 A:HIS139 2.8 39.0 1.0
CG A:HIS33 3.0 49.3 1.0
CE1 A:HIS33 3.0 49.3 1.0
CA A:HIS33 3.0 49.3 1.0
CE1 A:HIS139 3.2 39.0 1.0
CG A:HIS137 3.2 39.0 1.0
CB A:HIS33 3.2 49.3 1.0
CE1 A:HIS137 3.3 39.0 1.0
CB A:HIS137 3.4 39.0 1.0
O A:HOH626 3.5 37.4 1.0
O A:HOH639 3.9 43.2 1.0
CD2 A:HIS33 4.1 49.3 1.0
CG A:HIS139 4.1 39.0 1.0
NE2 A:HIS33 4.1 49.3 1.0
O A:HIS137 4.1 39.0 1.0
OE1 A:GLU35 4.1 45.5 1.0
ND1 A:HIS139 4.2 39.0 1.0
CD2 A:HIS137 4.4 39.0 1.0
NE2 A:HIS137 4.4 39.0 1.0
C A:HIS137 4.5 39.0 1.0
C A:HIS33 4.5 49.3 1.0
CA A:HIS137 4.6 39.0 1.0
OE2 A:GLU35 4.6 45.5 1.0
O A:HOH680 4.6 40.7 1.0
CD A:GLU35 4.8 45.5 1.0

Copper binding site 2 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:57.7
occ:1.00
 ND1 A:HIS48 2.0 39.3 1.0
ND1 A:HIS72 2.0 39.0 1.0
OE1 A:GLN404 2.4 45.9 1.0
CE1 A:HIS48 2.8 39.3 1.0
CG A:HIS48 3.0 39.3 1.0
CE1 A:HIS72 3.0 39.0 1.0
CG A:HIS72 3.0 39.0 1.0
CB A:HIS72 3.3 39.0 1.0
O A:HIS72 3.4 39.0 1.0
CB A:HIS48 3.5 39.3 1.0
CD A:GLN404 3.6 45.9 1.0
C A:HIS72 3.9 39.0 1.0
NE2 A:HIS48 3.9 39.3 1.0
CD2 A:LEU390 4.0 43.1 1.0
CD2 A:HIS48 4.0 39.3 1.0
CA A:PHE74 4.1 40.1 1.0
NE2 A:HIS72 4.1 39.0 1.0
CD2 A:HIS72 4.1 39.0 1.0
N A:PHE74 4.2 40.1 1.0
CA A:HIS72 4.2 39.0 1.0
N A:HIS48 4.2 39.3 1.0
CB A:PHE74 4.3 40.1 1.0
NE2 A:GLN404 4.4 45.9 1.0
CD1 A:PHE74 4.4 40.1 1.0
C A:VAL73 4.4 39.0 1.0
CA A:HIS48 4.5 39.3 1.0
CG A:GLN404 4.6 45.9 1.0
CG A:LEU390 4.6 43.1 1.0
N A:VAL73 4.7 39.0 1.0
O A:VAL73 4.7 39.0 1.0
CD1 A:LEU390 4.9 43.1 1.0
CG A:PHE74 4.9 40.1 1.0
N A:HIS72 5.0 39.0 1.0

Copper binding site 3 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu301

b:91.1
occ:1.00
 NE2 C:HIS245 1.5 38.1 1.0
NE2 C:HIS231 2.0 40.8 1.0
OD1 C:ASN227 2.2 39.6 1.0
CE1 C:HIS245 2.5 38.1 1.0
CD2 C:HIS245 2.6 38.1 1.0
CD2 C:HIS231 3.0 40.8 1.0
CE1 C:HIS231 3.0 40.8 1.0
CG C:ASN227 3.3 39.6 1.0
O C:HOH415 3.3 30.0 1.0
ND1 C:HIS245 3.6 38.1 1.0
CG C:HIS245 3.6 38.1 1.0
CD1 C:LEU244 3.7 39.8 1.0
ND2 C:ASN227 3.8 39.6 1.0
O C:HOH406 3.8 30.0 1.0
ND1 C:HIS231 4.1 40.8 1.0
CG C:HIS231 4.1 40.8 1.0
NH2 C:ARG165 4.2 43.4 1.0
CB C:ASN227 4.6 39.6 1.0
NH1 C:ARG165 4.7 43.4 1.0
CZ C:ARG165 4.8 43.4 1.0
CG C:LEU244 4.9 39.8 1.0
CE1 C:PHE248 5.0 37.5 1.0
CE1 C:PHE240 5.0 37.6 1.0

Copper binding site 4 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:55.7
occ:1.00
 ND1 E:HIS33 2.1 49.3 1.0
NE2 E:HIS139 2.1 39.0 1.0
ND1 E:HIS137 2.3 39.0 1.0
N E:HIS33 2.5 49.3 1.0
CD2 E:HIS139 2.8 39.0 1.0
CG E:HIS33 3.0 49.3 1.0
CE1 E:HIS33 3.0 49.3 1.0
CA E:HIS33 3.0 49.3 1.0
CE1 E:HIS139 3.2 39.0 1.0
CG E:HIS137 3.2 39.0 1.0
CB E:HIS33 3.2 49.3 1.0
CE1 E:HIS137 3.3 39.0 1.0
CB E:HIS137 3.4 39.0 1.0
O E:HOH625 3.5 39.9 1.0
O E:HOH638 3.9 42.8 1.0
CD2 E:HIS33 4.1 49.3 1.0
CG E:HIS139 4.1 39.0 1.0
NE2 E:HIS33 4.1 49.3 1.0
O E:HIS137 4.1 39.0 1.0
OE1 E:GLU35 4.1 45.5 1.0
ND1 E:HIS139 4.2 39.0 1.0
CD2 E:HIS137 4.4 39.0 1.0
NE2 E:HIS137 4.4 39.0 1.0
C E:HIS137 4.5 39.0 1.0
C E:HIS33 4.5 49.3 1.0
CA E:HIS137 4.6 39.0 1.0
OE2 E:GLU35 4.6 45.5 1.0
O E:HOH682 4.7 40.8 1.0
CD E:GLU35 4.8 45.5 1.0

Copper binding site 5 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu503

b:57.7
occ:1.00
 ND1 E:HIS48 2.0 39.3 1.0
ND1 E:HIS72 2.0 39.0 1.0
OE1 E:GLN404 2.4 45.9 1.0
CE1 E:HIS48 2.8 39.3 1.0
CG E:HIS48 3.0 39.3 1.0
CE1 E:HIS72 3.0 39.0 1.0
CG E:HIS72 3.0 39.0 1.0
CB E:HIS72 3.3 39.0 1.0
O E:HIS72 3.4 39.0 1.0
CB E:HIS48 3.5 39.3 1.0
CD E:GLN404 3.6 45.9 1.0
C E:HIS72 3.9 39.0 1.0
NE2 E:HIS48 3.9 39.3 1.0
CD2 E:LEU390 4.0 43.1 1.0
CD2 E:HIS48 4.0 39.3 1.0
CA E:PHE74 4.1 40.1 1.0
NE2 E:HIS72 4.1 39.0 1.0
CD2 E:HIS72 4.1 39.0 1.0
N E:PHE74 4.2 40.1 1.0
CA E:HIS72 4.2 39.0 1.0
N E:HIS48 4.2 39.3 1.0
CB E:PHE74 4.3 40.1 1.0
NE2 E:GLN404 4.4 45.9 1.0
CD1 E:PHE74 4.4 40.1 1.0
C E:VAL73 4.4 39.0 1.0
CA E:HIS48 4.5 39.3 1.0
CG E:GLN404 4.6 45.9 1.0
CG E:LEU390 4.6 43.1 1.0
N E:VAL73 4.7 39.0 1.0
O E:VAL73 4.7 39.0 1.0
CD1 E:LEU390 4.9 43.1 1.0
CG E:PHE74 4.9 40.1 1.0
N E:HIS72 5.0 39.0 1.0

Copper binding site 6 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu502

b:55.7
occ:1.00
 ND1 I:HIS33 2.1 49.3 1.0
NE2 I:HIS139 2.1 39.0 1.0
ND1 I:HIS137 2.3 39.0 1.0
N I:HIS33 2.5 49.3 1.0
CD2 I:HIS139 2.8 39.0 1.0
CG I:HIS33 3.0 49.3 1.0
CE1 I:HIS33 3.0 49.3 1.0
CA I:HIS33 3.0 49.3 1.0
CE1 I:HIS139 3.2 39.0 1.0
CG I:HIS137 3.2 39.0 1.0
CB I:HIS33 3.2 49.3 1.0
CE1 I:HIS137 3.3 39.0 1.0
CB I:HIS137 3.4 39.0 1.0
O I:HOH627 3.4 38.4 1.0
O I:HOH640 3.9 43.3 1.0
CD2 I:HIS33 4.1 49.3 1.0
CG I:HIS139 4.1 39.0 1.0
NE2 I:HIS33 4.1 49.3 1.0
O I:HIS137 4.1 39.0 1.0
OE1 I:GLU35 4.1 45.5 1.0
ND1 I:HIS139 4.2 39.0 1.0
CD2 I:HIS137 4.4 39.0 1.0
NE2 I:HIS137 4.4 39.0 1.0
C I:HIS137 4.5 39.0 1.0
C I:HIS33 4.5 49.3 1.0
CA I:HIS137 4.6 39.0 1.0
OE2 I:GLU35 4.6 45.5 1.0
O I:HOH680 4.6 41.7 1.0
CD I:GLU35 4.8 45.5 1.0

Copper binding site 7 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu503

b:57.7
occ:1.00
 ND1 I:HIS48 2.0 39.3 1.0
ND1 I:HIS72 2.0 39.0 1.0
OE1 I:GLN404 2.4 45.9 1.0
CE1 I:HIS48 2.8 39.3 1.0
CG I:HIS48 3.0 39.3 1.0
CE1 I:HIS72 3.0 39.0 1.0
CG I:HIS72 3.0 39.0 1.0
CB I:HIS72 3.3 39.0 1.0
O I:HIS72 3.4 39.0 1.0
CB I:HIS48 3.5 39.3 1.0
CD I:GLN404 3.6 45.9 1.0
C I:HIS72 3.9 39.0 1.0
NE2 I:HIS48 3.9 39.3 1.0
CD2 I:LEU390 4.0 43.1 1.0
CD2 I:HIS48 4.0 39.3 1.0
CA I:PHE74 4.1 40.1 1.0
NE2 I:HIS72 4.1 39.0 1.0
CD2 I:HIS72 4.1 39.0 1.0
N I:PHE74 4.2 40.1 1.0
CA I:HIS72 4.2 39.0 1.0
N I:HIS48 4.2 39.3 1.0
CB I:PHE74 4.3 40.1 1.0
NE2 I:GLN404 4.4 45.9 1.0
CD1 I:PHE74 4.4 40.1 1.0
C I:VAL73 4.4 39.0 1.0
CA I:HIS48 4.5 39.3 1.0
CG I:GLN404 4.6 45.9 1.0
CG I:LEU390 4.6 43.1 1.0
N I:VAL73 4.7 39.0 1.0
O I:VAL73 4.7 39.0 1.0
CD1 I:LEU390 4.9 43.1 1.0
CG I:PHE74 4.9 40.1 1.0
N I:HIS72 5.0 39.0 1.0

Copper binding site 8 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu302

b:91.1
occ:1.00
 NE2 G:HIS245 1.5 38.1 1.0
NE2 G:HIS231 2.0 40.8 1.0
OD1 G:ASN227 2.2 39.6 1.0
CE1 G:HIS245 2.5 38.1 1.0
CD2 G:HIS245 2.6 38.1 1.0
CD2 G:HIS231 3.0 40.8 1.0
CE1 G:HIS231 3.0 40.8 1.0
CG G:ASN227 3.3 39.6 1.0
O G:HOH413 3.3 30.0 1.0
ND1 G:HIS245 3.6 38.1 1.0
CG G:HIS245 3.6 38.1 1.0
CD1 G:LEU244 3.7 39.8 1.0
ND2 G:ASN227 3.8 39.6 1.0
O G:HOH405 3.8 30.0 1.0
ND1 G:HIS231 4.1 40.8 1.0
CG G:HIS231 4.1 40.8 1.0
NH2 G:ARG165 4.2 43.4 1.0
CB G:ASN227 4.6 39.6 1.0
NH1 G:ARG165 4.7 43.4 1.0
CZ G:ARG165 4.8 43.4 1.0
CG G:LEU244 4.9 39.8 1.0
CE1 G:PHE248 5.0 37.5 1.0
CE1 G:PHE240 5.0 37.6 1.0

Copper binding site 9 out of 9 in 7s4h

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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 2.14 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 2.14 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu302

b:91.1
occ:1.00
 NE2 K:HIS245 1.5 38.1 1.0
NE2 K:HIS231 2.0 40.8 1.0
OD1 K:ASN227 2.2 39.6 1.0
CE1 K:HIS245 2.5 38.1 1.0
CD2 K:HIS245 2.6 38.1 1.0
CD2 K:HIS231 3.0 40.8 1.0
CE1 K:HIS231 3.0 40.8 1.0
CG K:ASN227 3.3 39.6 1.0
O K:HOH413 3.3 30.0 1.0
ND1 K:HIS245 3.6 38.1 1.0
CG K:HIS245 3.6 38.1 1.0
CD1 K:LEU244 3.7 39.8 1.0
ND2 K:ASN227 3.8 39.6 1.0
O K:HOH405 3.8 30.0 1.0
ND1 K:HIS231 4.1 40.8 1.0
CG K:HIS231 4.1 40.8 1.0
NH2 K:ARG165 4.2 43.4 1.0
CB K:ASN227 4.6 39.6 1.0
NH1 K:ARG165 4.7 43.4 1.0
CZ K:ARG165 4.8 43.4 1.0
CG K:LEU244 4.9 39.8 1.0
CE1 K:PHE248 5.0 37.5 1.0
CE1 K:PHE240 5.0 37.6 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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