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Copper in PDB 7t4p: Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution

Enzymatic activity of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution

All present enzymatic activity of Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution (pdb code 7t4p). 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution, PDB code: 7t4p:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 7t4p

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Copper binding site 1 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:35.1
occ:1.00
 ND1 A:HIS33 1.8 49.3 1.0
NE2 A:HIS139 2.2 13.8 1.0
N A:HIS33 2.4 49.3 1.0
CG A:HIS33 2.6 49.3 1.0
ND1 A:HIS137 2.7 14.2 1.0
CD2 A:HIS139 2.8 13.8 1.0
CA A:HIS33 2.9 49.3 1.0
CE1 A:HIS33 2.9 49.3 1.0
CB A:HIS33 2.9 49.3 1.0
CG A:HIS137 3.1 14.2 1.0
CE1 A:HIS139 3.3 13.8 1.0
CE1 A:HIS137 3.4 14.2 1.0
CB A:HIS137 3.5 14.2 1.0
CD2 A:HIS33 3.8 49.3 1.0
NE2 A:HIS33 3.9 49.3 1.0
CD2 A:HIS137 3.9 14.2 1.0
CG A:HIS139 4.0 13.8 1.0
NE2 A:HIS137 4.0 14.2 1.0
ND1 A:HIS139 4.2 13.8 1.0
OE1 A:GLU35 4.2 28.1 1.0
O A:HIS137 4.3 14.2 1.0
C A:HIS33 4.3 49.3 1.0
OE2 A:GLU35 4.4 28.1 1.0
N A:GLY34 4.7 30.6 1.0
CD A:GLU35 4.8 28.1 1.0
CA A:HIS137 4.8 14.2 1.0
C A:HIS137 4.9 14.2 1.0

Copper binding site 2 out of 9 in 7t4p

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Copper binding site 2 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:35.0
occ:1.00
 ND1 A:HIS48 1.9 10.9 1.0
ND1 A:HIS72 1.9 10.1 1.0
CE1 A:HIS48 2.6 10.9 1.0
CE1 A:HIS72 2.8 10.1 1.0
CG A:HIS48 2.9 10.9 1.0
CG A:HIS72 3.0 10.1 1.0
O A:HIS72 3.1 10.1 1.0
CB A:HIS72 3.4 10.1 1.0
CB A:HIS48 3.4 10.9 1.0
NE2 A:HIS48 3.6 10.9 1.0
C A:HIS72 3.7 10.1 1.0
CD2 A:HIS48 3.8 10.9 1.0
CA A:PHE74 3.8 11.2 1.0
NE2 A:HIS72 3.9 10.1 1.0
N A:PHE74 4.0 11.2 1.0
CD2 A:HIS72 4.0 10.1 1.0
CD1 A:PHE74 4.0 11.2 1.0
CB A:PHE74 4.1 11.2 1.0
CA A:HIS72 4.2 10.1 1.0
N A:HIS48 4.2 10.9 1.0
C A:VAL73 4.2 10.1 1.0
NE2 A:GLN404 4.3 17.9 1.0
O A:VAL73 4.4 10.1 1.0
CA A:HIS48 4.4 10.9 1.0
CD2 A:LEU390 4.5 14.8 1.0
N A:VAL73 4.5 10.1 1.0
CG A:PHE74 4.6 11.2 1.0
CA A:VAL73 4.9 10.1 1.0
CG A:LEU390 4.9 14.8 1.0
CD A:GLN404 4.9 17.9 1.0
N A:HIS72 5.0 10.1 1.0

Copper binding site 3 out of 9 in 7t4p

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Copper binding site 3 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu301

b:91.1
occ:1.00
 NE2 C:HIS245 1.7 35.2 1.0
OD1 C:ASN227 2.1 37.8 1.0
CD2 C:HIS245 2.5 35.2 1.0
CE1 C:HIS245 2.8 35.2 1.0
NE2 C:HIS231 3.0 39.7 1.0
CG C:ASN227 3.1 37.8 1.0
CD2 C:HIS231 3.2 39.7 1.0
ND2 C:ASN227 3.4 37.8 1.0
CG C:HIS245 3.7 35.2 1.0
ND1 C:HIS245 3.8 35.2 1.0
CE1 C:PHE240 4.0 30.3 1.0
NH2 C:ARG165 4.2 41.4 1.0
CE1 C:HIS231 4.3 39.7 1.0
CB C:ASN227 4.4 37.8 1.0
CD1 C:PHE240 4.4 30.3 1.0
NH1 C:ARG165 4.5 41.4 1.0
CD1 C:LEU244 4.6 39.2 1.0
CG C:HIS231 4.6 39.7 1.0
CE1 C:HIS160 4.6 31.2 1.0
O C:ASN227 4.8 37.8 1.0
CA C:ASN227 4.8 37.8 1.0
CZ C:ARG165 4.8 41.4 1.0
NE2 C:HIS160 4.9 31.2 1.0
CG C:LEU244 4.9 39.2 1.0

Copper binding site 4 out of 9 in 7t4p

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Copper binding site 4 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu302

b:91.1
occ:1.00
 NE2 G:HIS245 1.7 35.2 1.0
OD1 G:ASN227 2.1 37.8 1.0
CD2 G:HIS245 2.5 35.2 1.0
CE1 G:HIS245 2.8 35.2 1.0
NE2 G:HIS231 3.0 39.7 1.0
CG G:ASN227 3.1 37.8 1.0
CD2 G:HIS231 3.2 39.7 1.0
ND2 G:ASN227 3.4 37.8 1.0
CG G:HIS245 3.7 35.2 1.0
ND1 G:HIS245 3.8 35.2 1.0
CE1 G:PHE240 4.0 30.3 1.0
NH2 G:ARG165 4.2 41.4 1.0
CE1 G:HIS231 4.3 39.7 1.0
CB G:ASN227 4.4 37.8 1.0
CD1 G:PHE240 4.4 30.3 1.0
NH1 G:ARG165 4.5 41.4 1.0
CD1 G:LEU244 4.6 39.2 1.0
CG G:HIS231 4.6 39.7 1.0
CE1 G:HIS160 4.6 31.2 1.0
O G:ASN227 4.8 37.8 1.0
CA G:ASN227 4.8 37.8 1.0
CZ G:ARG165 4.8 41.4 1.0
NE2 G:HIS160 4.9 31.2 1.0
CG G:LEU244 4.9 39.2 1.0

Copper binding site 5 out of 9 in 7t4p

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Copper binding site 5 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu302

b:91.1
occ:1.00
 NE2 K:HIS245 1.7 35.2 1.0
OD1 K:ASN227 2.1 37.8 1.0
CD2 K:HIS245 2.5 35.2 1.0
CE1 K:HIS245 2.8 35.2 1.0
NE2 K:HIS231 3.0 39.7 1.0
CG K:ASN227 3.1 37.8 1.0
CD2 K:HIS231 3.2 39.7 1.0
ND2 K:ASN227 3.4 37.8 1.0
CG K:HIS245 3.7 35.2 1.0
ND1 K:HIS245 3.8 35.2 1.0
CE1 K:PHE240 4.0 30.3 1.0
NH2 K:ARG165 4.2 41.4 1.0
CE1 K:HIS231 4.3 39.7 1.0
CB K:ASN227 4.4 37.8 1.0
CD1 K:PHE240 4.4 30.3 1.0
NH1 K:ARG165 4.5 41.4 1.0
CD1 K:LEU244 4.6 39.2 1.0
CG K:HIS231 4.6 39.7 1.0
CE1 K:HIS160 4.6 31.2 1.0
O K:ASN227 4.8 37.8 1.0
CA K:ASN227 4.8 37.8 1.0
CZ K:ARG165 4.8 41.4 1.0
NE2 K:HIS160 4.9 31.2 1.0
CG K:LEU244 4.9 39.2 1.0

Copper binding site 6 out of 9 in 7t4p

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Copper binding site 6 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:35.1
occ:1.00
 ND1 E:HIS33 1.8 49.3 1.0
NE2 E:HIS139 2.2 13.8 1.0
N E:HIS33 2.4 49.3 1.0
CG E:HIS33 2.6 49.3 1.0
ND1 E:HIS137 2.7 14.2 1.0
CD2 E:HIS139 2.8 13.8 1.0
CA E:HIS33 2.9 49.3 1.0
CE1 E:HIS33 2.9 49.3 1.0
CB E:HIS33 2.9 49.3 1.0
CG E:HIS137 3.1 14.2 1.0
CE1 E:HIS139 3.3 13.8 1.0
CE1 E:HIS137 3.4 14.2 1.0
CB E:HIS137 3.5 14.2 1.0
CD2 E:HIS33 3.8 49.3 1.0
NE2 E:HIS33 3.9 49.3 1.0
CD2 E:HIS137 3.9 14.2 1.0
CG E:HIS139 4.0 13.8 1.0
NE2 E:HIS137 4.0 14.2 1.0
ND1 E:HIS139 4.2 13.8 1.0
OE1 E:GLU35 4.2 28.1 1.0
O E:HIS137 4.3 14.2 1.0
C E:HIS33 4.3 49.3 1.0
OE2 E:GLU35 4.4 28.1 1.0
N E:GLY34 4.7 30.6 1.0
CD E:GLU35 4.8 28.1 1.0
CA E:HIS137 4.8 14.2 1.0
C E:HIS137 4.9 14.2 1.0

Copper binding site 7 out of 9 in 7t4p

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Copper binding site 7 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu503

b:35.0
occ:1.00
 ND1 E:HIS48 1.9 10.9 1.0
ND1 E:HIS72 1.9 10.1 1.0
CE1 E:HIS48 2.6 10.9 1.0
CE1 E:HIS72 2.8 10.1 1.0
CG E:HIS48 2.9 10.9 1.0
CG E:HIS72 3.0 10.1 1.0
O E:HIS72 3.1 10.1 1.0
CB E:HIS72 3.4 10.1 1.0
CB E:HIS48 3.4 10.9 1.0
NE2 E:HIS48 3.6 10.9 1.0
C E:HIS72 3.7 10.1 1.0
CD2 E:HIS48 3.8 10.9 1.0
CA E:PHE74 3.8 11.2 1.0
NE2 E:HIS72 3.9 10.1 1.0
N E:PHE74 4.0 11.2 1.0
CD2 E:HIS72 4.0 10.1 1.0
CD1 E:PHE74 4.0 11.2 1.0
CB E:PHE74 4.1 11.2 1.0
CA E:HIS72 4.2 10.1 1.0
N E:HIS48 4.2 10.9 1.0
C E:VAL73 4.2 10.1 1.0
NE2 E:GLN404 4.3 17.9 1.0
O E:VAL73 4.4 10.1 1.0
CA E:HIS48 4.4 10.9 1.0
CD2 E:LEU390 4.5 14.8 1.0
N E:VAL73 4.5 10.1 1.0
CG E:PHE74 4.6 11.2 1.0
CA E:VAL73 4.9 10.1 1.0
CG E:LEU390 4.9 14.8 1.0
CD E:GLN404 4.9 17.9 1.0
N E:HIS72 5.0 10.1 1.0

Copper binding site 8 out of 9 in 7t4p

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Copper binding site 8 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu502

b:35.1
occ:1.00
 ND1 I:HIS33 1.8 49.3 1.0
NE2 I:HIS139 2.2 13.8 1.0
N I:HIS33 2.4 49.3 1.0
CG I:HIS33 2.6 49.3 1.0
ND1 I:HIS137 2.7 14.2 1.0
CD2 I:HIS139 2.8 13.8 1.0
CA I:HIS33 2.9 49.3 1.0
CE1 I:HIS33 2.9 49.3 1.0
CB I:HIS33 2.9 49.3 1.0
CG I:HIS137 3.1 14.2 1.0
CE1 I:HIS139 3.3 13.8 1.0
CE1 I:HIS137 3.4 14.2 1.0
CB I:HIS137 3.5 14.2 1.0
CD2 I:HIS33 3.8 49.3 1.0
NE2 I:HIS33 3.9 49.3 1.0
CD2 I:HIS137 3.9 14.2 1.0
CG I:HIS139 4.0 13.8 1.0
NE2 I:HIS137 4.0 14.2 1.0
ND1 I:HIS139 4.2 13.8 1.0
OE1 I:GLU35 4.2 28.1 1.0
O I:HIS137 4.3 14.2 1.0
C I:HIS33 4.3 49.3 1.0
OE2 I:GLU35 4.4 28.1 1.0
N I:GLY34 4.7 30.6 1.0
CD I:GLU35 4.8 28.1 1.0
CA I:HIS137 4.8 14.2 1.0
C I:HIS137 4.9 14.2 1.0

Copper binding site 9 out of 9 in 7t4p

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Copper binding site 9 out of 9 in the Cryoem Structure of Methylococcus Capsulatus (Bath) Pmmo Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 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 Treated with Potassium Cyanide and Copper in A Native Lipid Nanodisc at 3.62 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu503

b:35.0
occ:1.00
 ND1 I:HIS48 1.9 10.9 1.0
ND1 I:HIS72 1.9 10.1 1.0
CE1 I:HIS48 2.6 10.9 1.0
CE1 I:HIS72 2.8 10.1 1.0
CG I:HIS48 2.9 10.9 1.0
CG I:HIS72 3.0 10.1 1.0
O I:HIS72 3.1 10.1 1.0
CB I:HIS72 3.4 10.1 1.0
CB I:HIS48 3.4 10.9 1.0
NE2 I:HIS48 3.6 10.9 1.0
C I:HIS72 3.7 10.1 1.0
CD2 I:HIS48 3.8 10.9 1.0
CA I:PHE74 3.8 11.2 1.0
NE2 I:HIS72 3.9 10.1 1.0
N I:PHE74 4.0 11.2 1.0
CD2 I:HIS72 4.0 10.1 1.0
CD1 I:PHE74 4.0 11.2 1.0
CB I:PHE74 4.1 11.2 1.0
CA I:HIS72 4.2 10.1 1.0
N I:HIS48 4.2 10.9 1.0
C I:VAL73 4.2 10.1 1.0
NE2 I:GLN404 4.3 17.9 1.0
O I:VAL73 4.4 10.1 1.0
CA I:HIS48 4.4 10.9 1.0
CD2 I:LEU390 4.5 14.8 1.0
N I:VAL73 4.5 10.1 1.0
CG I:PHE74 4.6 11.2 1.0
CA I:VAL73 4.9 10.1 1.0
CG I:LEU390 4.9 14.8 1.0
CD I:GLN404 4.9 17.9 1.0
N I:HIS72 5.0 10.1 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: Mon Jul 14 08:33:13 2025

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