Atomistry » Copper » PDB 6zut-7euu » 7deg
Atomistry »
  Copper »
    PDB 6zut-7euu »
      7deg »

Copper in PDB 7deg: Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism

Other elements in 7deg:

The structure of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism (pdb code 7deg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism, PDB code: 7deg:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7deg

Go back to Copper Binding Sites List in 7deg
Copper binding site 1 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:55.8
occ:1.00
CE1 A:HIS273 1.2 32.6 1.0
CE1 A:HIS222 1.8 30.1 1.0
ND1 A:HIS222 1.9 30.1 1.0
NE2 A:HIS273 1.9 32.6 1.0
NE2 A:HIS274 2.1 30.5 1.0
NE2 A:HIS222 2.2 30.1 1.0
CG A:HIS222 2.3 30.1 1.0
ND1 A:HIS273 2.3 32.6 1.0
CD2 A:HIS222 2.5 30.1 1.0
CD2 A:HIS274 2.6 30.5 1.0
CD2 A:HIS273 3.0 32.6 1.0
CG A:HIS273 3.2 32.6 1.0
CE1 A:HIS274 3.3 30.5 1.0
CB A:HIS222 3.5 30.1 1.0
CG A:HIS274 3.8 30.5 1.0
O A:VAL270 4.0 32.8 1.0
ND1 A:HIS274 4.1 30.5 1.0
CG2 A:VAL270 4.3 32.8 1.0
C1D A:HAS601 4.4 24.4 1.0
CA A:GLY271 4.6 32.1 1.0
C A:VAL270 4.6 32.8 1.0
CB A:HIS273 4.6 32.6 1.0
CA A:HIS222 4.6 30.1 1.0
ND A:HAS601 4.7 24.4 1.0
C2D A:HAS601 4.7 24.4 1.0
CHB A:HAS601 4.7 24.4 1.0
CG1 A:VAL270 4.7 32.8 1.0
N A:HIS274 4.8 30.5 1.0
C A:HIS273 4.8 32.6 1.0
OH A:TYR226 4.9 25.7 1.0
C4D A:HAS601 4.9 24.4 1.0
CG2 A:THR293 5.0 32.3 1.0

Copper binding site 2 out of 6 in 7deg

Go back to Copper Binding Sites List in 7deg
Copper binding site 2 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu600

b:34.5
occ:1.00
CU1 B:CUA600 0.0 34.5 1.0
ND1 B:HIS139 1.8 25.9 1.0
CE1 B:HIS139 2.2 25.9 1.0
O B:GLU133 2.5 29.9 1.0
CU2 B:CUA600 2.7 34.5 1.0
SG B:CYS135 2.8 28.1 1.0
SG B:CYS131 2.8 23.6 1.0
CB B:CYS135 3.1 28.1 1.0
CG B:HIS139 3.1 25.9 1.0
NE2 B:HIS139 3.4 25.9 1.0
N B:CYS135 3.4 28.1 1.0
C B:GLU133 3.7 29.9 1.0
CD2 B:HIS139 3.8 25.9 1.0
CA B:CYS135 3.8 28.1 1.0
C B:PHE134 3.9 26.3 1.0
CB B:HIS139 3.9 25.9 1.0
ND1 B:HIS96 4.0 31.1 1.0
CB B:CYS131 4.1 23.6 1.0
CA B:PHE134 4.1 26.3 1.0
CE1 B:HIS96 4.3 31.1 1.0
N B:PHE134 4.4 26.3 1.0
O B:CYS131 4.4 23.6 1.0
O B:PHE134 4.6 26.3 1.0
CA B:HIS139 4.6 25.9 1.0
C B:CYS131 4.7 23.6 1.0
C B:CYS135 4.8 28.1 1.0
CA B:GLU133 4.8 29.9 1.0
O B:HIS132 4.8 25.2 1.0
C B:HIS132 4.8 25.2 1.0
N B:GLU133 4.9 29.9 1.0
SD B:MET142 4.9 26.6 1.0
O B:HIS139 4.9 25.9 1.0

Copper binding site 3 out of 6 in 7deg

Go back to Copper Binding Sites List in 7deg
Copper binding site 3 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu600

b:34.5
occ:1.00
CU2 B:CUA600 0.0 34.5 1.0
ND1 B:HIS96 1.8 31.1 1.0
CE1 B:HIS96 2.0 31.1 1.0
CU1 B:CUA600 2.7 34.5 1.0
SD B:MET142 2.7 26.6 1.0
SG B:CYS135 2.8 28.1 1.0
CE B:MET142 3.0 26.6 1.0
SG B:CYS131 3.0 23.6 1.0
CG B:HIS96 3.2 31.1 1.0
NE2 B:HIS96 3.3 31.1 1.0
CB B:CYS135 3.3 28.1 1.0
CD2 B:HIS96 3.8 31.1 1.0
CG B:MET142 3.9 26.6 1.0
CB B:CYS131 4.0 23.6 1.0
ND1 B:HIS139 4.0 25.9 1.0
CB B:HIS96 4.1 31.1 1.0
CA B:HIS96 4.5 31.1 1.0
CB B:MET142 4.5 26.6 1.0
CE1 B:HIS139 4.5 25.9 1.0
CA B:CYS135 4.8 28.1 1.0
N B:TRP66 4.8 31.4 1.0
O B:GLU133 4.9 29.9 1.0
O B:ARG64 4.9 36.0 1.0

Copper binding site 4 out of 6 in 7deg

Go back to Copper Binding Sites List in 7deg
Copper binding site 4 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu604

b:55.8
occ:1.00
CE1 D:HIS273 1.2 32.6 1.0
CE1 D:HIS222 1.8 30.1 1.0
ND1 D:HIS222 1.9 30.1 1.0
NE2 D:HIS273 1.9 32.6 1.0
NE2 D:HIS274 2.1 30.5 1.0
NE2 D:HIS222 2.2 30.1 1.0
CG D:HIS222 2.3 30.1 1.0
ND1 D:HIS273 2.3 32.6 1.0
CD2 D:HIS222 2.5 30.1 1.0
CD2 D:HIS274 2.6 30.5 1.0
CD2 D:HIS273 3.0 32.6 1.0
CG D:HIS273 3.2 32.6 1.0
CE1 D:HIS274 3.3 30.5 1.0
CB D:HIS222 3.5 30.1 1.0
CG D:HIS274 3.8 30.5 1.0
O D:VAL270 4.0 32.8 1.0
ND1 D:HIS274 4.1 30.5 1.0
CG2 D:VAL270 4.3 32.8 1.0
C1D D:HAS602 4.4 24.4 1.0
CA D:GLY271 4.6 32.1 1.0
C D:VAL270 4.6 32.8 1.0
CB D:HIS273 4.6 32.6 1.0
CA D:HIS222 4.6 30.1 1.0
ND D:HAS602 4.7 24.4 1.0
C2D D:HAS602 4.7 24.4 1.0
CHB D:HAS602 4.7 24.4 1.0
CG1 D:VAL270 4.7 32.8 1.0
N D:HIS274 4.8 30.5 1.0
C D:HIS273 4.8 32.6 1.0
OH D:TYR226 4.9 25.7 1.0
C4D D:HAS602 4.9 24.4 1.0
CG2 D:THR293 5.0 32.3 1.0

Copper binding site 5 out of 6 in 7deg

Go back to Copper Binding Sites List in 7deg
Copper binding site 5 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu600

b:34.5
occ:1.00
CU1 E:CUA600 0.0 34.5 1.0
ND1 E:HIS139 1.8 25.9 1.0
CE1 E:HIS139 2.2 25.9 1.0
O E:GLU133 2.5 29.9 1.0
CU2 E:CUA600 2.7 34.5 1.0
SG E:CYS135 2.8 28.1 1.0
SG E:CYS131 2.8 23.6 1.0
CB E:CYS135 3.1 28.1 1.0
CG E:HIS139 3.1 25.9 1.0
NE2 E:HIS139 3.4 25.9 1.0
N E:CYS135 3.4 28.1 1.0
C E:GLU133 3.7 29.9 1.0
CD2 E:HIS139 3.8 25.9 1.0
CA E:CYS135 3.8 28.1 1.0
C E:PHE134 3.9 26.3 1.0
CB E:HIS139 3.9 25.9 1.0
ND1 E:HIS96 4.0 31.1 1.0
CB E:CYS131 4.1 23.6 1.0
CA E:PHE134 4.1 26.3 1.0
CE1 E:HIS96 4.3 31.1 1.0
N E:PHE134 4.4 26.3 1.0
O E:CYS131 4.4 23.6 1.0
O E:PHE134 4.6 26.3 1.0
CA E:HIS139 4.6 25.9 1.0
C E:CYS131 4.7 23.6 1.0
C E:CYS135 4.8 28.1 1.0
CA E:GLU133 4.8 29.9 1.0
O E:HIS132 4.8 25.2 1.0
C E:HIS132 4.8 25.2 1.0
N E:GLU133 4.9 29.9 1.0
SD E:MET142 4.9 26.6 1.0
O E:HIS139 4.9 25.9 1.0

Copper binding site 6 out of 6 in 7deg

Go back to Copper Binding Sites List in 7deg
Copper binding site 6 out of 6 in the Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cryo-Em Structure of A Heme-Copper Terminal Oxidase Dimer Provides Insights Into Its Catalytic Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu600

b:34.5
occ:1.00
CU2 E:CUA600 0.0 34.5 1.0
ND1 E:HIS96 1.8 31.1 1.0
CE1 E:HIS96 2.0 31.1 1.0
CU1 E:CUA600 2.7 34.5 1.0
SD E:MET142 2.7 26.6 1.0
SG E:CYS135 2.8 28.1 1.0
CE E:MET142 3.0 26.6 1.0
SG E:CYS131 3.0 23.6 1.0
CG E:HIS96 3.2 31.1 1.0
NE2 E:HIS96 3.3 31.1 1.0
CB E:CYS135 3.3 28.1 1.0
CD2 E:HIS96 3.8 31.1 1.0
CG E:MET142 3.9 26.6 1.0
CB E:CYS131 4.0 23.6 1.0
ND1 E:HIS139 4.0 25.9 1.0
CB E:HIS96 4.1 31.1 1.0
CA E:HIS96 4.5 31.1 1.0
CB E:MET142 4.5 26.6 1.0
CE1 E:HIS139 4.5 25.9 1.0
CA E:CYS135 4.8 28.1 1.0
N E:TRP66 4.8 31.4 1.0
O E:GLU133 4.8 29.9 1.0
O E:ARG64 4.9 36.0 1.0

Reference:

G.Zhu, H.Zeng, S.Zhang, J.Juli, L.Tai, D.Zhang, X.Pang, Y.Zhang, S.M.Lam, Y.Zhu, G.Peng, H.Michel, F.Sun. The Unusual Homodimer of A Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors. Angew.Chem.Int.Ed.Engl. V. 60 13323 2021.
ISSN: ESSN 1521-3773
PubMed: 33665933
DOI: 10.1002/ANIE.202016785
Page generated: Sat Aug 21 13:32:14 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy