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Copper in PDB 6adq: Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis

Enzymatic activity of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis

All present enzymatic activity of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis:
1.10.2.2; 1.15.1.1; 1.9.3.1;

Other elements in 6adq:

The structure of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis also contains other interesting chemical elements:

Iron (Fe) 16 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis (pdb code 6adq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis, PDB code: 6adq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6adq

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Copper binding site 1 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu401

b:48.4
occ:1.00
CU E:CU402 1.6 64.4 1.0
ND1 E:HIS281 2.3 34.4 1.0
SG E:CYS277 2.5 34.5 1.0
SG E:CYS273 2.5 34.5 1.0
CE1 E:HIS281 2.5 34.4 1.0
SD E:MET284 2.5 35.7 1.0
CB E:CYS277 3.0 34.5 1.0
CB E:HIS232 3.4 36.2 1.0
CE E:MET284 3.5 35.7 1.0
CG E:HIS232 3.6 36.2 1.0
CG E:HIS281 3.6 34.4 1.0
NE2 E:HIS281 3.8 34.4 1.0
CB E:CYS273 3.8 34.5 1.0
CD2 E:HIS232 4.0 36.2 1.0
N E:CYS277 4.0 34.5 1.0
CA E:CYS277 4.0 34.5 1.0
CG E:MET284 4.1 35.7 1.0
ND1 E:HIS232 4.2 36.2 1.0
O E:HIS281 4.3 34.4 1.0
CD2 E:HIS281 4.3 34.4 1.0
CB E:HIS281 4.5 34.4 1.0
CA E:HIS281 4.5 34.4 1.0
CB E:MET284 4.5 35.7 1.0
NE2 E:HIS232 4.7 36.2 1.0
CE1 E:HIS232 4.8 36.2 1.0
C E:MET276 4.8 32.4 1.0
CA E:HIS232 4.9 36.2 1.0
C E:HIS281 4.9 34.4 1.0
CA E:CYS273 5.0 34.5 1.0
C E:CYS273 5.0 34.5 1.0

Copper binding site 2 out of 8 in 6adq

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Copper binding site 2 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:64.4
occ:1.00
CU E:CU401 1.6 48.4 1.0
CG E:HIS232 2.4 36.2 1.0
SG E:CYS277 2.4 34.5 1.0
SG E:CYS273 2.4 34.5 1.0
CD2 E:HIS232 2.5 36.2 1.0
SD E:MET284 2.5 35.7 1.0
CE E:MET284 2.5 35.7 1.0
CB E:HIS232 2.8 36.2 1.0
ND1 E:HIS232 2.9 36.2 1.0
NE2 E:HIS232 3.0 36.2 1.0
CE1 E:HIS232 3.3 36.2 1.0
CB E:CYS277 3.7 34.5 1.0
ND1 E:HIS281 4.0 34.4 1.0
CE1 E:HIS281 4.0 34.4 1.0
CB E:CYS273 4.0 34.5 1.0
CG E:MET284 4.1 35.7 1.0
CA E:HIS232 4.3 36.2 1.0
CB E:MET284 4.4 35.7 1.0
CA E:CYS277 4.9 34.5 1.0
N E:GLY233 4.9 33.3 1.0

Copper binding site 3 out of 8 in 6adq

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Copper binding site 3 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu603

b:35.4
occ:1.00
ND1 F:HIS264 2.1 24.9 1.0
NE2 F:HIS314 2.2 27.8 1.0
CE1 F:HIS313 2.3 28.1 1.0
CE1 F:HIS314 2.3 27.8 1.0
NE2 F:HIS313 2.6 28.1 1.0
CE1 F:HIS264 2.9 24.9 1.0
CG F:HIS264 3.0 24.9 1.0
ND1 F:HIS313 3.4 28.1 1.0
CD2 F:HIS314 3.4 27.8 1.0
CB F:HIS264 3.5 24.9 1.0
ND1 F:HIS314 3.5 27.8 1.0
CD2 F:HIS313 3.8 28.1 1.0
NE2 F:HIS264 4.0 24.9 1.0
C1A F:HEA601 4.1 27.5 1.0
CD2 F:HIS264 4.1 24.9 1.0
CG F:HIS314 4.1 27.8 1.0
NA F:HEA601 4.1 27.5 1.0
CG F:HIS313 4.2 28.1 1.0
CA F:HIS264 4.3 24.9 1.0
C4D F:HEA601 4.3 27.5 1.0
ND F:HEA601 4.3 27.5 1.0
CHA F:HEA601 4.4 27.5 1.0
CG2 F:VAL267 4.5 24.6 1.0
C2A F:HEA601 4.5 27.5 1.0
C4A F:HEA601 4.5 27.5 1.0
FE F:HEA601 4.7 27.5 1.0
C3A F:HEA601 4.8 27.5 1.0
C3D F:HEA601 4.9 27.5 1.0
C1D F:HEA601 5.0 27.5 1.0
NB F:HEA601 5.0 27.5 1.0

Copper binding site 4 out of 8 in 6adq

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Copper binding site 4 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu604

b:48.5
occ:1.00
OD2 F:ASP390 2.8 30.8 1.0
OE2 E:GLU275 3.0 34.1 1.0
OH F:TYR154 3.2 31.4 1.0
OD1 F:ASP390 3.3 30.8 1.0
CG F:ASP390 3.3 30.8 1.0
OE1 E:GLU275 3.3 34.1 1.0
CD E:GLU275 3.6 34.1 1.0
O F:HIS314 3.8 27.8 1.0
CZ F:TYR154 4.1 31.4 1.0
CE2 F:TYR154 4.4 31.4 1.0
O2A F:HEA601 4.6 27.5 1.0
CB F:ASP390 4.7 30.8 1.0
OD2 E:ASP244 4.8 32.4 1.0

Copper binding site 5 out of 8 in 6adq

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Copper binding site 5 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu401

b:47.9
occ:1.00
CU Q:CU402 1.6 64.0 1.0
ND1 Q:HIS281 2.3 34.2 1.0
SG Q:CYS277 2.5 34.4 1.0
SG Q:CYS273 2.5 34.1 1.0
CE1 Q:HIS281 2.5 34.2 1.0
SD Q:MET284 2.5 35.9 1.0
CB Q:CYS277 3.0 34.4 1.0
CB Q:HIS232 3.4 35.9 1.0
CE Q:MET284 3.5 35.9 1.0
CG Q:HIS232 3.6 35.9 1.0
CG Q:HIS281 3.6 34.2 1.0
NE2 Q:HIS281 3.8 34.2 1.0
CB Q:CYS273 3.8 34.1 1.0
CD2 Q:HIS232 4.0 35.9 1.0
N Q:CYS277 4.0 34.4 1.0
CA Q:CYS277 4.0 34.4 1.0
CG Q:MET284 4.1 35.9 1.0
ND1 Q:HIS232 4.2 35.9 1.0
O Q:HIS281 4.3 34.2 1.0
CD2 Q:HIS281 4.4 34.2 1.0
CB Q:HIS281 4.5 34.2 1.0
CA Q:HIS281 4.5 34.2 1.0
CB Q:MET284 4.5 35.9 1.0
NE2 Q:HIS232 4.7 35.9 1.0
CE1 Q:HIS232 4.8 35.9 1.0
C Q:MET276 4.8 32.5 1.0
CA Q:HIS232 4.9 35.9 1.0
C Q:HIS281 4.9 34.2 1.0
CA Q:CYS273 5.0 34.1 1.0
C Q:CYS273 5.0 34.1 1.0

Copper binding site 6 out of 8 in 6adq

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Copper binding site 6 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Cu402

b:64.0
occ:1.00
CU Q:CU401 1.6 47.9 1.0
CG Q:HIS232 2.4 35.9 1.0
SG Q:CYS277 2.4 34.4 1.0
SG Q:CYS273 2.5 34.1 1.0
CD2 Q:HIS232 2.5 35.9 1.0
SD Q:MET284 2.5 35.9 1.0
CE Q:MET284 2.5 35.9 1.0
CB Q:HIS232 2.8 35.9 1.0
ND1 Q:HIS232 2.9 35.9 1.0
NE2 Q:HIS232 3.0 35.9 1.0
CE1 Q:HIS232 3.3 35.9 1.0
CB Q:CYS277 3.7 34.4 1.0
ND1 Q:HIS281 4.0 34.2 1.0
CE1 Q:HIS281 4.0 34.2 1.0
CB Q:CYS273 4.0 34.1 1.0
CG Q:MET284 4.1 35.9 1.0
CA Q:HIS232 4.3 35.9 1.0
CB Q:MET284 4.5 35.9 1.0
CA Q:CYS277 4.9 34.4 1.0
N Q:GLY233 4.9 32.8 1.0

Copper binding site 7 out of 8 in 6adq

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Copper binding site 7 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cu603

b:33.9
occ:1.00
ND1 R:HIS264 2.1 24.5 1.0
NE2 R:HIS314 2.2 27.5 1.0
CE1 R:HIS313 2.3 27.7 1.0
CE1 R:HIS314 2.3 27.5 1.0
NE2 R:HIS313 2.6 27.7 1.0
CE1 R:HIS264 2.9 24.5 1.0
CG R:HIS264 3.0 24.5 1.0
ND1 R:HIS313 3.4 27.7 1.0
CD2 R:HIS314 3.4 27.5 1.0
CB R:HIS264 3.5 24.5 1.0
ND1 R:HIS314 3.5 27.5 1.0
CD2 R:HIS313 3.8 27.7 1.0
NE2 R:HIS264 4.0 24.5 1.0
C1A R:HEA601 4.1 27.4 1.0
CD2 R:HIS264 4.1 24.5 1.0
CG R:HIS314 4.1 27.5 1.0
NA R:HEA601 4.1 27.4 1.0
CG R:HIS313 4.2 27.7 1.0
CA R:HIS264 4.3 24.5 1.0
C4D R:HEA601 4.3 27.4 1.0
ND R:HEA601 4.3 27.4 1.0
CHA R:HEA601 4.4 27.4 1.0
CG2 R:VAL267 4.5 24.2 1.0
C2A R:HEA601 4.5 27.4 1.0
C4A R:HEA601 4.5 27.4 1.0
FE R:HEA601 4.7 27.4 1.0
C3A R:HEA601 4.8 27.4 1.0
C3D R:HEA601 4.9 27.4 1.0
C1D R:HEA601 5.0 27.4 1.0
NB R:HEA601 5.0 27.4 1.0

Copper binding site 8 out of 8 in 6adq

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Copper binding site 8 out of 8 in the Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Respiratory Complex CIII2CIV2SOD2 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cu604

b:46.9
occ:1.00
OD2 R:ASP390 2.8 31.0 1.0
OE2 Q:GLU275 3.0 34.3 1.0
OH R:TYR154 3.2 30.9 1.0
OD1 R:ASP390 3.3 31.0 1.0
CG R:ASP390 3.3 31.0 1.0
OE1 Q:GLU275 3.3 34.3 1.0
CD Q:GLU275 3.6 34.3 1.0
O R:HIS314 3.8 27.5 1.0
CZ R:TYR154 4.1 30.9 1.0
CE2 R:TYR154 4.4 30.9 1.0
O2A R:HEA601 4.6 27.4 1.0
CB R:ASP390 4.7 31.0 1.0
OD2 Q:ASP244 4.8 32.4 1.0

Reference:

H.Gong, J.Li, A.Xu, Y.Tang, W.Ji, R.Gao, S.Wang, L.Yu, C.Tian, J.Li, H.Y.Yen, S.Man Lam, G.Shui, X.Yang, Y.Sun, X.Li, M.Jia, C.Yang, B.Jiang, Z.Lou, C.V.Robinson, L.L.Wong, L.W.Guddat, F.Sun, Q.Wang, Z.Rao. An Electron Transfer Path Connects Subunits of A Mycobacterial Respiratory Supercomplex. Science V. 362 2018.
ISSN: ESSN 1095-9203
PubMed: 30361386
DOI: 10.1126/SCIENCE.AAT8923
Page generated: Sun Dec 13 11:22:01 2020

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