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Copper in PDB 5u7n: Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop

Enzymatic activity of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop

All present enzymatic activity of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop, PDB code: 5u7n was solved by L.H.Otero, S.Klinke, A.Espinoza-Cara, A.J.Vila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.18 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.352, 100.701, 101.103, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.6

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop (pdb code 5u7n). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop, PDB code: 5u7n:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5u7n

Go back to Copper Binding Sites List in 5u7n
Copper binding site 1 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1000

b:35.0
occ:1.00
 ND1 A:HIS152 2.0 42.0 1.0
ND1 A:HIS114 2.3 27.2 1.0
SD A:MET155 2.3 36.7 1.0
SG A:CYS149 2.4 34.6 1.0
CE1 A:HIS152 3.0 41.6 1.0
CG A:HIS152 3.1 43.4 1.0
CE1 A:HIS114 3.2 26.9 1.0
CE A:MET155 3.3 30.0 1.0
CG A:HIS114 3.3 23.4 1.0
CB A:CYS149 3.4 30.4 1.0
CB A:HIS152 3.4 41.3 1.0
CB A:HIS114 3.5 19.3 1.0
CG A:MET155 3.8 35.2 1.0
CA A:HIS114 3.9 20.9 1.0
CB A:MET155 4.1 36.1 1.0
NE2 A:HIS152 4.1 44.7 1.0
CD2 A:HIS152 4.2 46.2 1.0
NE2 A:HIS114 4.4 25.5 1.0
CD2 A:HIS114 4.4 24.2 1.0
N A:HIS152 4.5 44.8 1.0
CD1 A:PHE88 4.5 35.8 1.0
O A:ILE113 4.5 30.0 1.0
CA A:HIS152 4.5 44.4 1.0
N A:GLY115 4.6 23.8 1.0
CG A:PRO151 4.7 50.6 1.0
CA A:CYS149 4.8 30.8 1.0
C A:HIS114 4.8 26.1 1.0
O A:HIS152 4.9 49.9 1.0
O A:PHE86 4.9 26.5 1.0
N A:HIS114 5.0 21.5 1.0

Copper binding site 2 out of 8 in 5u7n

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Copper binding site 2 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1000

b:35.5
occ:1.00
 ND1 B:HIS152 2.0 38.6 1.0
ND1 B:HIS114 2.2 30.0 1.0
SD B:MET155 2.4 33.3 1.0
SG B:CYS149 2.5 33.3 1.0
CE1 B:HIS152 2.9 38.8 1.0
CG B:HIS152 3.1 39.9 1.0
CE1 B:HIS114 3.2 29.6 1.0
CG B:HIS114 3.2 27.5 1.0
CE B:MET155 3.2 26.6 1.0
CB B:CYS149 3.4 29.1 1.0
CB B:HIS152 3.5 37.7 1.0
CB B:HIS114 3.5 23.6 1.0
CG B:MET155 3.7 32.0 1.0
CA B:HIS114 3.9 24.4 1.0
CB B:MET155 4.1 33.4 1.0
NE2 B:HIS152 4.1 41.6 1.0
CD2 B:HIS152 4.2 43.0 1.0
NE2 B:HIS114 4.3 29.3 1.0
CD2 B:HIS114 4.4 28.7 1.0
O B:ILE113 4.4 33.2 1.0
CD1 B:PHE88 4.5 37.8 1.0
N B:GLY115 4.5 23.2 1.0
N B:HIS152 4.5 42.1 1.0
CA B:HIS152 4.6 41.1 1.0
CG B:PRO151 4.8 49.4 1.0
C B:HIS114 4.8 26.6 1.0
O B:PHE86 4.9 26.5 1.0
CA B:CYS149 4.9 29.9 1.0
N B:HIS114 4.9 26.9 1.0
O B:HIS152 5.0 49.0 1.0

Copper binding site 3 out of 8 in 5u7n

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Copper binding site 3 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:35.8
occ:1.00
 ND1 C:HIS152 2.0 42.8 1.0
ND1 C:HIS114 2.2 25.6 1.0
SD C:MET155 2.4 34.0 1.0
SG C:CYS149 2.4 39.0 1.0
CE1 C:HIS152 2.9 42.4 1.0
CG C:HIS152 3.1 43.6 1.0
CE1 C:HIS114 3.2 24.2 1.0
CG C:HIS114 3.2 23.8 1.0
CE C:MET155 3.2 27.9 1.0
CB C:HIS114 3.5 21.5 1.0
CB C:CYS149 3.5 35.0 1.0
CB C:HIS152 3.5 41.9 1.0
CG C:MET155 3.8 33.8 1.0
CA C:HIS114 3.8 24.1 1.0
NE2 C:HIS152 4.1 44.5 1.0
CB C:MET155 4.2 35.2 1.0
CD2 C:HIS152 4.2 45.8 1.0
NE2 C:HIS114 4.3 23.9 1.0
CD2 C:HIS114 4.3 23.8 1.0
O C:ILE113 4.4 30.5 1.0
N C:GLY115 4.5 26.6 1.0
CD1 C:PHE88 4.5 31.1 1.0
N C:HIS152 4.5 47.1 1.0
CA C:HIS152 4.6 45.3 1.0
CG C:PRO151 4.7 55.4 1.0
C C:HIS114 4.8 30.6 1.0
O C:PHE86 4.8 25.8 1.0
N C:HIS114 4.9 25.7 1.0
CA C:CYS149 4.9 36.4 1.0

Copper binding site 4 out of 8 in 5u7n

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Copper binding site 4 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1000

b:31.7
occ:1.00
 ND1 D:HIS152 1.9 41.9 1.0
ND1 D:HIS114 2.2 24.6 1.0
SD D:MET155 2.3 29.8 1.0
SG D:CYS149 2.4 28.4 1.0
CE1 D:HIS152 2.8 42.4 1.0
CG D:HIS152 3.0 42.9 1.0
CE1 D:HIS114 3.1 23.8 1.0
CG D:HIS114 3.2 22.9 1.0
CE D:MET155 3.2 24.5 1.0
CB D:CYS149 3.4 24.8 1.0
CB D:HIS152 3.5 39.9 1.0
CB D:HIS114 3.5 20.3 1.0
CG D:MET155 3.8 29.4 1.0
CA D:HIS114 3.9 22.3 1.0
NE2 D:HIS152 4.0 45.4 1.0
CD2 D:HIS152 4.1 46.2 1.0
CB D:MET155 4.1 30.8 1.0
NE2 D:HIS114 4.3 24.1 1.0
CD2 D:HIS114 4.3 23.4 1.0
CD1 D:PHE88 4.5 32.8 1.0
O D:ILE113 4.5 29.1 1.0
N D:HIS152 4.5 42.7 1.0
N D:GLY115 4.6 23.3 1.0
CA D:HIS152 4.6 42.5 1.0
CG D:PRO151 4.7 48.7 1.0
CA D:CYS149 4.9 27.3 1.0
O D:PHE86 4.9 29.3 1.0
C D:HIS114 4.9 25.1 1.0
N D:HIS114 5.0 23.7 1.0

Copper binding site 5 out of 8 in 5u7n

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Copper binding site 5 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu1000

b:40.7
occ:1.00
 ND1 E:HIS152 2.0 50.9 1.0
SG E:CYS149 2.3 37.9 1.0
ND1 E:HIS114 2.3 28.3 1.0
SD E:MET155 2.3 35.9 1.0
CE1 E:HIS152 3.0 51.2 1.0
CG E:HIS152 3.1 51.9 1.0
CE E:MET155 3.1 29.1 1.0
CB E:CYS149 3.2 33.4 1.0
CG E:HIS114 3.3 25.6 1.0
CE1 E:HIS114 3.3 28.2 1.0
CB E:HIS152 3.5 48.8 1.0
CB E:HIS114 3.5 22.7 1.0
CG E:MET155 3.7 34.8 1.0
CA E:HIS114 3.9 25.3 1.0
CB E:MET155 4.0 36.1 1.0
NE2 E:HIS152 4.1 54.4 1.0
CD2 E:HIS152 4.2 55.4 1.0
CD2 E:HIS114 4.4 26.6 1.0
NE2 E:HIS114 4.4 27.7 1.0
N E:GLY115 4.4 25.7 1.0
O E:ILE113 4.5 32.9 1.0
CD1 E:PHE88 4.5 45.7 1.0
N E:HIS152 4.5 50.9 1.0
CA E:HIS152 4.6 50.8 1.0
CA E:CYS149 4.7 33.9 1.0
C E:HIS114 4.7 29.4 1.0
CG E:PRO151 4.8 55.7 1.0
O E:HIS152 4.9 53.8 1.0
O E:PHE86 4.9 33.3 1.0
N E:HIS114 4.9 27.1 1.0

Copper binding site 6 out of 8 in 5u7n

Go back to Copper Binding Sites List in 5u7n
Copper binding site 6 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu201

b:37.2
occ:1.00
 ND1 F:HIS152 2.0 33.1 1.0
ND1 F:HIS114 2.2 29.5 1.0
SD F:MET155 2.3 29.9 1.0
SG F:CYS149 2.4 34.2 1.0
CE1 F:HIS152 3.0 33.5 1.0
CG F:HIS152 3.1 32.6 1.0
CE1 F:HIS114 3.2 29.4 1.0
CG F:HIS114 3.2 27.9 1.0
CE F:MET155 3.2 24.6 1.0
CB F:CYS149 3.5 29.6 1.0
CB F:HIS152 3.5 29.5 1.0
CB F:HIS114 3.5 25.2 1.0
CG F:MET155 3.6 27.0 1.0
CA F:HIS114 3.9 26.9 1.0
CB F:MET155 4.0 25.9 1.0
NE2 F:HIS152 4.1 35.4 1.0
CD2 F:HIS152 4.2 35.6 1.0
NE2 F:HIS114 4.3 29.7 1.0
CD2 F:HIS114 4.4 29.1 1.0
O F:ILE113 4.4 35.5 1.0
CD1 F:PHE88 4.5 26.7 1.0
N F:HIS152 4.5 31.6 1.0
CA F:HIS152 4.6 30.8 1.0
N F:GLY115 4.6 31.5 1.0
CG F:PRO151 4.8 41.4 1.0
O F:PHE86 4.8 24.6 1.0
C F:HIS114 4.9 34.0 1.0
CA F:CYS149 4.9 30.5 1.0
O F:HIS152 5.0 34.7 1.0
N F:HIS114 5.0 28.1 1.0

Copper binding site 7 out of 8 in 5u7n

Go back to Copper Binding Sites List in 5u7n
Copper binding site 7 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu1000

b:39.2
occ:1.00
 ND1 G:HIS152 2.0 47.1 1.0
ND1 G:HIS114 2.1 34.9 1.0
SD G:MET155 2.4 36.1 1.0
SG G:CYS149 2.5 40.1 1.0
CE1 G:HIS152 3.0 46.8 1.0
CE G:MET155 3.1 30.7 1.0
CE1 G:HIS114 3.1 34.2 1.0
CG G:HIS114 3.1 32.6 1.0
CG G:HIS152 3.2 47.0 1.0
CB G:HIS114 3.4 28.9 1.0
CB G:CYS149 3.4 35.9 1.0
CB G:HIS152 3.6 44.0 1.0
CG G:MET155 3.7 35.0 1.0
CA G:HIS114 3.8 29.7 1.0
NE2 G:HIS152 4.1 48.7 1.0
CB G:MET155 4.1 36.0 1.0
CD2 G:HIS152 4.2 49.6 1.0
NE2 G:HIS114 4.3 34.3 1.0
CD2 G:HIS114 4.3 34.2 1.0
N G:GLY115 4.5 31.8 1.0
CD1 G:PHE88 4.5 35.6 1.0
O G:ILE113 4.6 36.9 1.0
N G:HIS152 4.6 46.9 1.0
CA G:HIS152 4.7 46.0 1.0
C G:HIS114 4.7 35.0 1.0
O G:PHE86 4.8 30.4 1.0
CG G:PRO151 4.8 54.9 1.0
CA G:CYS149 4.9 36.4 1.0
N G:HIS114 4.9 30.6 1.0

Copper binding site 8 out of 8 in 5u7n

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Copper binding site 8 out of 8 in the Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of A Chimeric Cua Domain (Subunit II) of Cytochrome BA3 From Thermus Thermophilus with the Amicyanin Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu1000

b:35.5
occ:1.00
 ND1 H:HIS152 2.0 42.3 1.0
ND1 H:HIS114 2.2 23.1 1.0
SG H:CYS149 2.4 32.8 1.0
SD H:MET155 2.4 34.2 1.0
CE1 H:HIS152 2.9 42.7 1.0
CG H:HIS152 3.1 42.9 1.0
CE1 H:HIS114 3.2 23.1 1.0
CG H:HIS114 3.2 20.6 1.0
CE H:MET155 3.3 27.7 1.0
CB H:CYS149 3.4 28.8 1.0
CB H:HIS152 3.5 40.4 1.0
CB H:HIS114 3.5 16.3 1.0
CG H:MET155 3.8 33.0 1.0
CA H:HIS114 3.9 19.3 1.0
NE2 H:HIS152 4.1 45.8 1.0
CB H:MET155 4.1 33.5 1.0
CD2 H:HIS152 4.2 46.4 1.0
NE2 H:HIS114 4.3 22.9 1.0
CD2 H:HIS114 4.3 21.5 1.0
CD1 H:PHE88 4.5 38.2 1.0
O H:ILE113 4.5 29.1 1.0
N H:HIS152 4.5 43.3 1.0
N H:GLY115 4.5 20.2 1.0
CA H:HIS152 4.6 43.1 1.0
CG H:PRO151 4.7 48.0 1.0
C H:HIS114 4.8 23.8 1.0
CA H:CYS149 4.9 29.5 1.0
O H:PHE86 4.9 27.9 1.0
N H:HIS114 5.0 21.5 1.0

Reference:

A.Espinoza-Cara, U.Zitare, D.Alvarez-Paggi, S.Klinke, L.H.Otero, D.H.Murgida, A.J.Vila. Engineering A Bifunctional Copper Site in the Cupredoxin Fold By Loop-Directed Mutagenesis. Chem Sci V. 9 6692 2018.
ISSN: ISSN 2041-6520
PubMed: 30310603
DOI: 10.1039/C8SC01444B
Page generated: Mon Jul 14 05:26:35 2025

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