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Copper in PDB 5zcp: Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days

Enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days

All present enzymatic activity of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days:
1.9.3.1;

Protein crystallography data

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5zcp was solved by A.Shimada, K.Hatano, H.Tadehara, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.320, 206.171, 177.625, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.7

Other elements in 5zcp:

The structure of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 6 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days (pdb code 5zcp). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days, PDB code: 5zcp:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5zcp

Go back to Copper Binding Sites List in 5zcp
Copper binding site 1 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:26.8
occ:1.00
N1 A:AZI607 1.4 24.3 0.6
NE2 A:HIS291 2.0 24.4 1.0
ND1 A:HIS240 2.0 24.3 1.0
NE2 A:HIS290 2.1 26.3 1.0
N2 A:AZI607 2.4 27.9 0.4
N2 A:AZI607 2.5 29.3 0.6
N3 A:AZI607 2.5 20.2 0.4
CE1 A:HIS291 2.9 23.9 1.0
CD2 A:HIS291 2.9 23.4 1.0
N1 A:AZI607 3.0 24.3 0.4
CE1 A:HIS240 3.0 23.0 1.0
CE1 A:HIS290 3.0 25.5 1.0
CG A:HIS240 3.0 22.5 1.0
CD2 A:HIS290 3.1 25.0 1.0
N3 A:AZI606 3.3 23.3 0.6
CB A:HIS240 3.3 22.1 1.0
N2 A:AZI606 3.5 24.0 0.6
N3 A:AZI607 3.7 23.0 0.6
CA A:HIS240 3.8 21.3 1.0
ND1 A:HIS291 4.0 23.5 1.0
CG A:HIS291 4.1 23.1 1.0
N1 A:AZI606 4.1 22.4 0.6
ND1 A:HIS290 4.1 25.1 1.0
NE2 A:HIS240 4.1 22.5 1.0
CD2 A:HIS240 4.2 24.1 1.0
CG A:HIS290 4.2 26.3 1.0
C1A A:HEA602 4.5 21.0 0.4
NA A:HEA602 4.6 22.4 0.4
ND A:HEA602 4.6 23.0 0.6
N A:HIS240 4.7 22.4 1.0
C4D A:HEA602 4.7 22.5 0.6
CG2 A:VAL243 4.8 23.8 1.0
CHA A:HEA602 4.8 22.9 0.6
C1A A:HEA602 4.8 24.8 0.6
CHA A:HEA602 4.8 22.4 0.4
C4A A:HEA602 4.8 22.8 0.4
C2A A:HEA602 4.9 20.6 0.4
NA A:HEA602 4.9 26.1 0.6
FE A:HEA602 4.9 23.0 0.4
C A:HIS240 4.9 20.9 1.0
FE A:HEA602 5.0 25.5 0.6

Copper binding site 2 out of 6 in 5zcp

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Copper binding site 2 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:28.1
occ:1.00
CU1 B:CUA302 0.0 28.1 1.0
ND1 B:HIS161 2.0 27.0 1.0
SG B:CYS196 2.3 26.9 1.0
SG B:CYS200 2.4 27.2 1.0
SD B:MET207 2.4 27.6 1.0
CU2 B:CUA302 2.5 27.4 1.0
O B:HOH402 2.7 0.2 1.0
CE1 B:HIS161 3.0 25.4 1.0
CE B:MET207 3.1 29.1 1.0
CG B:HIS161 3.2 27.4 1.0
CB B:CYS200 3.3 25.9 1.0
CB B:CYS196 3.4 25.8 1.0
CG B:MET207 3.5 28.0 1.0
CB B:HIS161 3.6 25.3 1.0
O B:HOH403 3.6 0.8 1.0
O B:GLU198 4.1 27.4 1.0
NE2 B:HIS161 4.2 26.3 1.0
CA B:HIS161 4.2 24.8 1.0
CD2 B:HIS161 4.2 26.1 1.0
ND1 B:HIS204 4.4 27.3 1.0
CA B:HIS204 4.7 25.7 1.0
CA B:CYS200 4.7 25.8 1.0
O B:HIS102 4.7 28.3 1.0
CD1 B:TRP104 4.7 27.8 1.0
O B:LEU160 4.7 26.6 1.0
CA B:CYS196 4.8 24.3 1.0
CB B:MET207 4.9 30.1 1.0
O B:HIS204 5.0 28.9 1.0
N B:CYS200 5.0 25.2 1.0

Copper binding site 3 out of 6 in 5zcp

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Copper binding site 3 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:27.4
occ:1.00
CU2 B:CUA302 0.0 27.4 1.0
ND1 B:HIS204 2.0 27.3 1.0
SG B:CYS200 2.3 27.2 1.0
SG B:CYS196 2.3 26.9 1.0
O B:GLU198 2.4 27.4 1.0
CU1 B:CUA302 2.5 28.1 1.0
O B:HOH402 2.7 0.2 1.0
CE1 B:HIS204 2.9 27.0 1.0
CG B:HIS204 3.0 26.9 1.0
CB B:CYS196 3.3 25.8 1.0
CB B:CYS200 3.4 25.9 1.0
CB B:HIS204 3.5 24.3 1.0
C B:GLU198 3.5 26.1 1.0
CA B:HIS204 3.6 25.7 1.0
N B:CYS200 3.7 25.2 1.0
O B:HIS204 3.8 28.9 1.0
O B:HOH403 4.0 0.8 1.0
NE2 B:HIS204 4.1 27.2 1.0
N B:GLU198 4.1 25.4 1.0
CD2 B:HIS204 4.1 27.1 1.0
ND1 B:HIS161 4.1 27.0 1.0
CA B:CYS200 4.2 25.8 1.0
C B:HIS204 4.2 26.7 1.0
C B:ILE199 4.2 26.2 1.0
C B:CYS196 4.2 23.8 1.0
O B:CYS196 4.2 25.6 1.0
CA B:ILE199 4.2 25.6 1.0
N B:ILE199 4.3 25.9 1.0
SD B:MET207 4.3 27.6 1.0
CA B:CYS196 4.4 24.3 1.0
CA B:GLU198 4.5 26.6 1.0
N B:SER197 4.7 27.7 1.0
CG B:MET207 4.7 28.0 1.0
N B:HIS204 4.8 29.3 1.0
CA B:HIS161 4.9 24.8 1.0

Copper binding site 4 out of 6 in 5zcp

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Copper binding site 4 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu604

b:30.1
occ:1.00
N1 N:AZI608 1.9 26.3 0.6
NE2 N:HIS291 2.0 29.9 1.0
ND1 N:HIS240 2.0 27.1 1.0
NE2 N:HIS290 2.0 28.0 1.0
N3 N:AZI608 2.3 38.2 0.4
N2 N:AZI608 2.8 24.9 0.6
N2 N:AZI608 2.9 29.1 0.4
CE1 N:HIS291 2.9 27.3 1.0
CD2 N:HIS291 3.0 29.3 1.0
CE1 N:HIS240 3.0 25.9 1.0
CG N:HIS240 3.0 26.4 1.0
CE1 N:HIS290 3.1 25.2 1.0
N3 N:AZI607 3.1 28.7 0.6
CD2 N:HIS290 3.1 27.1 1.0
CB N:HIS240 3.3 25.8 1.0
N2 N:AZI607 3.4 27.5 0.6
CA N:HIS240 3.8 24.6 1.0
N1 N:AZI608 3.8 40.0 0.4
N3 N:AZI608 4.0 26.3 0.6
ND1 N:HIS291 4.0 27.2 1.0
CG N:HIS291 4.1 27.6 1.0
N1 N:AZI607 4.1 23.5 0.6
NE2 N:HIS240 4.1 25.4 1.0
CD2 N:HIS240 4.2 26.8 1.0
ND1 N:HIS290 4.2 28.1 1.0
CG N:HIS290 4.2 29.3 1.0
C1A N:HEA603 4.5 23.0 0.4
NA N:HEA603 4.6 25.1 0.4
ND N:HEA603 4.6 27.4 0.6
C4D N:HEA603 4.6 27.1 0.6
N N:HIS240 4.7 24.3 1.0
C1A N:HEA603 4.7 27.1 0.6
CHA N:HEA603 4.7 25.6 0.6
CG2 N:VAL243 4.8 26.1 1.0
CHA N:HEA603 4.8 23.0 0.4
C4A N:HEA603 4.8 24.2 0.4
NA N:HEA603 4.9 29.4 0.6
C2A N:HEA603 4.9 25.8 0.4
FE N:HEA603 4.9 28.8 0.6
FE N:HEA603 4.9 24.6 0.4
C N:HIS240 4.9 25.7 1.0
O N:HOH701 5.0 33.8 0.2

Copper binding site 5 out of 6 in 5zcp

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Copper binding site 5 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:32.8
occ:1.00
CU1 O:CUA301 0.0 32.8 1.0
ND1 O:HIS161 2.1 33.9 1.0
SG O:CYS196 2.3 33.2 1.0
SG O:CYS200 2.3 32.1 1.0
SD O:MET207 2.4 33.2 1.0
CU2 O:CUA301 2.5 32.7 1.0
CE1 O:HIS161 2.9 30.0 1.0
CE O:MET207 3.1 31.2 1.0
CG O:HIS161 3.2 27.9 1.0
CB O:CYS200 3.3 28.6 1.0
CB O:CYS196 3.4 32.9 1.0
CG O:MET207 3.5 35.6 1.0
CB O:HIS161 3.6 27.8 1.0
O O:GLU198 4.0 29.8 1.0
NE2 O:HIS161 4.2 32.5 1.0
CA O:HIS161 4.2 29.1 1.0
CD2 O:HIS161 4.3 31.8 1.0
ND1 O:HIS204 4.4 33.3 1.0
CD1 O:TRP104 4.6 37.8 1.0
O O:LEU160 4.7 31.2 1.0
O O:HIS102 4.7 32.6 1.0
CA O:CYS200 4.7 30.8 1.0
CA O:HIS204 4.7 33.1 1.0
CA O:CYS196 4.8 33.4 1.0
CB O:MET207 4.9 37.1 1.0
O O:HIS204 5.0 34.0 1.0

Copper binding site 6 out of 6 in 5zcp

Go back to Copper Binding Sites List in 5zcp
Copper binding site 6 out of 6 in the Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azide-Bound Cytochrome C Oxidase Structure Determined Using the Crystals Exposed to 20 Mm Azide Solution For 2 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:32.7
occ:1.00
CU2 O:CUA301 0.0 32.7 1.0
ND1 O:HIS204 2.0 33.3 1.0
SG O:CYS200 2.3 32.1 1.0
SG O:CYS196 2.3 33.2 1.0
O O:GLU198 2.3 29.8 1.0
CU1 O:CUA301 2.5 32.8 1.0
CE1 O:HIS204 2.9 31.1 1.0
CG O:HIS204 3.1 31.1 1.0
CB O:CYS196 3.3 32.9 1.0
CB O:CYS200 3.3 28.6 1.0
C O:GLU198 3.5 29.8 1.0
CB O:HIS204 3.5 32.3 1.0
CA O:HIS204 3.6 33.1 1.0
N O:CYS200 3.7 33.4 1.0
O O:HIS204 3.9 34.0 1.0
NE2 O:HIS204 4.1 34.2 1.0
N O:GLU198 4.1 32.0 1.0
O O:CYS196 4.2 31.8 1.0
CD2 O:HIS204 4.2 33.1 1.0
CA O:CYS200 4.2 30.8 1.0
C O:HIS204 4.2 30.1 1.0
ND1 O:HIS161 4.2 33.9 1.0
C O:ILE199 4.2 32.3 1.0
C O:CYS196 4.2 33.3 1.0
N O:ILE199 4.3 30.2 1.0
CA O:ILE199 4.3 31.1 1.0
SD O:MET207 4.3 33.2 1.0
CA O:CYS196 4.4 33.4 1.0
CA O:GLU198 4.5 31.7 1.0
N O:SER197 4.7 33.3 1.0
CG O:MET207 4.7 35.6 1.0
N O:HIS204 4.8 34.2 1.0
CA O:HIS161 4.9 29.1 1.0

Reference:

A.Shimada, K.Hatano, H.Tadehara, N.Yano, K.Shinzawa-Itoh, E.Yamashita, K.Muramoto, T.Tsukihara, S.Yoshikawa. X-Ray Structural Analyses of Azide-Bound Cytochromecoxidases Reveal That the H-Pathway Is Critically Important For the Proton-Pumping Activity. J. Biol. Chem. V. 293 14868 2018.
ISSN: ESSN 1083-351X
PubMed: 30077971
DOI: 10.1074/JBC.RA118.003123
Page generated: Sun Dec 13 11:21:10 2020

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