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Copper in PDB 5x1f: Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K

Enzymatic activity of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K

All present enzymatic activity of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K:
1.9.3.1;

Protein crystallography data

The structure of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K, PDB code: 5x1f was solved by A.Shimada, M.Kubo, S.Baba, K.Yamashita, K.Hirata, G.Ueno, T.Nomura, T.Kimura, K.Shinzawa-Itoh, J.Baba, K.Hatano, Y.Eto, A.Miyamoto, H.Murakami, T.Kumasaka, S.Owada, K.Tono, M.Yabashi, Y.Yamaguchi, S.Yanagisawa, M.Sakaguchi, T.Ogura, R.Komiya, J.Yan, E.Yamashita, M.Yamamoto, H.Ago, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 184.806, 208.488, 177.885, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.9

Other elements in 5x1f:

The structure of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K (pdb code 5x1f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K, PDB code: 5x1f:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5x1f

Go back to Copper Binding Sites List in 5x1f
Copper binding site 1 out of 6 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:39.2
occ:1.00
 ND1 A:HIS240 1.9 34.5 1.0
NE2 A:HIS291 2.0 36.2 1.0
NE2 A:HIS290 2.1 35.3 1.0
O A:CMO606 2.4 48.4 1.0
CD2 A:HIS291 2.8 35.1 1.0
CE1 A:HIS240 2.9 30.9 1.0
CE1 A:HIS290 2.9 37.1 1.0
CG A:HIS240 2.9 34.9 1.0
CE1 A:HIS291 3.1 35.4 1.0
CD2 A:HIS290 3.1 36.4 1.0
CB A:HIS240 3.3 32.7 1.0
C A:CMO606 3.5 34.1 1.0
CA A:HIS240 3.9 34.9 1.0
NE2 A:HIS240 4.0 32.5 1.0
ND1 A:HIS290 4.0 34.5 1.0
CG A:HIS291 4.0 34.8 1.0
CD2 A:HIS240 4.0 32.0 1.0
ND1 A:HIS291 4.1 35.4 1.0
CG A:HIS290 4.2 39.2 1.0
N A:HIS240 4.7 38.5 1.0
CA A:TRP288 4.9 40.3 1.0
O A:TRP288 5.0 37.8 1.0
C A:HIS240 5.0 35.5 1.0
NA A:HEA602 5.0 40.4 1.0
CG2 A:VAL243 5.0 43.1 1.0

Copper binding site 2 out of 6 in 5x1f

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Copper binding site 2 out of 6 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:43.3
occ:1.00
 CU1 B:CUA301 0.0 43.3 1.0
ND1 B:HIS161 2.0 37.9 1.0
O B:HOH465 2.3 0.7 1.0
SG B:CYS196 2.4 39.2 1.0
SD B:MET207 2.4 44.4 1.0
SG B:CYS200 2.4 40.0 1.0
CU2 B:CUA301 2.6 44.2 1.0
CE1 B:HIS161 2.8 36.7 1.0
CG B:HIS161 3.1 38.0 1.0
CE B:MET207 3.2 39.9 1.0
CB B:CYS200 3.2 39.7 1.0
CB B:CYS196 3.4 39.3 1.0
CG B:MET207 3.5 38.5 1.0
CB B:HIS161 3.6 40.2 1.0
NE2 B:HIS161 4.1 38.2 1.0
CD2 B:HIS161 4.2 38.1 1.0
CA B:HIS161 4.2 38.2 1.0
O B:GLU198 4.3 40.5 1.0
CD1 B:TRP104 4.4 45.2 1.0
ND1 B:HIS204 4.4 39.6 1.0
CA B:CYS200 4.6 42.3 1.0
O B:LEU160 4.7 43.0 1.0
CA B:CYS196 4.8 38.4 1.0
O B:HIS102 4.8 47.6 1.0
CA B:HIS204 4.8 42.2 1.0
CB B:MET207 4.9 38.2 1.0
N B:CYS200 4.9 41.5 1.0
O B:HIS204 4.9 41.6 1.0

Copper binding site 3 out of 6 in 5x1f

Go back to Copper Binding Sites List in 5x1f
Copper binding site 3 out of 6 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:44.2
occ:1.00
 CU2 B:CUA301 0.0 44.2 1.0
ND1 B:HIS204 1.9 39.6 1.0
SG B:CYS196 2.3 39.2 1.0
SG B:CYS200 2.4 40.0 1.0
CU1 B:CUA301 2.6 43.3 1.0
O B:GLU198 2.7 40.5 1.0
CE1 B:HIS204 2.8 37.1 1.0
CG B:HIS204 3.0 42.7 1.0
CB B:CYS196 3.2 39.3 1.0
CB B:CYS200 3.4 39.7 1.0
CA B:HIS204 3.5 42.2 1.0
CB B:HIS204 3.6 39.9 1.0
N B:CYS200 3.6 41.5 1.0
O B:HIS204 3.7 41.6 1.0
C B:GLU198 3.7 38.5 1.0
O B:HOH465 3.9 0.7 1.0
NE2 B:HIS204 4.0 40.6 1.0
C B:HIS204 4.1 40.5 1.0
CA B:CYS200 4.1 42.3 1.0
CD2 B:HIS204 4.1 34.5 1.0
O B:CYS196 4.2 42.3 1.0
N B:GLU198 4.2 39.0 1.0
CA B:ILE199 4.2 38.5 1.0
C B:ILE199 4.2 38.4 1.0
C B:CYS196 4.2 40.8 1.0
ND1 B:HIS161 4.2 37.9 1.0
CA B:CYS196 4.3 38.4 1.0
SD B:MET207 4.4 44.4 1.0
N B:ILE199 4.4 38.4 1.0
CG B:MET207 4.6 38.5 1.0
CA B:GLU198 4.6 35.9 1.0
N B:HIS204 4.8 41.1 1.0
N B:SER197 4.8 40.2 1.0
C B:CYS200 5.0 44.8 1.0
CA B:HIS161 5.0 38.2 1.0

Copper binding site 4 out of 6 in 5x1f

Go back to Copper Binding Sites List in 5x1f
Copper binding site 4 out of 6 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cu603

b:45.4
occ:1.00
 ND1 N:HIS240 1.8 45.3 1.0
NE2 N:HIS291 2.0 34.4 1.0
NE2 N:HIS290 2.1 42.2 1.0
CE1 N:HIS240 2.8 34.9 1.0
O N:CMO606 2.8 49.3 1.0
CG N:HIS240 2.8 43.2 1.0
CE1 N:HIS291 2.9 39.3 1.0
CD2 N:HIS291 3.0 33.1 1.0
CE1 N:HIS290 3.0 45.9 1.0
CD2 N:HIS290 3.2 40.2 1.0
CB N:HIS240 3.2 41.1 1.0
C N:CMO606 3.2 43.8 1.0
CA N:HIS240 3.9 44.5 1.0
NE2 N:HIS240 3.9 42.8 1.0
ND1 N:HIS291 4.0 39.3 1.0
CD2 N:HIS240 4.0 36.0 1.0
CG N:HIS291 4.0 36.6 1.0
ND1 N:HIS290 4.2 39.8 1.0
CG N:HIS290 4.3 44.1 1.0
N N:HIS240 4.7 44.9 1.0
C1A N:HEA602 4.9 47.9 1.0
CG2 N:VAL287 4.9 39.5 1.0
NA N:HEA602 5.0 44.7 1.0
C N:HIS240 5.0 43.6 1.0
CA N:TRP288 5.0 47.5 1.0

Copper binding site 5 out of 6 in 5x1f

Go back to Copper Binding Sites List in 5x1f
Copper binding site 5 out of 6 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:55.4
occ:1.00
 CU1 O:CUA301 0.0 55.4 1.0
SG O:CYS200 1.6 66.8 1.0
ND1 O:HIS161 2.1 48.9 1.0
SG O:CYS196 2.2 58.5 1.0
SD O:MET207 2.4 48.3 1.0
O O:HOH480 2.6 34.4 1.0
CU2 O:CUA301 2.8 58.0 1.0
CB O:CYS200 2.9 50.4 1.0
O O:HOH417 2.9 32.1 1.0
CE1 O:HIS161 3.1 48.4 1.0
CB O:CYS196 3.1 51.1 1.0
CE O:MET207 3.1 42.4 1.0
CG O:HIS161 3.1 46.7 1.0
O O:HOH460 3.4 0.1 1.0
CB O:HIS161 3.5 40.1 1.0
CG O:MET207 3.5 48.4 1.0
CA O:HIS161 4.1 49.0 1.0
NE2 O:HIS161 4.2 44.5 1.0
CD2 O:HIS161 4.3 47.4 1.0
CA O:CYS200 4.4 51.6 1.0
O O:GLU198 4.5 50.1 1.0
CA O:CYS196 4.5 44.9 1.0
CD1 O:TRP104 4.6 51.4 1.0
ND1 O:HIS204 4.8 49.6 1.0
N O:CYS200 4.8 52.1 1.0
O O:LEU160 4.8 54.0 1.0
O O:HIS102 4.8 49.9 1.0
CB O:MET207 4.9 45.7 1.0
CA O:HIS204 5.0 50.0 1.0

Copper binding site 6 out of 6 in 5x1f

Go back to Copper Binding Sites List in 5x1f
Copper binding site 6 out of 6 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Cu301

b:58.0
occ:1.00
 CU2 O:CUA301 0.0 58.0 1.0
SG O:CYS196 1.4 58.5 1.0
SG O:CYS200 2.0 66.8 1.0
ND1 O:HIS204 2.0 49.6 1.0
O O:HOH417 2.6 32.1 1.0
O O:GLU198 2.7 50.1 1.0
O O:HOH480 2.8 34.4 1.0
CE1 O:HIS204 2.8 49.2 1.0
CU1 O:CUA301 2.8 55.4 1.0
CB O:CYS196 2.9 51.1 1.0
CG O:HIS204 3.0 48.5 1.0
CB O:CYS200 3.1 50.4 1.0
N O:CYS200 3.2 52.1 1.0
CA O:HIS204 3.5 50.0 1.0
CB O:HIS204 3.5 52.5 1.0
C O:GLU198 3.7 43.4 1.0
O O:HIS204 3.7 47.5 1.0
CA O:CYS200 3.8 51.6 1.0
NE2 O:HIS204 4.0 50.6 1.0
C O:ILE199 4.0 49.4 1.0
C O:HIS204 4.0 48.3 1.0
CA O:ILE199 4.1 48.8 1.0
CD2 O:HIS204 4.1 51.8 1.0
C O:CYS196 4.1 46.2 1.0
CA O:CYS196 4.1 44.9 1.0
O O:CYS196 4.2 42.2 1.0
N O:GLU198 4.3 46.9 1.0
N O:ILE199 4.3 47.3 1.0
ND1 O:HIS161 4.5 48.9 1.0
SD O:MET207 4.6 48.3 1.0
CA O:GLU198 4.6 48.6 1.0
N O:SER197 4.7 42.6 1.0
N O:HIS204 4.7 44.9 1.0
C O:CYS200 4.8 54.7 1.0
CG O:MET207 4.8 48.4 1.0

Reference:

A.Shimada, M.Kubo, S.Baba, K.Yamashita, K.Hirata, G.Ueno, T.Nomura, T.Kimura, K.Shinzawa-Itoh, J.Baba, K.Hatano, Y.Eto, A.Miyamoto, H.Murakami, T.Kumasaka, S.Owada, K.Tono, M.Yabashi, Y.Yamaguchi, S.Yanagisawa, M.Sakaguchi, T.Ogura, R.Komiya, J.Yan, E.Yamashita, M.Yamamoto, H.Ago, S.Yoshikawa, T.Tsukihara. A Nanosecond Time-Resolved Xfel Analysis of Structural Changes Associated with Co Release From Cytochrome C Oxidase. Sci Adv V. 3 03042 2017.
ISSN: ESSN 2375-2548
PubMed: 28740863
DOI: 10.1126/SCIADV.1603042
Page generated: Mon Jul 14 05:32:58 2025

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