Atomistry » Copper » PDB 5wbd-5z84 » 5x1f
Atomistry »
  Copper »
    PDB 5wbd-5z84 »
      5x1f »

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

Go back to Copper Binding Sites List in 5x1f
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: Sun Dec 13 11:20:20 2020

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