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Sodium 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
Copper (Cu) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K, PDB code: 5x1f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5x1f

Go back to Sodium Binding Sites List in 5x1f
Sodium binding site 1 out of 2 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na605

b:43.7
occ:1.00
O A:GLU40 2.2 43.1 1.0
OE1 A:GLU40 2.3 52.0 1.0
O A:SER441 2.3 47.1 1.0
O A:HOH817 2.4 43.2 1.0
O A:GLY45 2.5 56.5 1.0
CD A:GLU40 3.2 52.6 1.0
C A:GLU40 3.3 44.0 1.0
O A:HOH804 3.4 54.2 1.0
CG A:GLU40 3.6 44.6 1.0
C A:SER441 3.6 43.8 1.0
C A:GLY45 3.6 48.2 1.0
CA A:ASP442 4.0 42.7 1.0
CB A:ASP442 4.0 43.4 1.0
CA A:THR46 4.1 54.1 1.0
O A:GLN43 4.1 47.8 1.0
CA A:GLU40 4.2 45.7 1.0
N A:LEU41 4.2 43.9 1.0
N A:ASP442 4.3 39.0 1.0
CA A:LEU41 4.3 41.1 1.0
OD1 A:ASP442 4.3 46.4 1.0
N A:THR46 4.3 50.6 1.0
CG A:ASP442 4.3 47.0 1.0
OE2 A:GLU40 4.3 52.9 1.0
N A:LEU47 4.4 54.8 1.0
CB A:GLU40 4.4 45.1 1.0
CD2 A:LEU41 4.6 40.5 1.0
N A:GLY45 4.6 40.5 1.0
CA A:SER441 4.7 42.8 1.0
C A:THR46 4.7 57.0 1.0
CA A:GLY45 4.8 41.7 1.0
CB A:SER441 5.0 41.4 1.0

Sodium binding site 2 out of 2 in 5x1f

Go back to Sodium Binding Sites List in 5x1f
Sodium binding site 2 out of 2 in the Co Bound Cytochrome C Oxidase Without Pump Laser Irradiation at 278K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
N:Na605

b:53.0
occ:1.00
O N:HOH803 2.2 53.1 1.0
O N:GLU40 2.3 44.7 1.0
O N:GLY45 2.3 67.8 1.0
O N:SER441 2.4 52.1 1.0
OE1 N:GLU40 2.6 53.0 1.0
O N:HOH783 3.4 73.1 1.0
C N:GLU40 3.5 46.1 1.0
C N:GLY45 3.5 60.9 1.0
CD N:GLU40 3.6 55.4 1.0
C N:SER441 3.6 50.3 1.0
CG N:GLU40 3.8 48.3 1.0
CB N:ASP442 3.9 50.1 1.0
CA N:ASP442 3.9 51.7 1.0
O N:GLN43 3.9 62.0 1.0
OD1 N:ASP442 4.0 57.2 1.0
CA N:THR46 4.0 64.0 1.0
CG N:ASP442 4.0 57.4 1.0
N N:ASP442 4.2 47.4 1.0
N N:THR46 4.2 64.1 1.0
O N:HOH794 4.3 65.1 1.0
N N:LEU41 4.3 46.4 1.0
CA N:GLU40 4.3 46.2 1.0
CA N:LEU41 4.4 48.4 1.0
N N:GLY45 4.4 55.2 1.0
N N:LEU47 4.4 67.8 1.0
CD2 N:LEU41 4.5 46.5 1.0
C N:THR46 4.6 63.2 1.0
CB N:GLU40 4.6 46.6 1.0
CA N:GLY45 4.6 56.3 1.0
OE2 N:GLU40 4.7 60.7 1.0
CA N:SER441 4.7 52.5 1.0
C N:PRO44 4.8 53.0 1.0
OD2 N:ASP442 4.8 54.1 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: Tue Dec 15 11:48:25 2020

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