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Sodium in PDB 5x1b: Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center

Enzymatic activity of Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center

All present enzymatic activity of Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center:
1.9.3.1;

Protein crystallography data

The structure of Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center, PDB code: 5x1b 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) 15.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 185.849, 209.485, 179.524, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23

Other elements in 5x1b:

The structure of Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center 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 at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center (pdb code 5x1b). 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 at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center, PDB code: 5x1b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5x1b

Go back to Sodium Binding Sites List in 5x1b
Sodium binding site 1 out of 2 in the Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center


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 at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:59.9
occ:1.00
 O A:SER441 2.4 57.6 1.0
O A:GLU40 2.4 55.3 1.0
OE1 A:GLU40 2.4 55.2 1.0
O A:HOH793 2.5 51.4 1.0
O A:GLY45 2.5 70.5 1.0
CD A:GLU40 3.3 58.2 1.0
CG A:GLU40 3.4 66.0 1.0
C A:GLU40 3.4 57.7 1.0
C A:SER441 3.6 57.2 1.0
C A:GLY45 3.6 66.3 1.0
O A:HOH790 3.7 66.0 1.0
O A:HOH801 3.7 0.0 1.0
CA A:THR46 3.9 63.2 1.0
CA A:GLU40 4.1 56.3 1.0
N A:THR46 4.2 63.2 1.0
N A:LEU47 4.2 67.1 1.0
CD2 A:LEU41 4.2 44.7 1.0
CA A:ASP442 4.2 53.3 1.0
O A:GLN43 4.3 61.3 1.0
CB A:ASP442 4.3 52.2 1.0
CB A:GLU40 4.3 55.5 1.0
N A:LEU41 4.3 49.7 1.0
OD1 A:ASP442 4.3 62.6 1.0
N A:ASP442 4.4 56.8 1.0
CA A:LEU41 4.4 51.8 1.0
OE2 A:GLU40 4.4 62.3 1.0
CG A:ASP442 4.5 53.5 1.0
C A:THR46 4.5 65.2 1.0
CA A:SER441 4.7 53.4 1.0
N A:GLY45 4.7 56.0 1.0
CA A:GLY45 4.8 60.7 1.0
CB A:THR46 4.9 65.3 1.0

Sodium binding site 2 out of 2 in 5x1b

Go back to Sodium Binding Sites List in 5x1b
Sodium binding site 2 out of 2 in the Co Bound Cytochrome C Oxidase at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center


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 at 20 Nsec After Pump Laser Irradiation to Release Co From O2 Reduction Center within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:70.2
occ:1.00
 O N:GLY45 2.3 77.1 1.0
O N:GLU40 2.4 56.3 1.0
O N:HOH774 2.5 69.8 1.0
O N:SER441 2.6 64.9 1.0
OE1 N:GLU40 2.6 60.9 1.0
O N:HOH714 3.1 78.9 1.0
C N:GLY45 3.4 72.7 1.0
O N:GLN43 3.5 67.3 1.0
C N:GLU40 3.5 59.5 1.0
CD N:GLU40 3.6 68.8 1.0
OD1 N:ASP442 3.6 78.9 1.0
C N:SER441 3.7 60.2 1.0
CG N:GLU40 3.9 61.7 1.0
CG N:ASP442 4.0 72.3 1.0
CA N:THR46 4.1 83.9 1.0
N N:THR46 4.1 75.4 1.0
CA N:ASP442 4.1 62.5 1.0
N N:GLY45 4.2 72.8 1.0
CA N:LEU41 4.3 63.1 1.0
CB N:ASP442 4.4 67.0 1.0
CA N:GLY45 4.4 76.5 1.0
N N:LEU41 4.4 60.8 1.0
N N:ASP442 4.4 56.3 1.0
C N:PRO44 4.4 69.2 1.0
C N:THR46 4.5 83.5 1.0
CA N:GLU40 4.5 60.3 1.0
C N:GLN43 4.7 64.7 1.0
OE2 N:GLU40 4.7 70.3 1.0
CD2 N:LEU41 4.7 62.1 1.0
N N:LEU47 4.7 87.6 1.0
O N:PRO44 4.8 72.6 1.0
CB N:GLU40 4.8 58.9 1.0
OD2 N:ASP442 4.8 71.7 1.0
CA N:PRO44 4.9 65.0 1.0
CA N:SER441 4.9 62.7 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 Oct 8 01:06:50 2024

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