Magnesium in PDB 5x1f: 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;

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

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

Zinc	(Zn)	2 atoms
Iron	(Fe)	4 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	2 atoms

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

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604 b:39.2 occ:1.00 OD2 A:ASP369 2.1 42.4 1.0 OE1 B:GLU198 2.1 41.5 1.0 O B:HOH479 2.1 36.0 1.0 O B:HOH435 2.2 35.8 1.0 NE2 A:HIS368 2.2 34.8 1.0 O B:HOH409 2.2 40.0 1.0 CE1 A:HIS368 3.2 33.7 1.0 CD2 A:HIS368 3.2 35.2 1.0 CG A:ASP369 3.3 40.9 1.0 CD B:GLU198 3.3 42.6 1.0 O B:SER197 3.8 44.0 1.0 O A:HOH836 4.0 38.3 1.0 OE2 B:GLU198 4.0 43.4 1.0 OD2 B:ASP173 4.1 43.9 1.0 CB A:ASP369 4.1 37.2 1.0 OD1 A:ASP369 4.2 41.0 1.0 O A:HOH708 4.2 40.4 1.0 CB B:GLU198 4.3 36.5 1.0 CG B:GLU198 4.3 40.7 1.0 ND1 A:HIS368 4.3 36.0 1.0 O A:HOH764 4.3 37.0 1.0 CG A:HIS368 4.4 39.8 1.0 O A:HOH749 4.4 38.2 1.0 OD1 B:ASP173 4.4 39.2 1.0 CA B:GLU198 4.6 35.9 1.0 O A:HOH787 4.6 36.8 1.0 OG1 A:THR294 4.6 45.6 1.0 O B:HOH406 4.6 47.5 0.7 O A:HOH786 4.7 36.6 1.0 CG B:ASP173 4.7 40.7 1.0 C B:SER197 4.9 43.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604 b:46.0 occ:1.00 O O:HOH448 2.0 45.6 1.0 OE1 O:GLU198 2.0 47.0 1.0 OD2 N:ASP369 2.0 53.7 1.0 O O:HOH405 2.1 49.4 1.0 O O:HOH456 2.2 39.1 1.0 NE2 N:HIS368 2.2 41.5 1.0 CE1 N:HIS368 3.2 41.5 1.0 CD2 N:HIS368 3.2 43.1 1.0 CG N:ASP369 3.2 47.1 1.0 CD O:GLU198 3.3 54.3 1.0 O N:HOH813 4.0 44.1 1.0 OE2 O:GLU198 4.0 45.8 1.0 CB N:ASP369 4.0 43.1 1.0 O O:SER197 4.1 51.0 1.0 OD2 O:ASP173 4.1 47.4 1.0 OD1 N:ASP369 4.2 43.6 1.0 O N:HOH774 4.3 41.0 1.0 ND1 N:HIS368 4.3 45.2 1.0 O N:HOH722 4.3 42.6 1.0 CG O:GLU198 4.3 46.2 1.0 CG N:HIS368 4.4 43.0 1.0 CB O:GLU198 4.4 46.8 1.0 O N:HOH822 4.4 43.9 1.0 OG1 N:THR294 4.4 48.5 1.0 O O:HOH432 4.5 46.5 1.0 OD1 O:ASP173 4.5 44.3 1.0 O N:HOH793 4.5 45.8 1.0 CA O:GLU198 4.6 48.6 1.0 CG O:ASP173 4.8 45.1 1.0 O O:HOH438 4.8 61.1 0.7

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