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

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5x1f

Go back to Zinc Binding Sites List in 5x1f
Zinc 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 Zinc with other atoms in the Zn 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
F:Zn101

b:52.1
occ:1.00
SG F:CYS60 2.3 50.1 1.0
SG F:CYS62 2.3 48.4 1.0
SG F:CYS82 2.4 46.3 1.0
SG F:CYS85 2.5 50.2 1.0
CB F:CYS82 3.1 52.7 1.0
CB F:CYS60 3.2 44.1 1.0
CB F:CYS85 3.3 44.4 1.0
CB F:CYS62 3.4 49.2 1.0
CA F:CYS62 3.6 55.5 1.0
N F:CYS85 3.7 53.6 1.0
N F:CYS62 4.0 52.1 1.0
CA F:CYS85 4.1 53.6 1.0
O F:CYS60 4.2 49.1 1.0
C F:CYS60 4.4 46.5 1.0
CA F:CYS60 4.4 44.8 1.0
O F:HOH224 4.5 78.2 1.0
CB F:SER84 4.5 56.8 1.0
CA F:CYS82 4.6 56.5 1.0
OG F:SER84 4.6 56.4 1.0
C F:SER84 4.7 56.7 1.0
CG2 F:THR87 4.7 47.6 1.0
C F:ILE61 4.8 53.0 1.0
C F:CYS85 4.9 53.5 1.0
N F:SER84 4.9 51.5 1.0
CA F:SER84 4.9 52.1 1.0
N F:GLY86 4.9 53.3 1.0
C F:CYS62 4.9 54.9 1.0

Zinc binding site 2 out of 2 in 5x1f

Go back to Zinc Binding Sites List in 5x1f
Zinc 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 Zinc with other atoms in the Zn 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
S:Zn101

b:56.1
occ:1.00
SG S:CYS62 2.3 53.2 1.0
SG S:CYS60 2.3 49.4 1.0
SG S:CYS85 2.4 56.4 1.0
SG S:CYS82 2.4 53.8 1.0
CB S:CYS82 3.1 54.6 1.0
CB S:CYS60 3.1 47.2 1.0
CB S:CYS85 3.4 50.9 1.0
CB S:CYS62 3.4 57.3 1.0
N S:CYS85 3.6 63.6 1.0
CA S:CYS62 3.7 60.5 1.0
N S:CYS62 4.1 63.5 1.0
CA S:CYS85 4.1 57.1 1.0
O S:CYS60 4.2 55.4 1.0
CA S:CYS60 4.4 54.3 1.0
C S:CYS60 4.4 54.6 1.0
CB S:SER84 4.5 60.5 1.0
OG S:SER84 4.5 62.8 1.0
CA S:CYS82 4.6 59.5 1.0
C S:SER84 4.7 66.7 1.0
CG2 S:THR87 4.7 55.5 1.0
CG1 S:ILE70 4.8 49.4 1.0
C S:CYS85 4.8 57.5 1.0
CA S:SER84 4.9 59.3 1.0
C S:ILE61 4.9 54.8 1.0
N S:GLY86 4.9 64.1 1.0
CB S:ILE70 4.9 45.0 1.0
N S:SER84 4.9 62.0 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: Wed Dec 16 11:19:15 2020

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