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Zinc in PDB 5x19: Co Bound Cytochrome C Oxidase at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center

Enzymatic activity of Co Bound Cytochrome C Oxidase at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center

All present enzymatic activity of Co Bound Cytochrome C Oxidase at 100 Micro Sec 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 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center, PDB code: 5x19 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 (°) 185.034, 208.846, 178.046, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21

Other elements in 5x19:

The structure of Co Bound Cytochrome C Oxidase at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center 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 at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center (pdb code 5x19). 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 at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center, PDB code: 5x19:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5x19

Go back to Zinc Binding Sites List in 5x19
Zinc binding site 1 out of 2 in the Co Bound Cytochrome C Oxidase at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center


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 at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:57.5
occ:1.00
 SG F:CYS60 2.3 51.5 1.0
SG F:CYS62 2.3 50.4 1.0
SG F:CYS82 2.3 52.2 1.0
SG F:CYS85 2.5 55.9 1.0
CB F:CYS82 3.2 52.9 1.0
CB F:CYS60 3.2 44.5 1.0
CB F:CYS62 3.3 48.6 1.0
CB F:CYS85 3.4 51.2 1.0
CA F:CYS62 3.6 56.8 1.0
N F:CYS85 3.7 56.3 1.0
N F:CYS62 4.1 54.6 1.0
CA F:CYS85 4.2 56.2 1.0
O F:CYS60 4.3 53.0 1.0
CB F:SER84 4.3 62.6 1.0
C F:CYS60 4.4 53.2 1.0
CA F:CYS60 4.4 46.1 1.0
CG2 F:THR87 4.5 49.2 1.0
OG F:SER84 4.6 64.4 1.0
CA F:CYS82 4.6 55.3 1.0
C F:SER84 4.7 56.8 1.0
C F:CYS85 4.9 56.3 1.0
CG1 F:ILE70 4.9 45.7 1.0
C F:ILE61 4.9 55.5 1.0
CA F:SER84 4.9 52.7 1.0
N F:SER84 4.9 54.3 1.0
CB F:ILE70 5.0 46.6 1.0
N F:ILE61 5.0 52.6 1.0

Zinc binding site 2 out of 2 in 5x19

Go back to Zinc Binding Sites List in 5x19
Zinc binding site 2 out of 2 in the Co Bound Cytochrome C Oxidase at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center


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 at 100 Micro Sec After Pump Laser Irradiation to Release Co From O2 Reduction Center within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn101

b:64.4
occ:1.00
 SG S:CYS62 2.3 63.1 1.0
SG S:CYS60 2.3 59.1 1.0
SG S:CYS82 2.4 59.5 1.0
SG S:CYS85 2.5 66.9 1.0
CB S:CYS82 3.1 60.0 1.0
CB S:CYS60 3.2 58.9 1.0
CB S:CYS62 3.4 54.8 1.0
CB S:CYS85 3.5 55.7 1.0
N S:CYS85 3.6 65.3 1.0
CA S:CYS62 3.7 71.1 1.0
NZ N:LYS514 4.1 0.6 1.0
N S:CYS62 4.1 69.2 1.0
CA S:CYS85 4.1 62.0 1.0
O S:CYS60 4.4 61.3 1.0
C S:CYS60 4.4 57.9 1.0
CA S:CYS60 4.4 60.6 1.0
CB S:SER84 4.5 64.1 1.0
CA S:CYS82 4.6 63.2 1.0
C S:SER84 4.6 74.1 1.0
CG2 S:THR87 4.6 63.4 1.0
CG1 S:ILE70 4.7 46.0 1.0
OG S:SER84 4.8 57.3 1.0
C S:ILE61 4.8 62.7 1.0
C S:CYS85 4.9 62.6 1.0
CA S:SER84 4.9 67.9 1.0
CB S:ILE70 4.9 51.8 1.0
N S:SER84 4.9 66.7 1.0
C S:CYS82 5.0 65.5 1.0
N S:ILE61 5.0 54.9 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: Mon Oct 28 14:45:09 2024

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