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Magnesium in PDB 3wg7: A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography

Enzymatic activity of A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography

All present enzymatic activity of A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography:
1.9.3.1;

Protein crystallography data

The structure of A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography, PDB code: 3wg7 was solved by K.Hirata, K.Shinzawa-Itoh, N.Yano, S.Takemura, K.Kato, M.Hatanaka, K.Muramoto, T.Kawahara, T.Tsukihara, E.Yamashita, K.Tono, G.Ueno, T.Hikima, H.Murakami, Y.Inubushi, M.Yabashi, T.Ishikawa, M.Yamamoto, T.Ogura, H.Sugimoto, J.R.Shen, S.Yoshikawa, H.Ago, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.600, 204.510, 178.290, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23

Other elements in 3wg7:

The structure of A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography (pdb code 3wg7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography, PDB code: 3wg7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3wg7

Go back to Magnesium Binding Sites List in 3wg7
Magnesium binding site 1 out of 2 in the A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:14.5
occ:1.00
 NE2 A:HIS368 2.1 12.3 1.0
OD1 A:ASP369 2.1 11.8 1.0
OE1 B:GLU198 2.2 13.8 1.0
O A:HOH722 2.3 11.8 1.0
O B:HOH411 2.3 11.0 1.0
O B:HOH410 2.3 11.7 1.0
CD2 A:HIS368 3.1 12.5 1.0
CE1 A:HIS368 3.1 13.0 1.0
CD B:GLU198 3.2 13.5 1.0
CG A:ASP369 3.3 15.8 1.0
OE2 B:GLU198 3.5 14.9 1.0
O B:SER197 3.8 13.9 1.0
O A:HOH724 3.9 13.2 1.0
CB A:ASP369 4.0 14.0 1.0
OD1 B:ASP173 4.2 16.2 1.0
ND1 A:HIS368 4.2 11.7 1.0
CG A:HIS368 4.2 11.1 1.0
OD2 A:ASP369 4.3 13.7 1.0
O A:HOH727 4.3 13.6 1.0
OD2 B:ASP173 4.4 15.9 1.0
OG1 A:THR294 4.4 13.4 1.0
O B:HOH519 4.5 34.7 1.0
CG B:GLU198 4.5 12.5 1.0
O A:HOH717 4.5 20.2 1.0
O A:HOH708 4.5 12.0 1.0
O A:HOH714 4.6 20.3 1.0
CB B:GLU198 4.7 11.5 1.0
CG B:ASP173 4.7 14.7 1.0
CA A:ASP369 5.0 12.8 1.0
CA B:GLU198 5.0 12.6 1.0

Magnesium binding site 2 out of 2 in 3wg7

Go back to Magnesium Binding Sites List in 3wg7
Magnesium binding site 2 out of 2 in the A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A 1.9 Angstrom Radiation Damage Free X-Ray Structure of Large (420KDA) Protein By Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg604

b:17.7
occ:1.00
 NE2 N:HIS368 2.1 13.9 1.0
OD1 N:ASP369 2.1 13.3 1.0
OE1 O:GLU198 2.2 19.0 1.0
O O:HOH411 2.2 13.9 1.0
O O:HOH412 2.3 14.9 1.0
O O:HOH401 2.3 14.7 1.0
CE1 N:HIS368 3.1 13.6 1.0
CD2 N:HIS368 3.1 14.3 1.0
CD O:GLU198 3.2 13.7 1.0
CG N:ASP369 3.3 16.6 1.0
OE2 O:GLU198 3.6 11.8 1.0
O O:SER197 3.8 12.8 1.0
CB N:ASP369 4.0 15.4 1.0
O N:HOH723 4.0 13.9 1.0
ND1 N:HIS368 4.2 14.8 1.0
CG N:HIS368 4.2 14.1 1.0
OD2 N:ASP369 4.2 15.1 1.0
OD2 O:ASP173 4.3 18.8 1.0
OD1 O:ASP173 4.3 15.0 1.0
OG1 N:THR294 4.4 13.1 1.0
O O:HOH497 4.4 42.2 1.0
O N:HOH726 4.4 11.2 1.0
O N:HOH717 4.4 11.3 1.0
CG O:GLU198 4.5 14.6 1.0
O N:HOH708 4.5 10.2 1.0
O N:HOH714 4.6 14.5 1.0
CB O:GLU198 4.7 12.7 1.0
CG O:ASP173 4.7 16.7 1.0
CA N:ASP369 4.9 14.6 1.0

Reference:

K.Hirata, K.Shinzawa-Itoh, N.Yano, S.Takemura, K.Kato, M.Hatanaka, K.Muramoto, T.Kawahara, T.Tsukihara, E.Yamashita, K.Tono, G.Ueno, T.Hikima, H.Murakami, Y.Inubushi, M.Yabashi, T.Ishikawa, M.Yamamoto, T.Ogura, H.Sugimoto, J.R.Shen, S.Yoshikawa, H.Ago. Determination of Damage-Free Crystal Structure of An X-Ray-Sensitive Protein Using An Xfel. Nat.Methods 2014.
ISSN: ESSN 1548-7105
PubMed: 24813624
DOI: 10.1038/NMETH.2962
Page generated: Thu Aug 15 13:24:13 2024

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