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Sodium 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:

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 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3wg7

Go back to Sodium Binding Sites List in 3wg7
Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na605

b:14.3
occ:1.00
 O A:HOH720 2.3 14.0 1.0
O A:SER441 2.3 14.5 1.0
O A:GLY45 2.3 15.6 1.0
O A:GLU40 2.3 11.9 1.0
OE1 A:GLU40 2.3 15.2 1.0
CD A:GLU40 3.3 15.6 1.0
C A:GLU40 3.4 13.2 1.0
C A:SER441 3.5 13.2 1.0
C A:GLY45 3.5 17.2 1.0
O A:HOH900 3.5 21.1 1.0
CG A:GLU40 3.5 15.1 1.0
CA A:ASP442 3.9 13.0 1.0
OD2 A:ASP442 4.0 12.4 1.0
O A:GLN43 4.0 15.5 1.0
CB A:ASP442 4.1 11.5 1.0
CA A:THR46 4.1 18.5 1.0
CG A:ASP442 4.1 15.1 1.0
CA A:GLU40 4.2 15.8 1.0
N A:ASP442 4.2 12.6 1.0
N A:THR46 4.2 16.1 1.0
N A:LEU41 4.3 14.4 1.0
N A:LEU47 4.3 18.4 1.0
CB A:GLU40 4.4 14.0 1.0
N A:GLY45 4.4 15.4 1.0
OE2 A:GLU40 4.4 16.4 1.0
CA A:LEU41 4.5 12.2 1.0
CA A:GLY45 4.6 17.5 1.0
C A:THR46 4.6 19.0 1.0
CA A:SER441 4.7 13.6 1.0
CD2 A:LEU41 4.7 11.9 1.0
OD1 A:ASP442 4.9 15.1 1.0
CB A:SER441 4.9 11.6 1.0

Sodium binding site 2 out of 4 in 3wg7

Go back to Sodium Binding Sites List in 3wg7
Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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
C:Na301

b:37.3
occ:1.00
 O C:HOH404 1.4 24.9 1.0
NE2 C:HIS232 2.1 18.5 1.0
NE2 C:HIS148 2.1 26.9 1.0
OE1 C:GLU236 2.2 51.6 1.0
CD C:GLU236 2.8 37.4 1.0
CD2 C:HIS232 2.9 17.8 1.0
CG C:GLU236 3.1 31.8 1.0
CD2 C:HIS148 3.1 26.0 1.0
CE1 C:HIS148 3.1 28.3 1.0
CE1 C:HIS232 3.3 18.5 1.0
OE2 C:GLU236 3.8 39.0 1.0
O C:HOH539 4.1 55.1 1.0
CG C:HIS232 4.1 16.4 1.0
ND1 C:HIS148 4.2 25.6 1.0
CG C:HIS148 4.2 23.7 1.0
SD C:MET152 4.3 25.4 1.0
ND1 C:HIS232 4.3 17.3 1.0
CG C:MET152 4.4 18.8 1.0
CB C:GLU236 4.6 19.6 1.0
O C:HOH406 4.8 50.2 1.0

Sodium binding site 3 out of 4 in 3wg7

Go back to Sodium Binding Sites List in 3wg7
Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na binding site number 3 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:Na605

b:12.9
occ:1.00
 OE1 N:GLU40 2.2 12.1 1.0
O N:GLY45 2.3 13.6 1.0
O N:SER441 2.3 13.4 1.0
O N:GLU40 2.3 10.7 1.0
O N:HOH720 2.3 14.8 1.0
CD N:GLU40 3.2 11.9 1.0
O N:HOH740 3.2 18.4 1.0
C N:GLU40 3.4 11.3 1.0
C N:GLY45 3.5 15.1 1.0
CG N:GLU40 3.5 11.0 1.0
C N:SER441 3.5 11.6 1.0
O N:GLN43 3.9 14.7 1.0
OD2 N:ASP442 4.0 14.9 1.0
CA N:ASP442 4.0 13.0 1.0
CA N:THR46 4.1 15.8 1.0
CG N:ASP442 4.1 14.1 1.0
CB N:ASP442 4.2 12.9 1.0
N N:LEU41 4.2 12.6 1.0
CA N:GLU40 4.2 11.6 1.0
N N:ASP442 4.2 12.1 1.0
N N:THR46 4.2 13.9 1.0
OE2 N:GLU40 4.4 11.9 1.0
CA N:LEU41 4.4 11.3 1.0
N N:LEU47 4.4 17.9 1.0
N N:GLY45 4.4 14.2 1.0
CB N:GLU40 4.5 9.8 1.0
CA N:GLY45 4.6 15.1 1.0
CD2 N:LEU41 4.6 9.8 1.0
CA N:SER441 4.6 13.3 1.0
C N:THR46 4.7 18.4 1.0
CB N:SER441 4.9 12.4 1.0
OD1 N:ASP442 5.0 13.1 1.0

Sodium binding site 4 out of 4 in 3wg7

Go back to Sodium Binding Sites List in 3wg7
Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na binding site number 4 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
P:Na302

b:29.9
occ:1.00
 OE1 P:GLU236 2.2 58.8 1.0
NE2 P:HIS148 2.2 27.9 1.0
NE2 P:HIS232 2.2 16.9 1.0
CD P:GLU236 3.0 48.4 1.0
CE1 P:HIS148 3.0 24.5 1.0
CD2 P:HIS232 3.1 16.8 1.0
CE1 P:HIS232 3.2 15.6 1.0
CD2 P:HIS148 3.4 23.6 1.0
CG P:GLU236 3.4 35.6 1.0
OE2 P:GLU236 3.9 39.1 1.0
O P:HOH471 4.0 42.5 1.0
SD P:MET152 4.1 27.4 1.0
CG P:MET152 4.2 20.9 1.0
ND1 P:HIS148 4.2 26.2 1.0
CG P:HIS232 4.3 14.1 1.0
ND1 P:HIS232 4.3 13.6 1.0
CG P:HIS148 4.4 21.6 1.0
O P:HOH535 4.5 58.2 1.0
O P:HOH404 4.8 50.9 1.0
CB P:GLU236 4.9 21.5 1.0
O P:HOH432 5.0 20.2 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: Mon Oct 7 13:56:43 2024

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