Atomistry » Sodium » PDB 3wc3-3wxo » 3wg7
Atomistry »
  Sodium »
    PDB 3wc3-3wxo »
      3wg7 »

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: Tue Dec 15 06:29:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy