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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3wg7

Go back to Zinc Binding Sites List in 3wg7
Zinc 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 Zinc with other atoms in the Zn 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
F:Zn101

b:19.0
occ:1.00
SG F:CYS62 2.3 16.9 1.0
SG F:CYS82 2.4 19.5 1.0
SG F:CYS85 2.4 19.5 1.0
SG F:CYS60 2.4 19.5 1.0
CB F:CYS82 3.2 17.4 1.0
CB F:CYS62 3.3 16.6 1.0
CB F:CYS85 3.4 17.3 1.0
CB F:CYS60 3.4 20.2 1.0
CA F:CYS62 3.6 21.2 1.0
N F:CYS85 3.8 17.5 1.0
N F:CYS62 4.1 19.7 1.0
CA F:CYS85 4.2 18.8 1.0
O F:CYS60 4.3 14.9 1.0
C F:CYS60 4.4 17.8 1.0
CA F:CYS60 4.5 17.7 1.0
O F:HOH222 4.6 41.1 1.0
CB F:SER84 4.6 19.6 1.0
OG F:SER84 4.7 24.7 1.0
CA F:CYS82 4.7 19.5 1.0
C F:SER84 4.7 19.7 1.0
CG2 F:THR87 4.9 27.0 1.0
C F:ILE61 4.9 24.4 1.0
C F:CYS62 4.9 26.1 1.0
CB F:ILE70 4.9 17.9 1.0
CA F:SER84 5.0 19.0 1.0
N F:SER84 5.0 21.5 1.0
C F:CYS85 5.0 18.5 1.0

Zinc binding site 2 out of 2 in 3wg7

Go back to Zinc Binding Sites List in 3wg7
Zinc 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 Zinc with other atoms in the Zn 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
S:Zn101

b:18.2
occ:1.00
SG S:CYS82 2.3 16.1 1.0
SG S:CYS62 2.3 17.9 1.0
SG S:CYS85 2.4 16.0 1.0
SG S:CYS60 2.4 15.8 1.0
CB S:CYS82 3.2 15.4 1.0
CB S:CYS60 3.3 15.8 1.0
CB S:CYS62 3.3 14.0 1.0
CB S:CYS85 3.4 17.6 1.0
N S:CYS85 3.7 18.0 1.0
CA S:CYS62 3.7 17.7 1.0
CA S:CYS85 4.1 18.4 1.0
N S:CYS62 4.2 15.8 1.0
CB S:SER84 4.3 21.5 1.0
OG1 S:THR87 4.4 35.1 1.0
O S:CYS60 4.4 16.4 1.0
O S:HOH222 4.4 29.6 1.0
C S:CYS60 4.5 17.4 1.0
CA S:CYS60 4.5 15.8 1.0
CA S:CYS82 4.7 17.2 1.0
C S:SER84 4.7 20.1 1.0
OG S:SER84 4.7 24.4 1.0
C S:CYS85 4.9 18.5 1.0
CA S:SER84 4.9 22.0 1.0
CG2 S:THR87 4.9 26.5 1.0
N S:GLY86 4.9 17.3 1.0
C S:ILE61 5.0 16.6 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: Wed Dec 16 04:57:24 2020

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