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

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 3wg7

Go back to Iron Binding Sites List in 3wg7
Iron 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 Iron with other atoms in the Fe 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:Fe601

b:15.5
occ:1.00
 FE A:HEA601 0.0 15.5 1.0
NE2 A:HIS61 2.0 18.5 1.0
ND A:HEA601 2.1 13.6 1.0
NB A:HEA601 2.1 12.7 1.0
NC A:HEA601 2.2 12.1 1.0
NE2 A:HIS378 2.2 17.9 1.0
NA A:HEA601 2.3 13.1 1.0
CE1 A:HIS61 3.0 15.4 1.0
CD2 A:HIS61 3.0 17.9 1.0
CD2 A:HIS378 3.0 13.5 1.0
C1D A:HEA601 3.0 12.5 1.0
C4D A:HEA601 3.1 13.1 1.0
C4B A:HEA601 3.1 12.9 1.0
C4C A:HEA601 3.1 12.3 1.0
C1B A:HEA601 3.1 13.1 1.0
C1C A:HEA601 3.1 11.9 1.0
C4A A:HEA601 3.2 11.4 1.0
C1A A:HEA601 3.2 11.9 1.0
CE1 A:HIS378 3.2 14.3 1.0
CHB A:HEA601 3.4 12.0 1.0
CHD A:HEA601 3.4 11.0 1.0
CHC A:HEA601 3.4 12.6 1.0
CHA A:HEA601 3.5 12.5 1.0
ND1 A:HIS61 4.1 14.1 1.0
CG A:HIS61 4.1 15.2 1.0
CG A:HIS378 4.2 13.4 1.0
C2D A:HEA601 4.3 14.2 1.0
C3D A:HEA601 4.3 13.9 1.0
ND1 A:HIS378 4.3 14.5 1.0
C2C A:HEA601 4.3 12.4 1.0
C3C A:HEA601 4.3 12.8 1.0
C3B A:HEA601 4.3 12.7 1.0
C2B A:HEA601 4.4 12.3 1.0
C2A A:HEA601 4.4 12.2 1.0
C3A A:HEA601 4.5 11.7 1.0
CE2 A:PHE377 4.8 11.5 1.0

Iron binding site 2 out of 4 in 3wg7

Go back to Iron Binding Sites List in 3wg7
Iron 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 Iron with other atoms in the Fe 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
A:Fe602

b:14.8
occ:1.00
 FE A:HEA602 0.0 14.8 1.0
ND A:HEA602 2.0 11.0 1.0
NB A:HEA602 2.0 11.7 1.0
NE2 A:HIS376 2.1 13.3 1.0
NC A:HEA602 2.1 13.0 1.0
NA A:HEA602 2.2 11.2 1.0
O1 A:PER606 2.4 10.2 0.9
C4D A:HEA602 3.0 10.6 1.0
C4B A:HEA602 3.1 12.7 1.0
CD2 A:HIS376 3.1 13.1 1.0
CE1 A:HIS376 3.1 15.2 1.0
C4C A:HEA602 3.1 11.7 1.0
C4A A:HEA602 3.1 12.2 1.0
C1B A:HEA602 3.1 12.8 1.0
C1D A:HEA602 3.1 10.4 1.0
C1C A:HEA602 3.1 11.7 1.0
C1A A:HEA602 3.1 11.8 1.0
CHB A:HEA602 3.4 11.6 1.0
CHA A:HEA602 3.5 11.2 1.0
CHC A:HEA602 3.5 12.4 1.0
CHD A:HEA602 3.5 11.4 1.0
O2 A:PER606 3.8 12.7 0.9
O1 A:PER606 3.8 11.7 0.1
ND1 A:HIS376 4.2 15.0 1.0
CG A:HIS376 4.2 13.5 1.0
C3D A:HEA602 4.3 11.1 1.0
C3B A:HEA602 4.3 12.9 1.0
C3C A:HEA602 4.3 12.3 1.0
C2C A:HEA602 4.3 13.5 1.0
C2B A:HEA602 4.3 12.4 1.0
C2D A:HEA602 4.3 10.2 1.0
C2A A:HEA602 4.3 14.0 1.0
C3A A:HEA602 4.4 12.5 1.0
O2 A:PER606 4.8 11.2 0.1
CU A:CU603 4.9 15.8 1.0
CA A:GLY355 5.0 11.4 1.0

Iron binding site 3 out of 4 in 3wg7

Go back to Iron Binding Sites List in 3wg7
Iron 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 Iron with other atoms in the Fe 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:Fe601

b:13.9
occ:1.00
 FE N:HEA601 0.0 13.9 1.0
NB N:HEA601 2.0 12.3 1.0
NE2 N:HIS378 2.0 12.3 1.0
NE2 N:HIS61 2.0 12.2 1.0
ND N:HEA601 2.1 13.1 1.0
NA N:HEA601 2.1 14.8 1.0
NC N:HEA601 2.2 13.6 1.0
CD2 N:HIS378 3.0 13.2 1.0
CE1 N:HIS378 3.0 14.8 1.0
CD2 N:HIS61 3.0 13.8 1.0
C4B N:HEA601 3.0 12.2 1.0
C1B N:HEA601 3.0 12.8 1.0
CE1 N:HIS61 3.1 12.5 1.0
C4D N:HEA601 3.1 12.4 1.0
C1D N:HEA601 3.1 15.4 1.0
C4A N:HEA601 3.1 12.7 1.0
C1A N:HEA601 3.1 12.7 1.0
C4C N:HEA601 3.1 13.9 1.0
C1C N:HEA601 3.2 12.5 1.0
CHA N:HEA601 3.4 13.3 1.0
CHB N:HEA601 3.5 12.4 1.0
CHD N:HEA601 3.5 14.5 1.0
CHC N:HEA601 3.5 11.1 1.0
ND1 N:HIS378 4.1 12.9 1.0
CG N:HIS378 4.1 12.7 1.0
ND1 N:HIS61 4.2 13.4 1.0
CG N:HIS61 4.2 13.0 1.0
C2B N:HEA601 4.2 10.7 1.0
C3B N:HEA601 4.2 11.3 1.0
C3A N:HEA601 4.3 14.1 1.0
C2D N:HEA601 4.3 14.4 1.0
C3D N:HEA601 4.3 13.0 1.0
C2A N:HEA601 4.3 12.6 1.0
C3C N:HEA601 4.4 12.8 1.0
C2C N:HEA601 4.4 12.5 1.0
CE2 N:PHE377 4.9 11.7 1.0

Iron binding site 4 out of 4 in 3wg7

Go back to Iron Binding Sites List in 3wg7
Iron 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 Iron with other atoms in the Fe 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
N:Fe602

b:14.1
occ:1.00
 FE N:HEA602 0.0 14.1 1.0
NB N:HEA602 2.0 13.3 1.0
ND N:HEA602 2.0 11.2 1.0
NA N:HEA602 2.1 12.3 1.0
NC N:HEA602 2.1 11.9 1.0
NE2 N:HIS376 2.2 11.1 1.0
O1 N:PER606 2.4 10.2 0.9
C1B N:HEA602 3.0 11.3 1.0
C4D N:HEA602 3.0 11.0 1.0
C1D N:HEA602 3.0 12.5 1.0
C1A N:HEA602 3.1 11.0 1.0
C4B N:HEA602 3.1 12.9 1.0
C4A N:HEA602 3.1 11.6 1.0
C4C N:HEA602 3.1 12.7 1.0
C1C N:HEA602 3.1 12.7 1.0
CD2 N:HIS376 3.1 12.0 1.0
CE1 N:HIS376 3.2 11.2 1.0
CHB N:HEA602 3.4 11.4 1.0
CHD N:HEA602 3.5 11.6 1.0
CHA N:HEA602 3.5 10.5 1.0
CHC N:HEA602 3.5 12.6 1.0
O1 N:PER606 3.7 11.7 0.1
O2 N:PER606 3.8 12.7 0.9
C2B N:HEA602 4.2 10.7 1.0
C3B N:HEA602 4.2 11.3 1.0
C2D N:HEA602 4.2 11.3 1.0
C3D N:HEA602 4.2 11.2 1.0
C2A N:HEA602 4.2 11.3 1.0
C3A N:HEA602 4.3 11.3 1.0
ND1 N:HIS376 4.3 12.1 1.0
CG N:HIS376 4.3 11.2 1.0
C2C N:HEA602 4.3 13.0 1.0
C3C N:HEA602 4.4 13.8 1.0
O2 N:PER606 4.7 11.2 0.1
CG2 N:VAL243 4.9 9.8 1.0
CU N:CU603 4.9 14.7 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: Sun Aug 4 22:39:57 2024

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