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Copper 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
Sodium (Na) 4 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 6 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3wg7

Go back to Copper Binding Sites List in 3wg7
Copper binding site 1 out of 6 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 Copper with other atoms in the Cu 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:Cu603

b:15.8
occ:1.00
 NE2 A:HIS291 1.9 19.1 1.0
O2 A:PER606 2.0 11.2 0.1
NE2 A:HIS290 2.0 13.9 1.0
ND1 A:HIS240 2.1 16.3 1.0
O2 A:PER606 2.1 12.7 0.9
O1 A:PER606 2.7 10.2 0.9
CE1 A:HIS291 2.9 13.7 1.0
CD2 A:HIS291 2.9 13.9 1.0
CE1 A:HIS290 3.0 14.2 1.0
CG A:HIS240 3.0 14.0 1.0
CD2 A:HIS290 3.0 13.4 1.0
CE1 A:HIS240 3.1 13.9 1.0
O1 A:PER606 3.1 11.7 0.1
CB A:HIS240 3.3 12.6 1.0
CA A:HIS240 3.9 12.6 1.0
ND1 A:HIS291 4.0 14.8 1.0
CG A:HIS291 4.0 15.4 1.0
ND1 A:HIS290 4.1 13.9 1.0
CD2 A:HIS240 4.2 15.2 1.0
NE2 A:HIS240 4.2 15.7 1.0
CG A:HIS290 4.2 13.8 1.0
C1A A:HEA602 4.5 11.8 1.0
NA A:HEA602 4.6 11.2 1.0
C4A A:HEA602 4.6 12.2 1.0
N A:HIS240 4.7 13.2 1.0
C2A A:HEA602 4.8 14.0 1.0
C3A A:HEA602 4.9 12.5 1.0
FE A:HEA602 4.9 14.8 1.0
CG2 A:VAL243 5.0 11.7 1.0

Copper binding site 2 out of 6 in 3wg7

Go back to Copper Binding Sites List in 3wg7
Copper binding site 2 out of 6 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 Copper with other atoms in the Cu 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
B:Cu302

b:14.8
occ:1.00
 CU1 B:CUA302 0.0 14.8 1.0
ND1 B:HIS161 2.0 13.8 1.0
SG B:CYS200 2.3 13.9 1.0
SG B:CYS196 2.3 15.3 1.0
SD B:MET207 2.4 14.9 1.0
CU2 B:CUA302 2.5 15.2 1.0
CE1 B:HIS161 2.9 12.4 1.0
CG B:HIS161 3.2 13.0 1.0
CE B:MET207 3.2 15.9 1.0
CB B:CYS196 3.4 13.9 1.0
CB B:CYS200 3.4 12.1 1.0
CG B:MET207 3.5 12.8 1.0
CB B:HIS161 3.6 12.1 1.0
O B:GLU198 3.8 13.2 1.0
NE2 B:HIS161 4.0 13.1 1.0
CA B:HIS161 4.2 11.9 1.0
CD2 B:HIS161 4.2 13.0 1.0
ND1 B:HIS204 4.5 14.5 1.0
O B:LEU160 4.7 11.4 1.0
O B:HIS102 4.8 13.6 1.0
CA B:CYS196 4.8 14.6 1.0
CA B:HIS204 4.8 13.2 1.0
CD1 B:TRP104 4.8 13.6 1.0
CA B:CYS200 4.8 12.4 1.0
CB B:MET207 4.8 12.2 1.0
O B:HIS204 4.9 12.3 1.0

Copper binding site 3 out of 6 in 3wg7

Go back to Copper Binding Sites List in 3wg7
Copper binding site 3 out of 6 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 Copper with other atoms in the Cu 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
B:Cu302

b:15.2
occ:1.00
 CU2 B:CUA302 0.0 15.2 1.0
ND1 B:HIS204 2.0 14.5 1.0
O B:GLU198 2.2 13.2 1.0
SG B:CYS200 2.3 13.9 1.0
SG B:CYS196 2.3 15.3 1.0
CU1 B:CUA302 2.5 14.8 1.0
CE1 B:HIS204 2.9 13.0 1.0
CG B:HIS204 3.1 12.3 1.0
C B:GLU198 3.3 10.4 1.0
CB B:CYS200 3.4 12.1 1.0
CB B:CYS196 3.5 13.9 1.0
CB B:HIS204 3.5 13.6 1.0
CA B:HIS204 3.6 13.2 1.0
N B:CYS200 3.7 14.3 1.0
O B:HIS204 3.8 12.3 1.0
NE2 B:HIS204 4.0 15.6 1.0
C B:ILE199 4.1 12.7 1.0
N B:GLU198 4.1 13.8 1.0
CD2 B:HIS204 4.1 12.8 1.0
ND1 B:HIS161 4.1 13.8 1.0
N B:ILE199 4.2 11.6 1.0
C B:HIS204 4.2 12.9 1.0
CA B:CYS200 4.2 12.4 1.0
CA B:ILE199 4.2 13.4 1.0
C B:CYS196 4.3 15.1 1.0
O B:CYS196 4.3 12.6 1.0
SD B:MET207 4.4 14.9 1.0
CA B:GLU198 4.4 12.6 1.0
CA B:CYS196 4.5 14.6 1.0
CG B:MET207 4.7 12.8 1.0
N B:SER197 4.7 14.1 1.0
N B:HIS204 4.8 13.2 1.0
O B:ILE199 4.9 14.6 1.0
CE1 B:HIS161 4.9 12.4 1.0
CA B:HIS161 4.9 11.9 1.0

Copper binding site 4 out of 6 in 3wg7

Go back to Copper Binding Sites List in 3wg7
Copper binding site 4 out of 6 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 Copper with other atoms in the Cu 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:Cu603

b:14.7
occ:1.00
 O2 N:PER606 2.0 11.2 0.1
NE2 N:HIS291 2.0 17.7 1.0
ND1 N:HIS240 2.1 13.2 1.0
O2 N:PER606 2.1 12.7 0.9
NE2 N:HIS290 2.1 15.2 1.0
O1 N:PER606 2.7 10.2 0.9
CE1 N:HIS291 2.9 11.3 1.0
CD2 N:HIS291 2.9 12.3 1.0
CD2 N:HIS290 3.0 13.8 1.0
CG N:HIS240 3.0 13.1 1.0
O1 N:PER606 3.1 11.7 0.1
CE1 N:HIS240 3.1 14.1 1.0
CE1 N:HIS290 3.2 16.4 1.0
CB N:HIS240 3.3 13.3 1.0
CA N:HIS240 3.9 13.7 1.0
ND1 N:HIS291 4.0 13.2 1.0
CG N:HIS291 4.0 12.7 1.0
CD2 N:HIS240 4.2 13.6 1.0
NE2 N:HIS240 4.2 16.1 1.0
CG N:HIS290 4.2 14.9 1.0
ND1 N:HIS290 4.3 13.8 1.0
C1A N:HEA602 4.6 11.0 1.0
NA N:HEA602 4.6 12.3 1.0
C4A N:HEA602 4.6 11.6 1.0
N N:HIS240 4.8 13.5 1.0
C2A N:HEA602 4.8 11.3 1.0
C3A N:HEA602 4.9 11.3 1.0
FE N:HEA602 4.9 14.1 1.0
CG2 N:VAL243 4.9 9.8 1.0

Copper binding site 5 out of 6 in 3wg7

Go back to Copper Binding Sites List in 3wg7
Copper binding site 5 out of 6 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 Copper with other atoms in the Cu binding site number 5 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
O:Cu301

b:14.2
occ:1.00
 CU1 O:CUA301 0.0 14.2 1.0
ND1 O:HIS161 2.0 12.9 1.0
SG O:CYS200 2.3 13.0 1.0
SG O:CYS196 2.3 15.3 1.0
SD O:MET207 2.4 14.4 1.0
CU2 O:CUA301 2.6 15.6 1.0
CE1 O:HIS161 2.8 11.8 1.0
CE O:MET207 3.1 11.2 1.0
CG O:HIS161 3.2 13.6 1.0
CB O:CYS200 3.3 12.4 1.0
CB O:CYS196 3.4 12.2 1.0
CG O:MET207 3.5 12.5 1.0
CB O:HIS161 3.7 14.0 1.0
O O:GLU198 3.9 10.1 1.0
NE2 O:HIS161 4.0 13.2 1.0
CA O:HIS161 4.2 13.4 1.0
CD2 O:HIS161 4.2 12.3 1.0
ND1 O:HIS204 4.5 12.2 1.0
CA O:HIS204 4.6 12.2 1.0
CA O:CYS200 4.7 12.1 1.0
O O:LEU160 4.7 13.8 1.0
O O:HIS102 4.8 13.1 1.0
CA O:CYS196 4.8 13.4 1.0
CD1 O:TRP104 4.9 11.7 1.0
CB O:MET207 4.9 11.5 1.0
O O:HIS204 4.9 10.7 1.0

Copper binding site 6 out of 6 in 3wg7

Go back to Copper Binding Sites List in 3wg7
Copper binding site 6 out of 6 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 Copper with other atoms in the Cu binding site number 6 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
O:Cu301

b:15.6
occ:1.00
 CU2 O:CUA301 0.0 15.6 1.0
ND1 O:HIS204 2.0 12.2 1.0
O O:GLU198 2.2 10.1 1.0
SG O:CYS200 2.3 13.0 1.0
SG O:CYS196 2.3 15.3 1.0
CU1 O:CUA301 2.6 14.2 1.0
CE1 O:HIS204 2.9 12.2 1.0
CG O:HIS204 3.0 11.2 1.0
CB O:CYS200 3.3 12.4 1.0
C O:GLU198 3.3 10.5 1.0
CB O:HIS204 3.4 12.2 1.0
CB O:CYS196 3.4 12.2 1.0
CA O:HIS204 3.6 12.2 1.0
N O:CYS200 3.6 12.6 1.0
O O:HIS204 3.9 10.7 1.0
NE2 O:HIS204 4.0 10.3 1.0
C O:ILE199 4.1 13.4 1.0
CA O:CYS200 4.1 12.1 1.0
CD2 O:HIS204 4.1 10.8 1.0
N O:ILE199 4.1 11.8 1.0
N O:GLU198 4.1 10.7 1.0
C O:HIS204 4.1 12.9 1.0
ND1 O:HIS161 4.2 12.9 1.0
CA O:ILE199 4.2 13.2 1.0
C O:CYS196 4.3 13.9 1.0
O O:CYS196 4.3 11.2 1.0
CA O:GLU198 4.4 12.0 1.0
SD O:MET207 4.4 14.4 1.0
CA O:CYS196 4.5 13.4 1.0
CG O:MET207 4.8 12.5 1.0
N O:SER197 4.8 12.2 1.0
N O:HIS204 4.9 12.6 1.0
O O:ILE199 4.9 11.7 1.0
CA O:HIS161 4.9 13.4 1.0
CE1 O:HIS161 4.9 11.8 1.0
C O:CYS200 5.0 13.8 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 Dec 13 11:12:42 2020

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