Atomistry » Copper » PDB 3t6w-3x1n » 3wg7
Atomistry »
  Copper »
    PDB 3t6w-3x1n »
      3wg7 »

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: Wed Jul 31 02:21:25 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy