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Copper in PDB 1v6p: Crystal Structure of Cobrotoxin

Protein crystallography data

The structure of Crystal Structure of Cobrotoxin, PDB code: 1v6p was solved by X.Lou, X.Tu, J.Wang, M.Teng, L.Niu, Q.Liu, Q.Huang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 0.87
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 46.808, 47.287, 90.018, 90.00, 90.00, 90.00
R / Rfree (%) 11.9 / 15.3

Other elements in 1v6p:

The structure of Crystal Structure of Cobrotoxin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 4 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Cobrotoxin (pdb code 1v6p). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 18 binding sites of Copper where determined in the Crystal Structure of Cobrotoxin, PDB code: 1v6p:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 18 in 1v6p

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Copper binding site 1 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:6.4
occ:0.57
 CU A:CU302 0.0 6.4 0.6
CU A:CU302 0.7 7.7 0.2
CU A:CU302 0.8 9.7 0.1
CU A:CU302 1.5 26.6 0.2
NE2 A:HIS4 2.0 8.2 1.0
OD1 A:ASN62 2.0 8.8 0.7
OD1 A:ASN62 2.2 17.5 0.3
O A:HOH1219 2.3 7.8 0.8
CD2 A:HIS4 3.0 7.8 1.0
CE1 A:HIS4 3.0 8.6 1.0
CG A:ASN62 3.0 8.0 0.7
ND2 A:ASN62 3.4 9.1 0.7
CG A:ASN62 3.4 11.5 0.3
NA A:NA501 3.4 40.5 0.5
CB A:PRO12 4.0 9.6 1.0
O A:ARG59 4.0 7.6 1.0
ND1 A:HIS4 4.1 7.8 1.0
ND2 A:ASN62 4.1 13.9 0.3
CG A:HIS4 4.1 6.8 1.0
CG A:PRO12 4.2 10.4 1.0
NA A:NA501 4.3 8.2 0.5
CB A:ASN62 4.4 8.3 0.7
CB A:ASN62 4.5 12.5 0.3
CA A:ASN62 4.7 10.5 0.3
CB A:ARG59 4.8 7.3 1.0
O A:HOH1214 4.8 13.4 1.0
CA A:ASN62 4.8 7.7 0.7

Copper binding site 2 out of 18 in 1v6p

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Copper binding site 2 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:7.7
occ:0.16
 CU A:CU302 0.0 7.7 0.2
CU A:CU302 0.7 6.4 0.6
CU A:CU302 1.2 9.7 0.1
NE2 A:HIS4 2.0 8.2 1.0
CU A:CU302 2.1 26.6 0.2
OD1 A:ASN62 2.6 8.8 0.7
CE1 A:HIS4 2.8 8.6 1.0
OD1 A:ASN62 2.8 17.5 0.3
O A:HOH1219 2.8 7.8 0.8
CD2 A:HIS4 3.2 7.8 1.0
NA A:NA501 3.4 40.5 0.5
CB A:PRO12 3.4 9.6 1.0
CG A:ASN62 3.6 8.0 0.7
CG A:PRO12 3.6 10.4 1.0
ND1 A:HIS4 3.9 7.8 1.0
CG A:ASN62 4.0 11.5 0.3
ND2 A:ASN62 4.0 9.1 0.7
CG A:HIS4 4.1 6.8 1.0
NA A:NA501 4.4 8.2 0.5
O A:ARG59 4.7 7.6 1.0
ND2 A:ASN62 4.7 13.9 0.3
O A:HOH1214 4.8 13.4 1.0
CB A:ASN62 4.9 8.3 0.7
CA A:PRO12 5.0 8.0 1.0
CD A:PRO12 5.0 10.5 1.0

Copper binding site 3 out of 18 in 1v6p

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Copper binding site 3 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:9.7
occ:0.09
 CU A:CU302 0.0 9.7 0.1
CU A:CU302 0.8 6.4 0.6
CU A:CU302 1.2 7.7 0.2
CU A:CU302 1.2 26.6 0.2
O A:HOH1219 1.7 7.8 0.8
NE2 A:HIS4 2.2 8.2 1.0
OD1 A:ASN62 2.6 17.5 0.3
OD1 A:ASN62 2.7 8.8 0.7
CE1 A:HIS4 3.0 8.6 1.0
CD2 A:HIS4 3.4 7.8 1.0
CG A:ASN62 3.5 8.0 0.7
ND2 A:ASN62 3.6 9.1 0.7
CG A:ASN62 3.8 11.5 0.3
O A:ARG59 3.8 7.6 1.0
NA A:NA501 4.1 40.5 0.5
ND2 A:ASN62 4.2 13.9 0.3
ND1 A:HIS4 4.3 7.8 1.0
CB A:ARG59 4.3 7.3 1.0
CG A:HIS4 4.4 6.8 1.0
CB A:PRO12 4.5 9.6 1.0
CG A:PRO12 4.8 10.4 1.0
C A:ARG59 4.8 6.6 1.0
CB A:ASN62 5.0 8.3 0.7
NA A:NA501 5.0 8.2 0.5

Copper binding site 4 out of 18 in 1v6p

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Copper binding site 4 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu302

b:26.6
occ:0.18
 CU A:CU302 0.0 26.6 0.2
O A:HOH1219 1.2 7.8 0.8
CU A:CU302 1.2 9.7 0.1
CU A:CU302 1.5 6.4 0.6
CU A:CU302 2.1 7.7 0.2
NE2 A:HIS4 2.1 8.2 1.0
OD1 A:ASN62 2.4 17.5 0.3
OD1 A:ASN62 2.4 8.8 0.7
O A:ARG59 2.7 7.6 1.0
CD2 A:HIS4 2.9 7.8 1.0
CG A:ASN62 3.1 8.0 0.7
CE1 A:HIS4 3.1 8.6 1.0
ND2 A:ASN62 3.3 9.1 0.7
CG A:ASN62 3.3 11.5 0.3
CB A:ARG59 3.6 7.3 1.0
C A:ARG59 3.7 6.6 1.0
ND2 A:ASN62 3.9 13.9 0.3
CG A:HIS4 4.0 6.8 1.0
ND1 A:HIS4 4.1 7.8 1.0
CA A:ARG59 4.2 6.5 1.0
CB A:ASN62 4.5 12.5 0.3
CB A:ASN62 4.5 8.3 0.7
CG A:ARG59 4.6 7.9 1.0
NA A:NA501 4.6 40.5 0.5
CA A:ASN62 4.7 10.5 0.3
N A:ASN62 4.8 9.3 0.7
CA A:ASN62 4.9 7.7 0.7
N A:ASN62 4.9 6.4 0.3
N A:CYS60 4.9 6.5 1.0

Copper binding site 5 out of 18 in 1v6p

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Copper binding site 5 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu303

b:8.0
occ:0.77
 OE1 A:GLU2 1.9 8.6 0.5
O A:HOH1205 2.0 7.5 0.4
OE1 A:GLU2 2.0 9.0 0.4
OD2 A:ASP58 2.1 10.7 1.0
O A:HOH1206 2.4 13.1 1.0
OD1 A:ASP58 2.7 8.6 1.0
CG A:ASP58 2.7 8.0 1.0
CD A:GLU2 2.9 8.5 0.5
CD A:GLU2 3.0 8.1 0.4
CU A:CU307 3.1 6.2 0.1
OE2 A:GLU2 3.2 10.9 0.5
O A:HOH1281 3.3 10.1 0.2
OE2 A:GLU2 3.3 10.8 0.4
CG A:GLU2 4.0 9.1 0.1
OE2 A:GLU2 4.0 9.6 0.1
O A:HOH1208 4.1 10.3 0.2
O A:HOH1207 4.1 10.5 0.9
N A:GLU2 4.1 7.1 0.5
N A:GLU2 4.1 7.1 0.1
CA A:LEU1 4.2 8.3 1.0
CB A:ASP58 4.2 7.7 1.0
N A:GLU2 4.2 6.7 0.4
CG A:GLU2 4.2 8.0 0.5
N A:LEU1 4.3 10.7 1.0
CG A:GLU2 4.4 9.1 0.4
C A:LEU1 4.4 7.6 1.0
CD A:GLU2 4.5 9.1 0.1
O A:HOH1218 4.6 16.2 0.4
CB A:GLU2 4.7 7.6 0.5
CB A:GLU2 4.7 8.2 0.1
CB A:GLU2 4.7 8.3 0.4
O A:HOH1276 5.0 10.8 0.4

Copper binding site 6 out of 18 in 1v6p

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Copper binding site 6 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu304

b:9.7
occ:0.11
 OE2 A:GLU51 2.0 15.2 0.5
O A:HOH1271 2.0 19.1 0.7
O A:HOH1270 2.6 17.9 0.3
CD A:GLU51 2.9 13.0 0.5
O A:HOH1271 3.2 17.0 0.3
OE1 A:GLU51 3.2 21.2 0.5
O A:HOH1249 3.2 45.7 0.6
O A:HOH1287 3.5 26.0 0.6
O A:HOH1267 4.2 19.6 0.4
OE2 A:GLU51 4.2 29.7 0.5
CG A:GLU51 4.3 11.3 0.5
OE1 A:GLU51 4.5 27.1 0.5
CD A:GLU51 4.5 19.2 0.5
O A:HOH1248 4.6 19.8 0.4

Copper binding site 7 out of 18 in 1v6p

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Copper binding site 7 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu305

b:9.1
occ:0.45
 NH2 A:ARG59 3.1 9.3 1.0
O A:HOH1288 3.2 24.2 1.0
CZ A:ARG59 4.1 7.5 1.0
NH1 A:ARG59 4.2 8.1 1.0

Copper binding site 8 out of 18 in 1v6p

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Copper binding site 8 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu306

b:18.9
occ:0.38
 CU A:CU306 0.0 18.9 0.4
CU A:CU306 1.2 15.7 0.2
O B:HOH375 1.6 7.8 0.4
O B:HOH376 1.6 26.2 0.4
O B:HOH375 1.6 13.9 0.3
OD2 B:ASP58 1.9 22.5 1.0
OD2 A:ASP31 2.1 25.4 0.4
CG B:ASP58 2.8 16.7 1.0
OD1 A:ASP31 2.8 23.6 0.6
OD1 B:ASP58 2.9 17.8 1.0
OE1 B:GLU2 3.1 26.1 0.3
OD2 A:ASP31 3.1 28.9 0.6
CG A:ASP31 3.2 24.6 0.4
CG A:ASP31 3.3 23.4 0.6
O B:HOH321 3.5 30.8 0.5
OD1 A:ASP31 3.5 26.0 0.4
O A:HOH1244 4.0 34.1 1.0
O A:HOH1255 4.1 73.7 1.0
CD B:GLU2 4.2 20.7 0.3
CB B:ASP58 4.2 13.8 1.0
OE2 B:GLU2 4.4 26.2 0.3
O A:HOH1257 4.5 20.6 1.0
CB A:ASP31 4.6 22.0 0.4
CB A:ASP31 4.7 21.1 0.6
CA B:LEU1 4.8 14.8 1.0
N B:LEU1 5.0 17.9 1.0
CD A:ARG36 5.0 20.7 0.3

Copper binding site 9 out of 18 in 1v6p

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Copper binding site 9 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu306

b:15.7
occ:0.22
 CU A:CU306 0.0 15.7 0.2
CU A:CU306 1.2 18.9 0.4
OD2 A:ASP31 1.8 25.4 0.4
OD2 B:ASP58 2.0 22.5 1.0
OD1 A:ASP31 2.0 23.6 0.6
O B:HOH376 2.2 26.2 0.4
O B:HOH375 2.7 7.8 0.4
O B:HOH375 2.8 13.9 0.3
CG A:ASP31 2.8 23.4 0.6
OD2 A:ASP31 2.9 28.9 0.6
CG A:ASP31 2.9 24.6 0.4
CG B:ASP58 3.1 16.7 1.0
OD1 B:ASP58 3.5 17.8 1.0
OD1 A:ASP31 3.6 26.0 0.4
O A:HOH1257 3.9 20.6 1.0
CB A:ASP31 4.1 22.0 0.4
OE1 B:GLU2 4.1 26.1 0.3
CD A:ARG36 4.2 20.7 0.3
O A:HOH1244 4.2 34.1 1.0
CB A:ASP31 4.2 21.1 0.6
CB B:ASP58 4.2 13.8 1.0
O B:HOH321 4.7 30.8 0.5
NH1 A:ARG36 4.8 23.3 0.3
O A:HOH1255 4.9 73.7 1.0
NE A:ARG36 5.0 23.7 0.3

Copper binding site 10 out of 18 in 1v6p

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Copper binding site 10 out of 18 in the Crystal Structure of Cobrotoxin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Cobrotoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu307

b:6.2
occ:0.13
 OE2 A:GLU2 1.6 10.8 0.4
OE2 A:GLU2 1.9 10.9 0.5
O A:HOH1208 2.0 10.3 0.2
O A:HOH1205 2.0 7.5 0.4
O A:HOH1218 2.1 16.2 0.4
O A:HOH1281 2.1 10.1 0.2
CD A:GLU2 2.7 8.1 0.4
CD A:GLU2 2.7 8.5 0.5
OE1 A:GLU2 3.0 8.6 0.5
OE1 A:GLU2 3.0 9.0 0.4
O A:HOH1206 3.1 13.1 1.0
CU A:CU303 3.1 8.0 0.8
O A:HOH1209 3.7 47.4 0.5
CG A:GLU2 4.0 9.1 0.4
CG A:GLU2 4.0 8.0 0.5
N A:LEU1 4.3 10.7 1.0
O A:HOH1204 4.8 15.2 1.0
C A:LEU1 4.8 7.6 1.0
CA A:LEU1 4.9 8.3 1.0
OD2 A:ASP58 5.0 10.7 1.0

Reference:

X.Lou, Q.Liu, X.Tu, J.Wang, M.Teng, L.Niu, D.J.Schuller, Q.Huang, Q.Hao. The Atomic Resolution Crystal Structure of Atratoxin Determined By Single Wavelength Anomalous Diffraction Phasing J.Biol.Chem. V. 279 39094 2004.
ISSN: ISSN 0021-9258
PubMed: 15252034
DOI: 10.1074/JBC.M403863200
Page generated: Mon Jul 14 00:32:23 2025

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