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Calcium in PDB 5etl: E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution

Enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution

All present enzymatic activity of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution:
2.7.6.3;

Protein crystallography data

The structure of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution, PDB code: 5etl was solved by M.L.Dennis, T.S.Peat, J.D.Swarbrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.81 / 1.82
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.447, 36.179, 121.330, 90.00, 90.32, 90.00
R / Rfree (%) 20.2 / 24.1

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution (pdb code 5etl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution, PDB code: 5etl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 5etl

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Calcium binding site 1 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:13.4
occ:1.00
 O A:HOH324 2.2 20.5 1.0
O2A A:ATP205 2.3 13.4 1.0
OD1 A:ASP95 2.3 8.8 1.0
O1B A:ATP205 2.3 14.6 1.0
O A:HOH368 2.3 13.2 1.0
OD1 A:ASP97 2.4 15.0 1.0
CG A:ASP95 3.3 13.6 1.0
PA A:ATP205 3.4 18.1 1.0
PB A:ATP205 3.4 17.5 1.0
OD2 A:ASP95 3.6 19.4 1.0
O3A A:ATP205 3.6 22.5 1.0
CG A:ASP97 3.6 15.2 1.0
O5' A:ATP205 3.8 17.3 1.0
CA A:CA202 3.8 18.9 1.0
OD2 A:ASP97 4.1 18.7 1.0
NH1 A:ARG82 4.1 17.2 1.0
O2B A:ATP205 4.3 20.0 1.0
OE2 A:GLU77 4.3 12.1 1.0
O A:LEU96 4.4 13.2 1.0
O A:HOH313 4.4 26.6 1.0
NH2 A:ARG82 4.4 13.6 1.0
NH1 A:ARG92 4.5 34.7 1.0
O A:HOH358 4.6 14.2 1.0
CB A:ASP95 4.6 10.7 1.0
C A:LEU96 4.7 12.1 1.0
C2 A:ATP205 4.7 15.3 1.0
O1A A:ATP205 4.7 17.7 1.0
O3B A:ATP205 4.7 17.2 1.0
CB A:ASP97 4.8 13.3 1.0
CZ A:ARG82 4.8 19.0 1.0
N3 A:ATP205 4.8 13.8 1.0
N A:LEU96 4.8 9.5 1.0
CA A:ASP97 4.8 11.7 1.0
O1G A:ATP205 4.9 18.8 1.0
N A:ASP97 4.9 10.0 1.0
O2G A:ATP205 4.9 18.8 1.0

Calcium binding site 2 out of 11 in 5etl

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Calcium binding site 2 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:18.9
occ:1.00
 O2G A:ATP205 2.3 18.8 1.0
O A:HOH413 2.3 24.8 1.0
OD2 A:ASP97 2.4 18.7 1.0
OD2 A:ASP95 2.4 19.4 1.0
O A:HOH415 2.4 25.1 1.0
O1B A:ATP205 2.4 14.6 1.0
CG A:ASP97 3.2 15.2 1.0
OD1 A:ASP97 3.3 15.0 1.0
CG A:ASP95 3.4 13.6 1.0
PB A:ATP205 3.5 17.5 1.0
PG A:ATP205 3.5 17.2 1.0
O3B A:ATP205 3.7 17.2 1.0
OD1 A:ASP95 3.8 8.8 1.0
CA A:CA201 3.8 13.4 1.0
NH1 A:ARG121 4.0 10.2 1.0
O2B A:ATP205 4.2 20.0 1.0
O A:HOH315 4.2 21.9 1.0
O1G A:ATP205 4.2 18.8 1.0
O A:HOH388 4.2 22.6 1.0
O A:HOH405 4.5 33.4 1.0
CB A:ASP97 4.6 13.3 1.0
CB A:ASP95 4.7 10.7 1.0
O3G A:ATP205 4.8 14.4 1.0
NE2 A:HIS115 4.8 11.8 1.0
N18 A:5RV206 4.8 19.6 1.0
NH1 A:ARG92 4.9 34.7 1.0
O3A A:ATP205 4.9 22.5 1.0
O A:HOH419 4.9 22.1 1.0

Calcium binding site 3 out of 11 in 5etl

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Calcium binding site 3 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:23.3
occ:1.00
 O B:HOH372 2.3 17.4 1.0
O A:HOH359 2.3 27.8 1.0
O B:HOH354 2.3 28.7 1.0
O A:HOH372 2.4 23.8 1.0
O A:HOH302 2.5 34.2 1.0
O B:HOH311 2.6 28.1 1.0
OD2 B:ASP117 4.3 8.0 1.0
O A:HOH426 4.4 31.9 1.0
OD2 A:ASP117 4.4 9.2 1.0
O B:HOH403 4.6 26.3 1.0
CB A:ASN120 4.6 8.4 1.0
O A:HOH421 4.6 26.4 1.0
OD1 B:ASP117 4.7 6.2 1.0
OD1 A:ASP117 4.7 7.3 1.0
CG B:ASP117 4.9 8.8 1.0
O A:ASN120 4.9 7.7 1.0
CG A:ASP117 5.0 9.4 1.0

Calcium binding site 4 out of 11 in 5etl

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Calcium binding site 4 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:28.8
occ:1.00
 O A:HOH430 2.9 24.5 1.0
O A:HOH425 3.0 29.2 1.0
CG A:ASP139 3.3 13.1 1.0
OD1 A:ASP139 3.3 11.4 1.0
N A:ASP139 3.4 7.5 1.0
NZ A:LYS119 3.6 19.0 1.0
CD A:PRO138 3.6 9.8 1.0
CB A:ASP139 3.6 11.0 1.0
CB A:PHE137 3.7 7.3 1.0
CG A:PRO114 3.7 7.2 1.0
N A:PRO138 3.8 7.9 1.0
OD2 A:ASP139 3.9 16.8 1.0
CE A:LYS119 4.0 15.5 1.0
O A:HOH327 4.1 35.2 1.0
CB A:PRO138 4.1 9.1 1.0
CA A:ASP139 4.1 9.0 1.0
CG A:PRO138 4.2 10.9 1.0
CD2 A:PHE137 4.3 11.3 1.0
C A:PRO138 4.3 7.6 1.0
CA A:PRO138 4.3 8.2 1.0
CG A:PHE137 4.3 8.5 1.0
C A:PHE137 4.4 6.5 1.0
CD A:PRO114 4.6 9.2 1.0
CA A:PHE137 4.6 6.7 1.0
CB A:PRO114 4.6 7.7 1.0

Calcium binding site 5 out of 11 in 5etl

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Calcium binding site 5 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:15.4
occ:1.00
 O B:HOH306 2.2 19.9 1.0
OD1 B:ASP95 2.2 12.9 1.0
O1A B:ATP203 2.3 16.2 1.0
O2B B:ATP203 2.3 12.9 1.0
O B:HOH359 2.3 15.8 1.0
OD1 B:ASP97 2.4 15.1 1.0
CG B:ASP95 3.2 16.4 1.0
PA B:ATP203 3.4 19.0 1.0
PB B:ATP203 3.5 17.7 1.0
OD2 B:ASP95 3.5 20.1 1.0
O3A B:ATP203 3.5 31.4 1.0
CG B:ASP97 3.6 12.2 1.0
O5' B:ATP203 3.8 20.4 1.0
CA B:CA202 3.8 17.3 1.0
OD2 B:ASP97 4.1 23.0 1.0
NH1 B:ARG82 4.1 22.1 1.0
OE2 B:GLU77 4.3 14.0 1.0
O B:LEU96 4.3 15.7 1.0
O1B B:ATP203 4.5 20.1 1.0
O B:HOH371 4.5 16.0 1.0
NH2 B:ARG82 4.5 24.8 1.0
CB B:ASP95 4.6 9.8 1.0
C B:LEU96 4.6 12.1 1.0
NH1 B:ARG92 4.7 34.3 1.0
N B:LEU96 4.7 7.8 1.0
N3 B:ATP203 4.7 12.7 1.0
O3B B:ATP203 4.7 17.0 1.0
C2 B:ATP203 4.7 15.4 1.0
O2A B:ATP203 4.8 19.4 1.0
CB B:ASP97 4.8 10.8 1.0
CZ B:ARG82 4.8 22.0 1.0
O2G B:ATP203 4.8 19.6 1.0
CA B:ASP97 4.8 9.2 1.0
O1G B:ATP203 4.9 15.8 1.0
N B:ASP97 4.9 8.4 1.0
CA B:ASP95 5.0 8.0 1.0

Calcium binding site 6 out of 11 in 5etl

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Calcium binding site 6 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:17.3
occ:1.00
 O B:HOH387 2.2 22.4 1.0
O1G B:ATP203 2.2 15.8 1.0
O B:HOH395 2.4 23.4 1.0
O2B B:ATP203 2.4 12.9 1.0
OD2 B:ASP95 2.5 20.1 1.0
OD2 B:ASP97 2.5 23.0 1.0
CG B:ASP97 3.3 12.2 1.0
OD1 B:ASP97 3.3 15.1 1.0
PB B:ATP203 3.4 17.7 1.0
PG B:ATP203 3.5 17.5 1.0
CG B:ASP95 3.5 16.4 1.0
O3B B:ATP203 3.6 17.0 1.0
CA B:CA201 3.8 15.4 1.0
OD1 B:ASP95 3.8 12.9 1.0
NH1 B:ARG121 4.0 13.4 1.0
O1B B:ATP203 4.2 20.1 1.0
O B:HOH367 4.2 21.6 1.0
O2G B:ATP203 4.2 19.6 1.0
O B:HOH308 4.3 24.1 1.0
O3G B:ATP203 4.6 18.7 1.0
CB B:ASP95 4.7 9.8 1.0
CB B:ASP97 4.7 10.8 1.0
N18 B:5RV204 4.8 23.1 1.0
O3A B:ATP203 4.8 31.4 1.0
NE2 B:HIS115 4.8 14.0 1.0
NH1 B:ARG92 4.9 34.3 1.0

Calcium binding site 7 out of 11 in 5etl

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Calcium binding site 7 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:14.2
occ:1.00
 OD1 C:ASP97 2.2 12.9 1.0
O1A C:ATP204 2.2 18.3 1.0
OD1 C:ASP95 2.2 13.9 1.0
O2B C:ATP204 2.3 14.9 1.0
O C:HOH317 2.4 16.0 1.0
O C:HOH384 2.5 13.7 1.0
CG C:ASP95 3.2 14.8 1.0
PA C:ATP204 3.3 17.9 1.0
CG C:ASP97 3.4 14.3 1.0
PB C:ATP204 3.4 17.1 1.0
O3A C:ATP204 3.5 25.6 1.0
OD2 C:ASP95 3.5 18.9 1.0
O5' C:ATP204 3.8 19.4 1.0
CA C:CA202 3.8 16.0 1.0
OD2 C:ASP97 4.0 21.4 1.0
O C:LEU96 4.2 16.2 1.0
NH1 C:ARG82 4.2 19.3 1.0
O1B C:ATP204 4.3 17.1 1.0
OE2 C:GLU77 4.3 17.3 1.0
O C:HOH380 4.5 14.7 1.0
C C:LEU96 4.5 13.3 1.0
CB C:ASP95 4.6 12.2 1.0
CB C:ASP97 4.6 11.6 1.0
NH2 C:ARG82 4.6 28.4 1.0
C2 C:ATP204 4.6 13.6 1.0
N C:LEU96 4.6 10.1 1.0
O3B C:ATP204 4.6 16.0 1.0
CA C:ASP97 4.7 9.6 1.0
N3 C:ATP204 4.7 12.3 1.0
O2A C:ATP204 4.7 17.9 1.0
O2G C:ATP204 4.7 17.7 1.0
N C:ASP97 4.8 9.2 1.0
O1G C:ATP204 4.8 19.2 1.0
CZ C:ARG82 4.9 23.6 1.0
CA C:ASP95 5.0 11.9 1.0

Calcium binding site 8 out of 11 in 5etl

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Calcium binding site 8 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:16.0
occ:1.00
 OD2 C:ASP97 2.2 21.4 1.0
O1G C:ATP204 2.3 19.2 1.0
OD2 C:ASP95 2.3 18.9 1.0
O2B C:ATP204 2.3 14.9 1.0
O C:HOH385 2.4 18.3 1.0
O C:HOH410 2.5 18.1 1.0
CG C:ASP97 3.1 14.3 1.0
OD1 C:ASP97 3.2 12.9 1.0
CG C:ASP95 3.4 14.8 1.0
PB C:ATP204 3.4 17.1 1.0
PG C:ATP204 3.5 15.5 1.0
O3B C:ATP204 3.6 16.0 1.0
OD1 C:ASP95 3.8 13.9 1.0
CA C:CA201 3.8 14.2 1.0
NH1 C:ARG121 4.0 8.8 1.0
O1B C:ATP204 4.1 17.1 1.0
O C:HOH393 4.1 18.3 1.0
NH1 C:ARG92 4.1 47.4 1.0
O C:HOH337 4.2 16.5 1.0
O2G C:ATP204 4.3 17.7 1.0
CB C:ASP97 4.5 11.6 1.0
CB C:ASP95 4.6 12.2 1.0
O C:HOH417 4.7 19.3 1.0
O3G C:ATP204 4.7 16.5 1.0
NE2 C:HIS115 4.7 10.2 1.0
N18 C:5RV205 4.8 17.5 1.0
CE C:MET124 4.8 22.8 1.0
O3A C:ATP204 4.8 25.6 1.0

Calcium binding site 9 out of 11 in 5etl

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Calcium binding site 9 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca203

b:18.2
occ:1.00
 O C:HOH375 2.3 23.2 1.0
O D:HOH364 2.3 23.6 1.0
O D:HOH411 2.3 19.2 1.0
O C:HOH431 2.4 34.1 1.0
O C:HOH400 2.4 23.3 1.0
O D:HOH303 2.6 25.2 1.0
O C:HOH347 2.6 24.6 1.0
OD2 D:ASP117 4.1 7.2 1.0
OD2 C:ASP117 4.3 6.5 1.0
O D:HOH418 4.4 21.3 1.0
OD1 C:ASP117 4.5 4.9 1.0
O D:HOH425 4.5 27.9 1.0
OD1 D:ASP117 4.5 6.7 1.0
O C:HOH423 4.6 23.8 1.0
CB C:ASN120 4.6 6.9 1.0
O C:HOH419 4.6 31.1 1.0
CB D:ASN120 4.7 7.7 1.0
CG D:ASP117 4.7 10.1 1.0
CG C:ASP117 4.8 6.5 1.0
O C:HOH368 4.9 38.9 1.0

Calcium binding site 10 out of 11 in 5etl

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Calcium binding site 10 out of 11 in the E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of E. Coli 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Complexed with Ampcpp and Inhibitor at 1.82 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:12.4
occ:1.00
 OD1 D:ASP95 2.3 9.9 1.0
OD1 D:ASP97 2.3 13.1 1.0
O D:HOH378 2.3 11.7 1.0
O2A D:ATP203 2.3 12.4 1.0
O D:HOH317 2.3 17.0 1.0
O1B D:ATP203 2.4 13.0 1.0
PA D:ATP203 3.2 16.7 1.0
CG D:ASP95 3.3 10.2 1.0
PB D:ATP203 3.4 16.6 1.0
O3A D:ATP203 3.4 20.7 1.0
CG D:ASP97 3.5 11.2 1.0
OD2 D:ASP95 3.5 16.3 1.0
O5' D:ATP203 3.7 19.6 1.0
CA D:CA202 3.8 14.7 1.0
OD2 D:ASP97 4.0 17.9 1.0
NH1 D:ARG82 4.2 18.3 1.0
O2B D:ATP203 4.2 19.2 1.0
O D:LEU96 4.3 13.0 1.0
OE2 D:GLU77 4.3 15.3 1.0
O D:HOH327 4.4 26.6 1.0
O D:HOH402 4.5 15.2 1.0
O1A D:ATP203 4.5 15.6 1.0
NH2 D:ARG82 4.5 28.6 1.0
O3B D:ATP203 4.6 15.8 1.0
CB D:ASP95 4.6 9.8 1.0
C D:LEU96 4.6 12.0 1.0
CB D:ASP97 4.7 10.6 1.0
O1G D:ATP203 4.7 17.5 1.0
N3 D:ATP203 4.7 9.8 1.0
CA D:ASP97 4.7 11.4 1.0
C2 D:ATP203 4.7 13.0 1.0
N D:LEU96 4.8 11.0 1.0
CZ D:ARG82 4.9 29.0 1.0
N D:ASP97 4.9 10.4 1.0
O2G D:ATP203 4.9 13.3 1.0

Reference:

M.L.Dennis, N.P.Pitcher, M.D.Lee, A.J.Debono, Z.C.Wang, J.R.Harjani, R.Rahmani, B.Cleary, T.S.Peat, J.B.Baell, J.D.Swarbrick. Structural Basis For the Selective Binding of Inhibitors to 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase From Staphylococcus Aureus and Escherichia Coli. J.Med.Chem. V. 59 5248 2016.
ISSN: ISSN 0022-2623
PubMed: 27094768
DOI: 10.1021/ACS.JMEDCHEM.6B00002
Page generated: Sun Jul 14 18:49:13 2024

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