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Magnesium in PDB 3g6k: Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate

Enzymatic activity of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate

All present enzymatic activity of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate:
2.7.7.2;

Protein crystallography data

The structure of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate, PDB code: 3g6k was solved by C.Huerta, M.Machius, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.19 / 1.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 206.583, 81.481, 136.603, 90.00, 129.79, 90.00
R / Rfree (%) 15.3 / 18.7

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate (pdb code 3g6k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate, PDB code: 3g6k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 3g6k

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Magnesium binding site 1 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:7.6
occ:1.00
 O2A A:FAD306 2.0 10.0 1.0
O5 A:POP305 2.0 8.4 1.0
O2 A:POP305 2.1 8.3 1.0
O A:HOH314 2.1 9.3 1.0
OD2 A:ASP66 2.1 8.2 1.0
O A:HOH312 2.1 9.0 1.0
CG A:ASP66 3.1 7.7 1.0
P2 A:POP305 3.2 8.4 1.0
PA A:FAD306 3.2 12.0 1.0
P1 A:POP305 3.3 8.2 1.0
O A:POP305 3.4 8.3 1.0
CB A:ASP66 3.6 7.9 1.0
O1A A:FAD306 3.8 14.1 1.0
O A:HOH352 3.8 16.5 1.0
O5B A:FAD306 3.9 12.1 1.0
NZ A:LYS65 4.0 8.5 1.0
OD2 A:ASP168 4.0 10.1 1.0
OD1 A:ASP66 4.1 8.6 1.0
C5B A:FAD306 4.1 11.3 1.0
OD1 A:ASP168 4.1 13.7 1.0
O3 A:POP305 4.1 10.3 1.0
O6 A:POP305 4.2 8.8 1.0
O4 A:POP305 4.3 9.6 1.0
O1 A:POP305 4.3 9.3 1.0
NH1 A:ARG297 4.3 15.9 0.6
OE2 A:GLU296 4.4 12.7 1.0
O3P A:FAD306 4.4 14.5 1.0
CG A:ASP168 4.5 10.1 1.0
O A:GLY163 4.6 10.6 1.0
NH2 A:ARG165 4.6 9.4 1.0
O3B A:FAD306 4.7 10.7 1.0
CA A:ASP66 4.9 7.4 1.0
MG A:MG308 4.9 14.7 0.5
N A:ASP66 4.9 7.1 1.0

Magnesium binding site 2 out of 13 in 3g6k

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Magnesium binding site 2 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:14.7
occ:0.50
 O A:HOH668 1.7 17.5 0.5
O A:HOH1808 2.0 16.2 0.5
O1A A:FAD306 2.0 14.1 1.0
O A:HOH1809 2.1 17.6 0.5
O3 A:POP305 2.1 10.3 1.0
O A:LEU223 2.6 16.7 1.0
P1 A:POP305 3.4 8.2 1.0
PA A:FAD306 3.4 12.0 1.0
C A:LEU223 3.4 12.0 1.0
O A:HOH1829 3.6 12.8 0.5
O2 A:POP305 3.8 8.3 1.0
N A:LEU223 3.8 9.9 1.0
O1P A:FAD306 4.0 18.0 1.0
O4 A:POP305 4.1 9.6 1.0
CA A:LEU223 4.1 11.2 1.0
O2A A:FAD306 4.1 10.0 1.0
O A:POP305 4.2 8.3 1.0
O3P A:FAD306 4.2 14.5 1.0
O A:HOH352 4.2 16.5 1.0
N A:GLY224 4.3 10.4 1.0
OG A:SER222 4.5 12.4 1.0
O5B A:FAD306 4.5 12.1 1.0
O1 A:POP305 4.5 9.3 1.0
CB A:LEU223 4.5 12.4 1.0
CA A:GLY224 4.6 11.3 1.0
P2 A:POP305 4.6 8.4 1.0
O A:HOH593 4.7 22.7 0.5
ND2 A:ASN62 4.7 14.9 1.0
O5 A:POP305 4.7 8.4 1.0
O A:HOH934 4.7 28.9 1.0
P A:FAD306 4.8 19.3 1.0
NH1 A:ARG297 4.8 15.9 0.6
C A:SER222 4.8 10.6 1.0
MG A:MG307 4.9 7.6 1.0
O A:HOH1823 5.0 24.8 0.5

Magnesium binding site 3 out of 13 in 3g6k

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Magnesium binding site 3 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:20.7
occ:0.50
 O A:HOH1297 1.9 25.2 0.5
O A:HOH437 2.0 21.8 1.0
O A:HOH685 2.1 27.8 1.0
O A:HOH1342 2.1 21.1 0.5
O A:HOH1392 2.2 18.0 0.5
O A:SER135 4.1 13.3 1.0
OE1 A:GLU134 4.3 25.6 1.0
O A:HOH536 4.3 24.3 1.0
OE1 F:GLU265 4.3 40.5 1.0
OD2 A:ASP109 4.3 14.2 1.0
O F:HOH1569 4.5 39.8 1.0
N A:ARG137 4.5 14.3 1.0
O F:GLY-3 4.5 28.3 1.0
CB A:GLU134 4.6 14.6 1.0
O A:GLU134 4.8 14.4 1.0
CA A:ASP136 4.8 15.4 1.0
CB A:ARG137 4.9 17.6 1.0
C A:SER135 5.0 13.2 1.0

Magnesium binding site 4 out of 13 in 3g6k

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Magnesium binding site 4 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:9.6
occ:1.00
 O2A B:FAD306 2.0 11.9 1.0
O3 B:POP305 2.0 10.8 1.0
O4 B:POP305 2.1 10.6 1.0
OD2 B:ASP66 2.1 10.3 1.0
O B:HOH316 2.1 11.0 1.0
O B:HOH312 2.1 11.1 1.0
CG B:ASP66 3.1 10.3 1.0
P1 B:POP305 3.2 10.2 1.0
PA B:FAD306 3.2 13.7 1.0
P2 B:POP305 3.2 9.9 1.0
O B:POP305 3.4 10.1 1.0
CB B:ASP66 3.6 10.2 1.0
O B:HOH322 3.8 22.5 1.0
O1A B:FAD306 3.9 15.3 1.0
O5B B:FAD306 3.9 13.1 1.0
OD2 B:ASP168 4.0 13.5 1.0
NZ B:LYS65 4.0 10.0 1.0
OD1 B:ASP66 4.1 11.2 1.0
OD1 B:ASP168 4.1 17.2 1.0
C5B B:FAD306 4.1 13.4 1.0
O5 B:POP305 4.1 13.1 1.0
O1 B:POP305 4.2 10.5 1.0
O2 B:POP305 4.3 12.2 1.0
NH1 B:ARG297 4.3 18.6 0.5
O6 B:POP305 4.4 11.9 1.0
CG B:ASP168 4.4 13.7 1.0
OE2 B:GLU296 4.4 15.6 1.0
O3P B:FAD306 4.4 15.3 1.0
NH2 B:ARG165 4.6 12.9 1.0
O B:GLY163 4.6 12.6 1.0
O3B B:FAD306 4.6 12.2 1.0
CA B:ASP66 4.9 9.5 1.0
MG B:MG309 4.9 17.2 0.5
N B:ASP66 5.0 8.9 1.0

Magnesium binding site 5 out of 13 in 3g6k

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Magnesium binding site 5 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:20.6
occ:0.50
 O B:HOH1825 2.0 24.9 0.5
O B:HOH931 2.1 20.5 0.5
O1P B:FAD306 2.2 21.9 1.0
O B:HOH1341 2.2 24.1 0.5
O B:HOH1826 2.2 21.2 0.5
O B:HOH1127 2.2 27.2 0.5
MG B:MG309 3.6 17.2 0.5
P B:FAD306 3.6 18.5 1.0
O1A B:FAD306 3.8 15.3 1.0
O B:HOH1827 4.1 22.6 0.5
O B:HOH1038 4.3 29.1 0.5
O5' B:FAD306 4.3 18.7 1.0
O B:LEU223 4.4 17.4 1.0
C5' B:FAD306 4.4 20.0 1.0
N7A B:FAD306 4.4 13.7 1.0
O2P B:FAD306 4.4 22.5 1.0
O3P B:FAD306 4.5 15.3 1.0
PA B:FAD306 4.7 13.7 1.0
O B:HOH898 4.8 30.8 1.0
CA B:GLY224 4.8 13.5 1.0
C8A B:FAD306 4.8 13.2 1.0
O B:HOH395 4.9 20.2 1.0
O B:HOH1870 4.9 25.2 0.5

Magnesium binding site 6 out of 13 in 3g6k

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Magnesium binding site 6 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg309

b:17.2
occ:0.50
 O B:HOH1827 1.9 22.6 0.5
O1A B:FAD306 2.0 15.3 1.0
O B:HOH1826 2.1 21.2 0.5
O5 B:POP305 2.1 13.1 1.0
O B:LEU223 2.7 17.4 1.0
PA B:FAD306 3.4 13.7 1.0
C B:LEU223 3.4 14.0 1.0
P2 B:POP305 3.4 9.9 1.0
MG B:MG308 3.6 20.6 0.5
O B:HOH1341 3.6 24.1 0.5
O4 B:POP305 3.8 10.6 1.0
O1P B:FAD306 3.8 21.9 1.0
N B:LEU223 3.9 11.8 1.0
O2A B:FAD306 4.1 11.9 1.0
O2 B:POP305 4.1 12.2 1.0
CA B:LEU223 4.1 12.4 1.0
N B:GLY224 4.2 12.5 1.0
O3P B:FAD306 4.2 15.3 1.0
O B:POP305 4.2 10.1 1.0
O B:HOH322 4.3 22.5 1.0
O5B B:FAD306 4.5 13.1 1.0
OG B:SER222 4.5 16.4 1.0
CA B:GLY224 4.5 13.5 1.0
O6 B:POP305 4.5 11.9 1.0
CB B:LEU223 4.6 13.0 1.0
P B:FAD306 4.6 18.5 1.0
O B:HOH931 4.6 20.5 0.5
P1 B:POP305 4.7 10.2 1.0
O B:HOH1870 4.7 25.2 0.5
O B:HOH1825 4.7 24.9 0.5
ND2 B:ASN62 4.7 15.7 1.0
NH1 B:ARG297 4.7 18.6 0.5
O3 B:POP305 4.7 10.8 1.0
O B:HOH898 4.8 30.8 1.0
C B:SER222 4.8 11.8 1.0
MG B:MG307 4.9 9.6 1.0

Magnesium binding site 7 out of 13 in 3g6k

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Magnesium binding site 7 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg307

b:9.6
occ:1.00
 O2A C:FAD306 2.0 12.6 1.0
O3 C:POP305 2.0 10.3 1.0
O C:HOH312 2.1 11.2 1.0
O4 C:POP305 2.1 10.5 1.0
OD2 C:ASP66 2.1 10.4 1.0
O C:HOH309 2.1 11.3 1.0
CG C:ASP66 3.1 10.2 1.0
PA C:FAD306 3.2 14.5 1.0
P1 C:POP305 3.2 10.0 1.0
P2 C:POP305 3.3 10.2 1.0
O C:POP305 3.4 9.8 1.0
CB C:ASP66 3.6 9.6 1.0
O1A C:FAD306 3.8 16.0 1.0
O C:HOH353 3.9 19.6 1.0
O5B C:FAD306 3.9 13.8 1.0
NZ C:LYS65 4.0 9.8 1.0
OD2 C:ASP168 4.0 11.7 1.0
OD1 C:ASP168 4.1 15.3 1.0
C5B C:FAD306 4.1 13.2 1.0
OD1 C:ASP66 4.1 9.9 1.0
O5 C:POP305 4.2 11.9 1.0
O1 C:POP305 4.2 10.8 1.0
O2 C:POP305 4.3 11.3 1.0
NH2 C:ARG297 4.3 18.8 0.5
O6 C:POP305 4.3 10.8 1.0
O3P C:FAD306 4.4 16.9 1.0
CG C:ASP168 4.4 12.5 1.0
OE2 C:GLU296 4.4 14.8 1.0
NH2 C:ARG165 4.6 10.7 1.0
O C:GLY163 4.6 12.0 1.0
O3B C:FAD306 4.6 13.5 1.0
CA C:ASP66 4.9 9.1 1.0
N C:ASP66 5.0 9.1 1.0

Magnesium binding site 8 out of 13 in 3g6k

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Magnesium binding site 8 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg307

b:8.5
occ:1.00
 O4 D:POP305 2.0 9.4 1.0
O D:HOH315 2.1 9.5 1.0
O1A D:FAD306 2.1 10.7 1.0
OD2 D:ASP66 2.1 9.1 1.0
O3 D:POP305 2.1 9.2 1.0
O D:HOH311 2.1 9.3 1.0
CG D:ASP66 3.1 8.7 1.0
P2 D:POP305 3.3 8.9 1.0
P1 D:POP305 3.3 8.8 1.0
PA D:FAD306 3.3 13.2 1.0
O D:POP305 3.4 8.6 1.0
CB D:ASP66 3.6 8.7 1.0
O D:HOH338 3.9 15.5 1.0
O2A D:FAD306 3.9 14.2 1.0
O5B D:FAD306 3.9 11.9 1.0
NZ D:LYS65 4.0 9.3 1.0
OD2 D:ASP168 4.0 10.6 1.0
C5B D:FAD306 4.1 12.1 1.0
OD1 D:ASP66 4.1 9.1 1.0
O5 D:POP305 4.1 11.0 1.0
OD1 D:ASP168 4.1 12.9 1.0
O1 D:POP305 4.2 9.4 1.0
O2 D:POP305 4.3 9.5 1.0
O6 D:POP305 4.4 9.8 1.0
OE2 D:GLU296 4.4 14.9 1.0
O3P D:FAD306 4.5 15.8 1.0
CG D:ASP168 4.5 11.6 1.0
O D:GLY163 4.5 10.9 1.0
O3B D:FAD306 4.6 11.1 1.0
NH1 D:ARG297 4.6 17.8 0.5
NH2 D:ARG165 4.6 9.6 1.0
CA D:ASP66 4.9 8.5 1.0
N D:ASP66 5.0 7.9 1.0
C3B D:FAD306 5.0 10.2 1.0

Magnesium binding site 9 out of 13 in 3g6k

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Magnesium binding site 9 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg307

b:11.6
occ:1.00
 O2A E:FAD306 2.0 15.7 1.0
O2 E:POP305 2.0 12.1 1.0
O5 E:POP305 2.0 13.2 1.0
OD2 E:ASP66 2.1 11.5 1.0
O E:HOH309 2.1 12.9 1.0
O E:HOH308 2.1 12.6 1.0
CG E:ASP66 3.1 10.7 1.0
PA E:FAD306 3.2 19.0 1.0
P2 E:POP305 3.2 12.8 1.0
P1 E:POP305 3.3 12.0 1.0
O E:POP305 3.4 12.6 1.0
CB E:ASP66 3.6 11.1 1.0
O1A E:FAD306 3.8 22.3 1.0
O E:HOH342 3.9 18.9 1.0
O5B E:FAD306 3.9 18.7 1.0
NZ E:LYS65 4.0 11.4 1.0
OD1 E:ASP168 4.0 12.4 1.0
OD2 E:ASP168 4.1 15.1 1.0
OD1 E:ASP66 4.1 12.1 1.0
O3 E:POP305 4.1 14.3 1.0
C5B E:FAD306 4.1 18.1 1.0
O6 E:POP305 4.2 12.9 1.0
O4 E:POP305 4.3 13.7 1.0
O3P E:FAD306 4.3 22.3 1.0
O1 E:POP305 4.4 12.9 1.0
CG E:ASP168 4.4 12.0 1.0
OE2 E:GLU296 4.5 15.2 1.0
O E:GLY163 4.6 15.3 1.0
NH1 E:ARG165 4.6 12.1 1.0
O3B E:FAD306 4.7 17.0 1.0
CA E:ASP66 4.9 10.8 1.0
N E:ASP66 4.9 10.8 1.0

Magnesium binding site 10 out of 13 in 3g6k

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Magnesium binding site 10 out of 13 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fad and Inorganic Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg307

b:7.8
occ:1.00
 O5 F:POP305 2.0 8.5 1.0
O2A F:FAD306 2.1 10.3 1.0
O2 F:POP305 2.1 8.7 1.0
OD2 F:ASP66 2.1 8.3 1.0
O F:HOH314 2.1 9.2 1.0
O F:HOH315 2.1 9.9 1.0
CG F:ASP66 3.1 8.5 1.0
P1 F:POP305 3.2 8.4 1.0
P2 F:POP305 3.2 8.1 1.0
PA F:FAD306 3.3 11.5 1.0
O F:POP305 3.4 8.4 1.0
CB F:ASP66 3.6 7.6 1.0
O F:HOH367 3.8 20.5 1.0
O1A F:FAD306 3.8 13.6 1.0
O5B F:FAD306 3.9 10.4 1.0
OD2 F:ASP168 4.0 12.0 1.0
NZ F:LYS65 4.0 8.8 1.0
C5B F:FAD306 4.1 10.1 1.0
O3 F:POP305 4.1 11.5 1.0
OD1 F:ASP66 4.1 8.9 1.0
OD1 F:ASP168 4.1 15.0 1.0
O6 F:POP305 4.2 8.2 1.0
O4 F:POP305 4.2 9.6 1.0
NH2 F:ARG297 4.3 18.4 0.6
O1 F:POP305 4.3 10.1 1.0
OE2 F:GLU296 4.4 14.1 1.0
CG F:ASP168 4.4 12.8 1.0
O3P F:FAD306 4.5 14.7 1.0
O F:GLY163 4.6 11.0 1.0
NH2 F:ARG165 4.6 11.4 1.0
O3B F:FAD306 4.6 10.0 1.0
CA F:ASP66 4.9 7.3 1.0
MG F:MG308 5.0 15.2 0.5
C3B F:FAD306 5.0 9.2 1.0

Reference:

C.Huerta, D.Borek, M.Machius, N.V.Grishin, H.Zhang. Structure and Mechanism of A Eukaryotic Fmn Adenylyltransferase. J.Mol.Biol. V. 389 388 2009.
ISSN: ISSN 0022-2836
PubMed: 19375431
DOI: 10.1016/J.JMB.2009.04.022
Page generated: Wed Aug 14 14:06:28 2024

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