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Magnesium in PDB 3g5a: Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp

Enzymatic activity of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp

All present enzymatic activity of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp:
2.7.7.2;

Protein crystallography data

The structure of Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp, PDB code: 3g5a was solved by C.Huerta, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.07 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 207.831, 81.753, 136.698, 90.00, 129.67, 90.00
R / Rfree (%) 17.5 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp (pdb code 3g5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp, PDB code: 3g5a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3g5a

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Magnesium binding site 1 out of 6 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp


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 Fmn and Atp Analog Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:15.5
occ:1.00
 O3G A:APC305 1.9 8.7 0.5
O2A A:APC305 2.0 9.7 0.5
O A:HOH336 2.2 11.9 1.0
OD2 A:ASP66 2.2 7.6 1.0
O2B A:APC305 2.2 8.2 0.6
O A:HOH315 2.2 10.5 1.0
O A:HOH1788 2.3 15.0 0.6
O3G A:APC305 2.3 8.7 0.6
O2B A:APC305 2.3 8.5 0.5
CG A:ASP66 3.1 7.5 1.0
PG A:APC305 3.2 7.3 0.5
PA A:APC305 3.3 10.3 0.5
PB A:APC305 3.3 9.3 0.5
PB A:APC305 3.4 8.4 0.6
PG A:APC305 3.4 7.3 0.6
O3B A:APC305 3.5 7.8 0.6
O3B A:APC305 3.5 8.6 0.5
O2A A:APC305 3.6 10.3 0.6
CB A:ASP66 3.7 9.5 1.0
C3A A:APC305 3.8 9.3 0.5
NZ A:LYS65 3.8 6.7 1.0
OD2 A:ASP168 3.9 11.3 1.0
O1G A:APC305 4.0 7.3 0.5
OD1 A:ASP66 4.0 7.4 1.0
OE2 A:GLU296 4.1 14.7 1.0
OD1 A:ASP168 4.1 14.5 1.0
O1A A:APC305 4.3 9.6 0.5
O2G A:APC305 4.3 7.7 0.5
CG A:ASP168 4.3 13.0 1.0
O1G A:APC305 4.3 9.3 0.6
O5' A:APC305 4.4 10.1 0.5
C5' A:APC305 4.5 10.0 0.5
O1B A:APC305 4.5 9.1 0.6
C5' A:APC305 4.5 10.5 0.6
O2G A:APC305 4.5 8.2 0.6
C3A A:APC305 4.6 8.8 0.6
NH1 A:ARG297 4.6 19.5 1.0
PA A:APC305 4.6 9.7 0.6
O A:GLY163 4.6 10.4 1.0
O A:HOH1789 4.6 11.1 0.5
NH2 A:ARG165 4.7 14.8 1.0
O1B A:APC305 4.7 7.6 0.5
O A:HOH1787 4.8 6.6 0.5
NE A:ARG165 4.8 16.1 1.0
O5' A:APC305 4.9 10.6 0.6

Magnesium binding site 2 out of 6 in 3g5a

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Magnesium binding site 2 out of 6 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp


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 Fmn and Atp Analog Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:13.8
occ:1.00
 O1A B:APC305 2.0 15.5 1.0
O1G B:APC305 2.0 13.9 1.0
OD2 B:ASP66 2.0 8.7 1.0
O B:HOH313 2.2 10.5 1.0
O B:HOH315 2.2 12.2 1.0
O1B B:APC305 2.3 14.6 1.0
CG B:ASP66 3.1 9.5 1.0
PG B:APC305 3.2 14.6 1.0
PB B:APC305 3.3 15.7 1.0
PA B:APC305 3.3 15.8 1.0
O3B B:APC305 3.4 15.3 1.0
O B:HOH364 3.6 10.6 1.0
CB B:ASP66 3.8 9.4 1.0
C3A B:APC305 3.8 15.2 1.0
OD2 B:ASP168 3.9 17.9 1.0
NZ B:LYS65 3.9 8.9 1.0
OD1 B:ASP66 4.0 8.1 1.0
O2G B:APC305 4.0 15.4 1.0
OD1 B:ASP168 4.0 17.6 1.0
OE2 B:GLU296 4.1 15.3 1.0
CG B:ASP168 4.3 17.3 1.0
O3G B:APC305 4.3 15.5 1.0
O2A B:APC305 4.4 15.2 1.0
C5' B:APC305 4.4 12.8 1.0
O5' B:APC305 4.4 13.3 1.0
NH1 B:ARG297 4.5 11.6 1.0
O B:GLY163 4.6 8.8 1.0
O2B B:APC305 4.7 16.1 1.0
O B:HOH318 4.8 13.8 1.0
NE B:ARG165 4.9 13.1 1.0
NH2 B:ARG165 4.9 14.1 1.0
O B:HOH1202 4.9 17.0 1.0

Magnesium binding site 3 out of 6 in 3g5a

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Magnesium binding site 3 out of 6 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp


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 Fmn and Atp Analog Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg307

b:16.8
occ:1.00
 O1B C:APC305 2.0 17.4 1.0
OD2 C:ASP66 2.0 12.1 1.0
O C:HOH1201 2.2 9.8 1.0
O C:HOH316 2.2 8.7 1.0
O1G C:APC305 2.3 14.8 1.0
O C:HOH331 2.9 23.6 1.0
CG C:ASP66 3.0 12.5 1.0
PB C:APC305 3.2 19.1 1.0
PG C:APC305 3.4 18.5 1.0
O3B C:APC305 3.4 17.5 1.0
O2A C:APC305 3.5 20.9 1.0
CB C:ASP66 3.6 10.7 1.0
OD2 C:ASP168 3.8 10.1 1.0
O C:HOH327 3.8 23.4 1.0
OD1 C:ASP66 3.9 13.8 1.0
OD1 C:ASP168 4.0 12.5 1.0
NZ C:LYS65 4.1 9.5 1.0
O2B C:APC305 4.3 17.7 1.0
O2G C:APC305 4.3 17.1 1.0
CG C:ASP168 4.3 12.1 1.0
C5' C:APC305 4.3 16.4 1.0
OE2 C:GLU296 4.4 18.9 1.0
PA C:APC305 4.4 18.7 1.0
C3A C:APC305 4.5 18.8 1.0
O C:GLY163 4.5 15.3 1.0
NH2 C:ARG297 4.5 28.5 1.0
O3G C:APC305 4.6 15.3 1.0
NH2 C:ARG165 4.6 20.1 1.0
O5' C:APC305 4.8 17.8 1.0
CA C:ASP66 4.9 10.5 1.0
NH1 C:ARG297 5.0 31.2 1.0

Magnesium binding site 4 out of 6 in 3g5a

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Magnesium binding site 4 out of 6 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp


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 Fmn and Atp Analog Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg307

b:13.1
occ:1.00
 O D:HOH1782 2.1 10.1 1.0
O1B D:APC305 2.1 10.1 1.0
O1G D:APC305 2.1 8.4 1.0
OD2 D:ASP66 2.1 8.8 1.0
O D:HOH315 2.1 7.8 1.0
O D:HOH317 2.2 10.0 1.0
CG D:ASP66 3.1 10.3 1.0
PB D:APC305 3.3 10.9 1.0
PG D:APC305 3.3 10.4 1.0
O3B D:APC305 3.5 9.5 1.0
CB D:ASP66 3.6 10.5 1.0
O2A D:APC305 3.8 13.9 1.0
O D:HOH318 3.8 18.2 1.0
OD2 D:ASP168 3.9 12.4 1.0
OD1 D:ASP168 4.0 12.7 1.0
OD1 D:ASP66 4.0 12.0 1.0
NZ D:LYS65 4.0 8.6 1.0
O2G D:APC305 4.2 8.1 1.0
OE2 D:GLU296 4.3 14.2 1.0
O2B D:APC305 4.3 12.9 1.0
O D:GLY163 4.3 15.8 1.0
CG D:ASP168 4.3 12.3 1.0
NH2 D:ARG165 4.4 13.9 1.0
O3G D:APC305 4.4 10.1 1.0
C5' D:APC305 4.5 12.5 1.0
C3A D:APC305 4.6 11.9 1.0
PA D:APC305 4.7 12.7 1.0
O D:HOH1236 4.8 32.9 1.0
NE D:ARG165 4.9 15.8 1.0
CA D:ASP66 5.0 10.5 1.0

Magnesium binding site 5 out of 6 in 3g5a

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Magnesium binding site 5 out of 6 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp


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 Fmn and Atp Analog Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg307

b:17.1
occ:1.00
 OD2 E:ASP66 1.9 11.3 1.0
O1B E:APC305 2.0 13.1 1.0
O2G E:APC305 2.2 13.0 1.0
O E:HOH312 2.2 9.5 1.0
O E:HOH313 2.2 9.5 1.0
O E:HOH327 2.3 18.4 1.0
CG E:ASP66 2.9 11.3 1.0
PB E:APC305 3.2 13.6 1.0
PG E:APC305 3.3 15.1 1.0
O3B E:APC305 3.4 13.5 1.0
CB E:ASP66 3.5 11.5 1.0
O2A E:APC305 3.8 16.6 1.0
NZ E:LYS65 3.9 11.8 1.0
O E:HOH347 3.9 19.7 1.0
OD1 E:ASP66 3.9 12.1 1.0
OD1 E:ASP168 4.0 15.2 1.0
OD2 E:ASP168 4.0 12.8 1.0
O3G E:APC305 4.2 15.4 1.0
O2B E:APC305 4.2 12.7 1.0
OE2 E:GLU296 4.2 18.0 1.0
CG E:ASP168 4.3 14.0 1.0
O E:GLY163 4.4 17.3 1.0
C5' E:APC305 4.4 12.4 1.0
O1G E:APC305 4.4 12.7 1.0
C3A E:APC305 4.5 13.5 1.0
NH1 E:ARG165 4.6 14.4 1.0
PA E:APC305 4.6 14.5 1.0
CA E:ASP66 4.9 10.8 1.0
N E:ASP66 5.0 11.9 1.0

Magnesium binding site 6 out of 6 in 3g5a

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Magnesium binding site 6 out of 6 in the Crystal Structure of Candida Glabrata Fmn Adenylyltransferase in Complex with Fmn and Atp Analog Ampcpp


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 Fmn and Atp Analog Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg307

b:11.3
occ:1.00
 O1A F:APC305 2.0 12.8 1.0
OD2 F:ASP66 2.0 8.4 1.0
O3G F:APC305 2.0 13.0 1.0
O F:HOH426 2.1 9.1 1.0
O F:HOH320 2.1 6.2 1.0
O2B F:APC305 2.2 10.3 1.0
CG F:ASP66 3.0 8.4 1.0
PB F:APC305 3.3 12.1 1.0
PG F:APC305 3.3 11.8 1.0
PA F:APC305 3.4 11.2 1.0
O3B F:APC305 3.6 11.4 1.0
O F:HOH318 3.7 10.1 1.0
NZ F:LYS65 3.8 9.1 1.0
OD1 F:ASP66 3.8 11.1 1.0
OD2 F:ASP168 3.8 12.4 1.0
CB F:ASP66 3.9 9.5 1.0
C3A F:APC305 3.9 11.3 1.0
OD1 F:ASP168 4.0 12.1 1.0
OE2 F:GLU296 4.0 16.4 1.0
O1G F:APC305 4.0 13.4 1.0
CG F:ASP168 4.2 13.9 1.0
O2A F:APC305 4.3 10.6 1.0
O5' F:APC305 4.4 10.8 1.0
O2G F:APC305 4.4 12.2 1.0
C5' F:APC305 4.5 11.0 1.0
O F:GLY163 4.5 9.2 1.0
NH1 F:ARG297 4.5 13.3 1.0
O1B F:APC305 4.6 11.5 1.0
NE F:ARG165 4.7 11.8 1.0
NH2 F:ARG165 4.9 10.8 1.0
O F:HOH324 4.9 14.3 1.0
O F:HOH323 5.0 10.9 1.0
O F:HOH451 5.0 15.4 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 14:05:37 2024

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