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Magnesium in PDB 3fd6: Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate

Enzymatic activity of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate

All present enzymatic activity of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate:
2.7.9.3;

Protein crystallography data

The structure of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate, PDB code: 3fd6 was solved by K.T.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.96 / 1.95
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 67.618, 67.618, 182.551, 90.00, 90.00, 90.00
R / Rfree (%) 13.1 / 19.6

Other elements in 3fd6:

The structure of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate (pdb code 3fd6). 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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate, PDB code: 3fd6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3fd6

Go back to Magnesium Binding Sites List in 3fd6
Magnesium binding site 1 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg395

b:18.0
occ:1.00
 OD1 A:ASP110 2.1 18.7 1.0
OD1 A:ASP265 2.1 14.3 1.0
OD1 A:ASP69 2.2 19.4 1.0
O A:HOH399 2.3 14.7 1.0
O A:HOH425 2.4 14.6 1.0
O3B A:ADP393 2.5 32.9 1.0
CG A:ASP265 2.9 13.2 1.0
OD2 A:ASP265 3.0 15.8 1.0
CG A:ASP110 3.2 19.2 1.0
CG A:ASP69 3.3 22.2 1.0
PB A:ADP393 3.4 34.0 1.0
O2B A:ADP393 3.6 42.3 1.0
CB A:ASP69 3.7 14.7 1.0
MG A:MG396 3.7 16.0 1.0
OD2 A:ASP110 3.8 19.1 1.0
O1B A:ADP393 4.0 37.3 1.0
CA A:ASP69 4.2 13.1 1.0
O A:ASP265 4.2 12.9 1.0
OG1 A:THR267 4.2 15.9 1.0
CB A:ASP265 4.3 14.9 1.0
O A:HOH476 4.3 21.0 1.0
CB A:ASP110 4.3 13.6 1.0
OD2 A:ASP69 4.3 17.8 1.0
CA A:ASP110 4.4 14.3 1.0
N A:ASP265 4.5 13.1 1.0
OG1 A:THR264 4.7 21.5 1.0
CA A:ASP265 4.7 17.0 1.0
C A:ASP265 4.7 12.8 1.0
O A:HOH450 4.8 15.0 1.0
O3A A:ADP393 4.8 20.9 1.0
O A:ASP69 4.9 16.9 1.0
O A:HOH426 4.9 17.4 1.0

Magnesium binding site 2 out of 6 in 3fd6

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg396

b:16.0
occ:1.00
 O1 A:PO4394 2.1 13.4 1.0
O A:HOH426 2.2 17.4 1.0
OD2 A:ASP110 2.4 19.1 1.0
O A:HOH399 2.4 14.7 1.0
O A:HOH427 2.4 9.8 1.0
O1B A:ADP393 2.6 37.3 1.0
O2B A:ADP393 2.7 42.3 1.0
MG A:MG397 3.0 23.5 1.0
PB A:ADP393 3.1 34.0 1.0
CG A:ASP110 3.2 19.2 1.0
OD1 A:ASP110 3.4 18.7 1.0
P A:PO4394 3.4 17.6 1.0
MG A:MG395 3.7 18.0 1.0
O3 A:PO4394 3.8 19.6 1.0
O3B A:ADP393 3.9 32.9 1.0
O A:HOH470 4.0 15.2 1.0
O A:HOH447 4.0 14.5 1.0
OG1 A:THR267 4.0 15.9 1.0
O4 A:PO4394 4.1 18.0 1.0
OD1 A:ASP87 4.2 27.3 1.0
OD2 A:ASP265 4.4 15.8 1.0
O3A A:ADP393 4.4 20.9 1.0
O2 A:PO4394 4.5 14.0 1.0
CG2 A:THR267 4.6 20.2 1.0
CB A:ASP110 4.7 13.6 1.0
O1A A:ADP393 4.7 15.0 1.0
CG A:ASP87 4.7 20.3 1.0
CB A:THR267 4.7 19.9 1.0
NA A:NA398 4.8 36.1 1.0
O A:THR86 4.9 15.4 1.0
O A:ASN106 4.9 11.6 1.0
O A:HOH425 4.9 14.6 1.0
OE1 B:GLN163 4.9 20.7 1.0
CB A:ASP87 5.0 15.1 1.0

Magnesium binding site 3 out of 6 in 3fd6

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Magnesium binding site 3 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg397

b:23.5
occ:1.00
 O1A A:ADP393 2.1 15.0 1.0
O3 A:PO4394 2.2 19.6 1.0
O A:HOH447 2.3 14.5 1.0
OE1 B:GLN163 2.3 20.7 1.0
O A:HOH427 2.4 9.8 1.0
O1B A:ADP393 2.7 37.3 1.0
O2B A:ADP393 2.8 42.3 1.0
MG A:MG396 3.0 16.0 1.0
O1 A:PO4394 3.1 13.4 1.0
PB A:ADP393 3.1 34.0 1.0
P A:PO4394 3.2 17.6 1.0
PA A:ADP393 3.2 16.9 1.0
CD B:GLN163 3.3 15.1 1.0
O3A A:ADP393 3.4 20.9 1.0
NE2 B:GLN163 3.7 17.3 1.0
O4 A:PO4394 4.0 18.0 1.0
OD1 A:ASP87 4.1 27.3 1.0
O2A A:ADP393 4.1 26.2 1.0
O A:THR86 4.3 15.4 1.0
O2 A:PO4394 4.3 14.0 1.0
O5' A:ADP393 4.4 13.2 1.0
CE A:LYS32 4.5 17.2 1.0
O B:HOH618 4.5 23.6 1.0
O B:GLY162 4.6 25.9 1.0
NZ A:LYS32 4.6 19.8 1.0
O3B A:ADP393 4.6 32.9 1.0
OD2 A:ASP110 4.7 19.1 1.0
O A:HOH426 4.7 17.4 1.0
CG B:GLN163 4.7 13.6 1.0
O B:HOH429 4.9 7.0 1.0
O A:HOH399 4.9 14.7 1.0
CB B:GLN163 5.0 12.0 1.0

Magnesium binding site 4 out of 6 in 3fd6

Go back to Magnesium Binding Sites List in 3fd6
Magnesium binding site 4 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg395

b:32.3
occ:1.00
 O2B B:ADP393 2.0 14.5 1.0
OD1 B:ASP110 2.2 15.7 1.0
O B:HOH399 2.2 20.2 1.0
OD1 B:ASP69 2.2 13.5 1.0
OD1 B:ASP265 2.3 22.1 1.0
O B:HOH424 2.3 20.7 1.0
CG B:ASP110 3.2 16.5 1.0
PB B:ADP393 3.3 13.7 1.0
CG B:ASP265 3.3 19.1 1.0
CG B:ASP69 3.4 17.0 1.0
OD2 B:ASP110 3.5 16.5 1.0
O1B B:ADP393 3.5 10.5 1.0
OD2 B:ASP265 3.6 13.2 1.0
O B:HOH451 3.8 18.1 1.0
MG B:MG396 3.9 13.1 1.0
CB B:ASP69 4.0 16.9 1.0
OG1 B:THR267 4.1 18.9 1.0
O3A B:ADP393 4.2 19.8 1.0
O B:ASP265 4.2 15.2 1.0
O3B B:ADP393 4.2 6.3 1.0
CA B:ASP69 4.3 19.0 1.0
OD2 B:ASP69 4.4 10.6 1.0
CB B:ASP110 4.5 15.5 1.0
O B:HOH513 4.6 19.4 1.0
O1 B:PO4394 4.6 14.1 1.0
CB B:ASP265 4.6 14.9 1.0
N B:ASP265 4.7 21.6 1.0
OG1 B:THR264 4.7 25.6 1.0
C B:ASP265 4.8 16.0 1.0
CE1 B:HIS274 4.9 21.4 1.0
CA B:ASP110 4.9 13.7 1.0
CA B:ASP265 4.9 17.0 1.0

Magnesium binding site 5 out of 6 in 3fd6

Go back to Magnesium Binding Sites List in 3fd6
Magnesium binding site 5 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg396

b:13.1
occ:1.00
 O1 B:PO4394 2.1 14.1 1.0
O B:HOH423 2.1 14.0 1.0
OD2 B:ASP110 2.1 16.5 1.0
O1B B:ADP393 2.3 10.5 1.0
O B:HOH399 2.4 20.2 1.0
O B:HOH430 2.6 11.2 1.0
CG B:ASP110 3.2 16.5 1.0
MG B:MG397 3.4 22.2 1.0
P B:PO4394 3.4 19.8 1.0
PB B:ADP393 3.6 13.7 1.0
OD1 B:ASP110 3.7 15.7 1.0
O2 B:PO4394 3.7 20.6 1.0
OD1 B:ASP87 3.7 17.3 1.0
MG B:MG395 3.9 32.3 1.0
O2B B:ADP393 3.9 14.5 1.0
OG1 B:THR267 4.1 18.9 1.0
O B:HOH435 4.2 12.5 1.0
CG B:ASP87 4.2 19.3 1.0
O4 B:PO4394 4.2 26.3 1.0
O B:ASN106 4.3 18.2 1.0
O3B B:ADP393 4.4 6.3 1.0
CB B:ASP87 4.4 18.6 1.0
O3 B:PO4394 4.4 17.3 1.0
CB B:ASP110 4.5 15.5 1.0
ND2 B:ASN106 4.5 27.4 1.0
O B:THR86 4.5 17.7 1.0
O A:HOH421 4.6 30.7 1.0
NA B:NA398 4.6 20.9 1.0
OD2 B:ASP265 4.6 13.2 1.0
CG2 B:THR267 4.8 12.1 1.0
O3A B:ADP393 4.8 19.8 1.0
CB B:THR267 4.8 16.2 1.0
OD2 B:ASP87 4.9 16.4 1.0

Magnesium binding site 6 out of 6 in 3fd6

Go back to Magnesium Binding Sites List in 3fd6
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate


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 Human Selenophosphate Synthetase 1 Complex with Adp and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg397

b:22.2
occ:1.00
 O B:HOH430 2.1 11.2 1.0
OE1 A:GLN163 2.1 16.8 1.0
O2 B:PO4394 2.2 20.6 1.0
O1A B:ADP393 2.2 21.3 1.0
O1B B:ADP393 2.2 10.5 1.0
O A:HOH421 2.4 30.7 1.0
CD A:GLN163 3.1 16.6 1.0
PB B:ADP393 3.2 13.7 1.0
P B:PO4394 3.3 19.8 1.0
PA B:ADP393 3.3 21.8 1.0
MG B:MG396 3.4 13.1 1.0
O1 B:PO4394 3.4 14.1 1.0
NE2 A:GLN163 3.5 17.0 1.0
O3A B:ADP393 3.6 19.8 1.0
OD1 B:ASP87 3.7 17.3 1.0
O3B B:ADP393 3.7 6.3 1.0
O B:THR86 4.1 17.7 1.0
O3 B:PO4394 4.2 17.3 1.0
O B:HOH456 4.3 13.7 1.0
O2A B:ADP393 4.3 27.4 1.0
O4 B:PO4394 4.4 26.3 1.0
O A:GLY162 4.4 18.4 1.0
CG A:GLN163 4.5 12.7 1.0
O5' B:ADP393 4.5 16.2 1.0
NZ B:LYS32 4.5 17.7 1.0
O2B B:ADP393 4.5 14.5 1.0
OD2 B:ASP110 4.6 16.5 1.0
CG B:ASP87 4.7 19.3 1.0
CB A:GLN163 4.7 26.1 1.0
NA B:NA398 4.8 20.9 1.0
CE B:LYS32 4.8 18.5 1.0
O B:HOH399 4.9 20.2 1.0
CA A:GLN163 4.9 25.7 1.0
CB B:ASP87 4.9 18.6 1.0
CA B:ASP87 5.0 15.2 1.0

Reference:

K.T.Wang, J.Wang, L.F.Li, X.D.Su. Crystal Structures of Catalytic Intermediates of Human Selenophosphate Synthetase 1. J.Mol.Biol. V. 390 747 2009.
ISSN: ISSN 0022-2836
PubMed: 19477186
DOI: 10.1016/J.JMB.2009.05.032
Page generated: Wed Aug 14 13:43:26 2024

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