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Magnesium in PDB 3fd5: Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp

Enzymatic activity of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp

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

Protein crystallography data

The structure of Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp, PDB code: 3fd5 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) 14.93 / 1.90
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 66.734, 66.734, 181.168, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 19.5

Other elements in 3fd5:

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

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp (pdb code 3fd5). 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 Ampcp, PDB code: 3fd5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3fd5

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Magnesium binding site 1 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp


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 Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg395

b:23.2
occ:1.00
 OD1 A:ASP265 2.1 22.1 1.0
OD1 A:ASP110 2.1 20.9 1.0
OD1 A:ASP69 2.1 23.3 1.0
O3B A:AP2393 2.2 25.7 1.0
O A:HOH718 2.2 22.9 1.0
O A:HOH399 2.3 16.8 1.0
CG A:ASP69 3.1 25.1 1.0
CG A:ASP265 3.1 21.9 1.0
CG A:ASP110 3.2 18.3 1.0
PB A:AP2393 3.3 22.0 1.0
OD2 A:ASP265 3.5 23.9 1.0
CB A:ASP69 3.5 21.5 1.0
O2B A:AP2393 3.7 21.9 1.0
OD2 A:ASP110 3.7 13.8 1.0
CA A:ASP69 3.9 21.5 1.0
MG A:MG396 4.0 25.5 1.0
O A:HOH404 4.0 18.0 1.0
O1B A:AP2393 4.0 21.7 1.0
O A:ASP265 4.1 18.8 1.0
OD2 A:ASP69 4.2 25.8 1.0
N A:ASP265 4.2 18.1 1.0
OG1 A:THR264 4.3 28.2 1.0
OG1 A:THR267 4.3 22.9 1.0
CB A:ASP265 4.4 20.6 1.0
CB A:ASP110 4.4 18.5 1.0
CA A:ASP265 4.7 17.4 1.0
O A:HOH828 4.7 28.8 1.0
CA A:ASP110 4.7 17.5 1.0
C A:ASP265 4.7 17.2 1.0
C3A A:AP2393 4.7 11.7 1.0
K A:K398 4.9 26.3 1.0
N A:ASP69 4.9 19.1 1.0
C A:ASP69 5.0 18.5 1.0
CB A:ALA113 5.0 22.0 1.0
O A:ASP69 5.0 17.8 1.0

Magnesium binding site 2 out of 6 in 3fd5

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


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 Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg396

b:25.5
occ:1.00
 O1 A:PO4394 2.1 19.1 1.0
OD2 A:ASP87 2.2 29.9 1.0
O1B A:AP2393 2.3 21.7 1.0
OD2 A:ASP110 2.3 13.8 1.0
O A:HOH399 2.3 16.8 1.0
O A:HOH828 2.4 28.8 1.0
CG A:ASP87 3.0 27.1 1.0
OD1 A:ASP87 3.2 22.5 1.0
PB A:AP2393 3.3 22.0 1.0
CG A:ASP110 3.3 18.3 1.0
P A:PO4394 3.4 26.8 1.0
OD1 A:ASP110 3.6 20.9 1.0
O3B A:AP2393 3.6 25.7 1.0
MG A:MG397 3.6 31.7 1.0
O2B A:AP2393 3.8 21.9 1.0
O3 A:PO4394 3.9 24.9 1.0
MG A:MG395 4.0 23.2 1.0
O4 A:PO4394 4.0 21.3 1.0
K A:K398 4.1 26.3 1.0
OG1 A:THR267 4.1 22.9 1.0
O A:HOH401 4.3 19.3 1.0
CB A:ASP87 4.3 22.5 1.0
O A:ASN106 4.3 20.5 1.0
OD2 A:ASP265 4.4 23.9 1.0
CG2 A:THR267 4.4 24.4 1.0
O A:HOH658 4.5 20.7 1.0
O2 A:PO4394 4.5 29.2 1.0
CB A:THR267 4.6 22.9 1.0
CB A:ASP110 4.6 18.5 1.0
O A:HOH752 4.7 23.4 1.0
OD1 A:ASN106 4.7 29.7 1.0
O A:HOH718 4.8 22.9 1.0
C3A A:AP2393 4.9 11.7 1.0
OD1 A:ASP265 4.9 22.1 1.0

Magnesium binding site 3 out of 6 in 3fd5

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


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 Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg397

b:31.7
occ:1.00
 O3 A:PO4394 2.1 24.9 1.0
OD1 A:ASP87 2.1 22.5 1.0
O A:HOH658 2.1 20.7 1.0
OE1 B:GLN163 2.1 22.4 1.0
O1A A:AP2393 2.2 20.4 1.0
O1B A:AP2393 2.3 21.7 1.0
CD B:GLN163 3.1 29.1 1.0
P A:PO4394 3.1 26.8 1.0
CG A:ASP87 3.2 27.1 1.0
O1 A:PO4394 3.3 19.1 1.0
PB A:AP2393 3.4 22.0 1.0
PA A:AP2393 3.4 21.9 1.0
NE2 B:GLN163 3.5 29.6 1.0
OD2 A:ASP87 3.6 29.9 1.0
MG A:MG396 3.6 25.5 1.0
C3A A:AP2393 3.7 11.7 1.0
O4 A:PO4394 3.8 21.3 1.0
O2B A:AP2393 3.9 21.9 1.0
O A:THR86 4.2 27.5 1.0
K A:K398 4.2 26.3 1.0
CG B:GLN163 4.3 29.2 1.0
O B:HOH511 4.3 15.9 1.0
O A:HOH752 4.3 23.4 1.0
O B:GLY162 4.3 28.1 1.0
O2 A:PO4394 4.4 29.2 1.0
O2A A:AP2393 4.4 24.9 1.0
CB A:ASP87 4.5 22.5 1.0
NZ A:LYS32 4.5 28.2 1.0
CB B:GLN163 4.5 23.8 1.0
O5' A:AP2393 4.5 19.3 1.0
CE A:LYS32 4.6 21.5 1.0
O3B A:AP2393 4.7 25.7 1.0
CA A:ASP87 4.7 23.7 1.0
CA B:GLN163 4.7 25.0 1.0

Magnesium binding site 4 out of 6 in 3fd5

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Magnesium binding site 4 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp


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 Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg395

b:33.5
occ:1.00
 OD1 B:ASP110 2.0 25.7 1.0
O B:HOH399 2.1 21.6 1.0
O1B B:AP2393 2.2 24.1 1.0
OD1 B:ASP69 2.2 24.9 1.0
OD1 B:ASP265 2.2 25.4 1.0
O B:HOH590 2.3 23.3 1.0
CG B:ASP110 2.9 30.3 1.0
CG B:ASP265 3.0 28.9 1.0
PB B:AP2393 3.1 27.2 1.0
OD2 B:ASP265 3.2 30.1 1.0
OD2 B:ASP110 3.2 34.3 1.0
CG B:ASP69 3.3 21.6 1.0
O3B B:AP2393 3.4 39.7 1.0
MG B:MG396 3.5 27.3 1.0
O B:HOH414 3.6 23.6 1.0
O2B B:AP2393 3.6 28.5 1.0
CB B:ASP69 3.8 18.1 1.0
OG1 B:THR267 4.0 26.7 1.0
CA B:ASP69 4.2 21.2 1.0
CB B:ASP110 4.3 22.6 1.0
O B:ASP265 4.3 27.0 1.0
OD2 B:ASP69 4.4 21.4 1.0
CB B:ASP265 4.4 21.9 1.0
N B:ASP265 4.5 26.9 1.0
O1 B:PO4394 4.6 26.2 1.0
C3A B:AP2393 4.7 28.3 1.0
K B:K398 4.7 20.2 1.0
OG1 B:THR264 4.7 19.7 1.0
O B:HOH719 4.7 19.6 1.0
CA B:ASP110 4.8 19.9 1.0
CA B:ASP265 4.8 23.9 1.0
C B:ASP265 4.8 23.4 1.0
O3 B:PO4394 5.0 37.0 1.0

Magnesium binding site 5 out of 6 in 3fd5

Go back to Magnesium Binding Sites List in 3fd5
Magnesium binding site 5 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp


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 Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg396

b:27.3
occ:1.00
 O1 B:PO4394 2.1 26.2 1.0
OD2 B:ASP87 2.2 23.1 1.0
O B:HOH719 2.2 19.6 1.0
OD2 B:ASP110 2.2 34.3 1.0
O2B B:AP2393 2.2 28.5 1.0
O B:HOH399 2.3 21.6 1.0
CG B:ASP87 3.0 28.0 1.0
OD1 B:ASP87 3.2 20.7 1.0
P B:PO4394 3.3 29.4 1.0
CG B:ASP110 3.3 30.3 1.0
PB B:AP2393 3.3 27.2 1.0
MG B:MG395 3.5 33.5 1.0
MG B:MG397 3.5 23.6 1.0
K B:K398 3.7 20.2 1.0
O2 B:PO4394 3.7 31.2 1.0
O1B B:AP2393 3.7 24.1 1.0
OD1 B:ASP110 3.8 25.7 1.0
O3 B:PO4394 3.8 37.0 1.0
OG1 B:THR267 3.9 26.7 1.0
O3B B:AP2393 4.0 39.7 1.0
OD2 B:ASP265 4.3 30.1 1.0
CB B:ASP87 4.4 24.9 1.0
O B:HOH423 4.4 24.4 1.0
O4 B:PO4394 4.5 28.6 1.0
O B:ASN106 4.5 19.9 1.0
CG2 B:THR267 4.5 25.1 1.0
CB B:THR267 4.6 24.9 1.0
CB B:ASP110 4.6 22.6 1.0
OD1 B:ASN106 4.6 20.7 1.0
C3A B:AP2393 4.8 28.3 1.0
O A:HOH661 4.8 23.8 1.0
ND2 B:ASN106 5.0 24.5 1.0

Magnesium binding site 6 out of 6 in 3fd5

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Magnesium binding site 6 out of 6 in the Crystal Structure of Human Selenophosphate Synthetase 1 Complex with Ampcp


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 Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg397

b:23.6
occ:1.00
 OD1 B:ASP87 2.1 20.7 1.0
OE1 A:GLN163 2.2 28.2 1.0
O1A B:AP2393 2.2 26.3 1.0
O2B B:AP2393 2.2 28.5 1.0
O2 B:PO4394 2.2 31.2 1.0
O A:HOH661 2.5 23.8 1.0
CD A:GLN163 3.2 22.8 1.0
CG B:ASP87 3.2 28.0 1.0
P B:PO4394 3.3 29.4 1.0
PA B:AP2393 3.3 27.1 1.0
PB B:AP2393 3.4 27.2 1.0
MG B:MG396 3.5 27.3 1.0
C3A B:AP2393 3.6 28.3 1.0
O1 B:PO4394 3.6 26.2 1.0
NE2 A:GLN163 3.6 18.6 1.0
OD2 B:ASP87 3.7 23.1 1.0
O3 B:PO4394 3.7 37.0 1.0
O3B B:AP2393 3.9 39.7 1.0
K B:K398 4.1 20.2 1.0
O B:THR86 4.2 19.6 1.0
O2A B:AP2393 4.2 26.8 1.0
O B:HOH423 4.3 24.4 1.0
NZ B:LYS32 4.3 28.3 1.0
CE B:LYS32 4.4 26.2 1.0
CG A:GLN163 4.5 15.9 1.0
O A:GLY162 4.5 22.1 1.0
CB B:ASP87 4.5 24.9 1.0
O5' B:AP2393 4.5 29.9 1.0
O4 B:PO4394 4.6 28.6 1.0
O1B B:AP2393 4.7 24.1 1.0
CB A:GLN163 4.7 19.8 1.0
CA B:ASP87 4.8 20.8 1.0
CA A:GLN163 4.9 22.1 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 13:43:25 2024

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