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Magnesium in PDB 1kh3: Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor:
6.3.4.5;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor, PDB code: 1kh3 was solved by M.Goto, K.Hirotsu, I.Miyahara, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 229.100, 229.100, 160.600, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 25.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor (pdb code 1kh3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor, PDB code: 1kh3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1kh3

Go back to Magnesium Binding Sites List in 1kh3
Magnesium binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor


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 Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg550

b:42.7
occ:1.00
 O A:HOH1005 2.3 36.4 1.0
O3G A:ANP510 2.4 27.2 1.0
O2B A:ANP510 2.4 37.7 1.0
O A:HOH1006 2.4 34.7 1.0
O A:HOH1001 2.5 39.9 1.0
O2A A:ANP510 2.6 42.4 1.0
PB A:ANP510 3.3 32.3 1.0
PG A:ANP510 3.6 37.8 1.0
PA A:ANP510 3.7 35.4 1.0
N3B A:ANP510 3.8 34.9 1.0
O3A A:ANP510 3.8 34.6 1.0
C5' A:ANP510 4.1 36.1 1.0
O1G A:ANP510 4.1 33.9 1.0
O A:GLY114 4.2 26.3 1.0
OD2 A:ASP12 4.3 48.7 1.0
O5' A:ANP510 4.4 39.9 1.0
O A:ASP530 4.5 29.8 1.0
O1B A:ANP510 4.7 37.8 1.0
O2G A:ANP510 4.8 41.5 1.0
C A:ASP530 4.8 30.0 1.0
CG2 A:THR116 4.9 26.3 1.0
O3 A:SO4540 4.9 63.6 0.9
O1A A:ANP510 4.9 44.8 1.0
N A:ASP530 4.9 28.1 1.0
CA A:ASP530 5.0 27.9 1.0

Magnesium binding site 2 out of 4 in 1kh3

Go back to Magnesium Binding Sites List in 1kh3
Magnesium binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor


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 Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4550

b:38.9
occ:1.00
 O2G B:ANP4510 2.2 37.1 1.0
O2B B:ANP4510 2.4 37.7 1.0
O A:HOH1008 2.4 24.4 1.0
O B:HOH1002 2.4 40.6 1.0
O B:HOH1007 2.4 34.0 1.0
O2A B:ANP4510 2.6 40.8 1.0
PB B:ANP4510 3.2 30.2 1.0
PG B:ANP4510 3.3 37.8 1.0
N3B B:ANP4510 3.5 31.8 1.0
O3A B:ANP4510 3.7 31.8 1.0
PA B:ANP4510 3.7 35.3 1.0
C5' B:ANP4510 4.0 37.0 1.0
O3G B:ANP4510 4.0 37.4 1.0
O5' B:ANP4510 4.3 40.3 1.0
O B:GLY114 4.5 27.1 1.0
O A:ASP4530 4.5 30.0 1.0
OD2 B:ASP12 4.6 41.5 1.0
O1G B:ANP4510 4.6 39.1 1.0
O1B B:ANP4510 4.6 29.3 1.0
O3 B:SO44540 4.7 51.6 0.9
O2 B:SO44540 4.7 58.3 0.9
N A:ASP4530 4.9 25.4 1.0
O1A B:ANP4510 5.0 41.3 1.0

Magnesium binding site 3 out of 4 in 1kh3

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Magnesium binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor


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 Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2550

b:43.0
occ:1.00
 O C:HOH1009 2.3 41.9 1.0
O C:HOH1010 2.3 34.7 1.0
O2B C:ANP2510 2.4 43.2 1.0
O3G C:ANP2510 2.4 35.5 1.0
O2A C:ANP2510 2.5 55.6 1.0
O C:HOH1003 2.6 50.4 1.0
PB C:ANP2510 3.2 36.7 1.0
PG C:ANP2510 3.4 44.1 1.0
PA C:ANP2510 3.6 44.2 1.0
O3A C:ANP2510 3.6 37.4 1.0
N3B C:ANP2510 3.6 43.4 1.0
O1G C:ANP2510 3.8 38.8 1.0
C5' C:ANP2510 3.9 44.9 1.0
O5' C:ANP2510 4.2 47.3 1.0
OD2 C:ASP12 4.4 51.8 1.0
O C:GLY114 4.4 33.6 1.0
O A:ASP2530 4.5 25.4 1.0
O C:HOH1440 4.6 41.7 1.0
O1B C:ANP2510 4.6 42.3 1.0
O2G C:ANP2510 4.7 48.0 1.0
O3 C:SO42540 4.8 81.9 0.9
N A:ASP2530 4.8 27.0 1.0
O1A C:ANP2510 4.8 51.9 1.0
CG2 C:THR116 5.0 29.5 1.0

Magnesium binding site 4 out of 4 in 1kh3

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Magnesium binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor


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 Thermus Thermophilus HB8 Argininosuccinate Synthetase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3550

b:55.1
occ:1.00
 O2B D:ANP3510 2.3 61.4 1.0
O D:HOH1004 2.3 47.4 1.0
O3G D:ANP3510 2.3 46.6 1.0
O D:HOH1011 2.4 49.9 1.0
O D:HOH1012 2.4 37.2 1.0
O2A D:ANP3510 2.5 60.9 1.0
PB D:ANP3510 3.0 52.7 1.0
PG D:ANP3510 3.3 51.6 1.0
N3B D:ANP3510 3.3 52.5 1.0
O3A D:ANP3510 3.5 49.1 1.0
PA D:ANP3510 3.6 51.0 1.0
O1G D:ANP3510 3.8 47.0 1.0
C5' D:ANP3510 4.1 47.0 1.0
O A:ASP3530 4.4 28.5 1.0
O5' D:ANP3510 4.4 54.3 1.0
O1B D:ANP3510 4.4 54.7 1.0
OD2 D:ASP12 4.6 45.4 1.0
O2G D:ANP3510 4.6 56.7 1.0
O D:GLY114 4.6 26.7 1.0
N A:ASP3530 4.7 30.4 1.0
O3 D:SO43540 4.7 74.2 1.0
O1A D:ANP3510 4.8 62.1 1.0
C A:ASP3530 4.8 32.5 1.0
CA A:ASP3530 4.8 29.5 1.0
CG2 D:THR116 4.9 32.7 1.0

Reference:

M.Goto, R.Omi, I.Miyahara, M.Sugahara, K.Hirotsu. Structures of Argininosuccinate Synthetase in Enzyme-Atp Substrates and Enzyme-Amp Product Forms: Stereochemistry of the Catalytic Reaction J.Biol.Chem. V. 278 22964 2003.
ISSN: ISSN 0021-9258
PubMed: 12684518
DOI: 10.1074/JBC.M213198200
Page generated: Mon Dec 14 06:20:20 2020

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