Magnesium in PDB 6xru: Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates

All present enzymatic activity of Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates:
6.2.1.4; 6.2.1.5;

The structure of Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates, PDB code: 6xru was solved by J.Huang, M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.041, 81.246, 50.386, 90, 104.59, 90
R / Rfree (%)	16.9 / 18.4

The binding sites of Magnesium atom in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates (pdb code 6xru). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates, PDB code: 6xru:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:18.2 occ:1.00 HO4 B:SIN401 1.3 23.1 1.0 O3 A:PO4406 2.0 18.6 1.0 O A:HOH600 2.0 17.4 1.0 O B:HOH555 2.1 18.0 1.0 O A:HOH542 2.1 17.7 1.0 O4 B:SIN401 2.2 19.1 1.0 O A:HOH610 2.2 20.4 1.0 C4 B:SIN401 3.2 34.1 1.0 P A:PO4406 3.2 16.5 1.0 H B:ALA273 3.4 20.3 1.0 HA2 B:GLY272 3.4 19.3 1.0 O3 B:SIN401 3.4 32.5 1.0 O4 A:PO4406 3.6 18.2 1.0 H31 A:DCA401 3.6 24.7 1.0 H B:GLY298 3.7 23.8 1.0 O2 A:PO4406 3.8 20.6 1.0 HA2 B:GLY297 3.9 25.9 1.0 NE2 A:HIS259 4.0 18.2 1.0 HD2 A:HIS259 4.1 22.9 1.0 OE1 A:GLU105 4.1 22.6 1.0 OD2 B:ASP295 4.1 21.3 1.0 OE2 A:GLU105 4.2 22.4 1.0 N B:ALA273 4.2 16.8 1.0 OD1 B:ASP295 4.3 18.2 1.0 CA B:GLY272 4.3 16.0 1.0 N B:GLY298 4.3 19.7 1.0 CD2 A:HIS259 4.4 19.0 1.0 H22 B:SIN401 4.4 27.1 1.0 O1 A:PO4406 4.5 20.9 1.0 CD A:GLU105 4.5 24.2 1.0 HZ2 B:LYS258 4.5 60.8 1.0 C3 B:SIN401 4.5 27.7 1.0 HA3 B:GLY272 4.5 19.3 1.0 O B:ASN271 4.6 20.3 1.0 HB2 B:ALA273 4.6 17.8 1.0 HZ1 B:LYS258 4.6 60.8 1.0 OD1 A:ASN131 4.6 17.0 1.0 CG B:ASP295 4.6 19.2 1.0 C3P A:DCA401 4.6 20.5 1.0 O5P A:DCA401 4.7 20.0 1.0 HB3 B:ALA273 4.7 17.8 1.0 H21 B:SIN401 4.8 27.1 1.0 CA B:GLY297 4.8 21.5 1.0 C B:GLY272 4.8 15.1 1.0 C2 B:SIN401 4.8 22.5 1.0 H21 A:DCA401 4.8 30.8 1.0 HA3 B:GLY298 4.9 22.4 1.0 H32 A:DCA401 5.0 24.7 1.0 C B:GLY297 5.0 24.1 1.0 NZ B:LYS258 5.0 50.6 1.0

Magnesium binding site 2 out of 2 in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gtp-Specific Succinyl-Coa Synthetase Complexed with Desulfo-Coenzyme A, Magnesium Ions and Succinates within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:27.4 occ:1.00 O B:HOH580 2.0 27.8 1.0 O B:HOH725 2.0 35.0 1.0 O A:HOH826 2.0 35.5 1.0 O B:HOH627 2.1 33.0 1.0 O B:HOH618 2.1 26.5 1.0 O B:HOH576 2.3 29.5 1.0 HZ2 B:LYS222 3.7 42.6 1.0 O B:HOH745 3.8 24.5 1.0 HZ1 B:LYS222 4.0 42.6 1.0 HO4 A:SIN402 4.1 50.2 1.0 OE1 B:GLU141 4.2 29.1 1.0 O A:HOH502 4.2 33.5 1.0 OE2 B:GLU141 4.2 31.6 1.0 HE3 B:LYS222 4.2 69.3 1.0 O A:HOH606 4.3 39.4 1.0 NZ B:LYS222 4.3 35.4 1.0 HA2 A:GLY266 4.3 32.3 1.0 OE1 B:GLU204 4.3 24.1 1.0 OE2 B:GLU204 4.4 21.4 1.0 O3 A:SIN402 4.6 51.8 1.0 HG22 B:ILE140 4.6 43.1 1.0 CD B:GLU141 4.6 38.2 1.0 CE B:LYS222 4.8 57.6 1.0 CD B:GLU204 4.8 23.1 1.0 H A:GLY266 4.8 32.5 1.0 O4 A:SIN402 4.9 41.7 1.0 OD1 B:ASP139 4.9 41.4 1.0

J.Huang, M.E.Fraser. Second Distinct Conformation of the Phosphohistidine Loop in Succinyl-Coa Synthetase Acta Crystallogr.,Sect.D V. 77 357 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798321000334