Magnesium in PDB 7jmk: Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp in Space Group P32

All present enzymatic activity of Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp in Space Group P32:
6.2.1.4; 6.2.1.5;

The structure of Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp in Space Group P32, PDB code: 7jmk 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)	53.00 / 2.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	99.762, 99.762, 134.206, 90, 90, 120
R / Rfree (%)	24 / 26.9

The binding sites of Magnesium atom in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp in Space Group P32 (pdb code 7jmk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp in Space Group P32, PDB code: 7jmk:

Magnesium binding site 1 out of 1 in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp in Space Group P32


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 Mg-Gdp in Space Group P32 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:104.7 occ:1.00 HOA2 B:GDP401 1.8 130.6 0.5 O1B B:GDP401 2.1 105.9 0.5 O B:ASN206 2.1 101.8 1.0 PB B:GDP401 2.6 106.1 0.5 O2A B:GDP401 2.6 107.8 0.5 O3A B:GDP401 2.7 107.1 0.5 O3B B:GDP401 2.8 104.4 0.5 HB3 B:ASN206 2.8 134.6 1.0 HZ3 B:LYS222 3.0 125.1 1.0 O3A B:GDP401 3.0 105.5 0.5 OD2 B:ASP220 3.1 99.7 1.0 C B:ASN206 3.1 105.4 1.0 PA B:GDP401 3.3 106.8 0.5 HB3 B:ASP220 3.4 121.7 1.0 HD22 B:ASN206 3.4 136.5 1.0 H5' B:GDP401 3.4 128.8 0.5 CB B:ASN206 3.6 111.1 1.0 O2A B:GDP401 3.7 105.1 0.5 HZ1 B:LYS222 3.7 125.1 1.0 ND2 B:ASN206 3.7 112.7 1.0 NZ B:LYS222 3.7 103.2 1.0 HOB2 B:GDP401 3.7 131.9 0.5 HOB3 B:GDP401 3.8 126.5 0.5 HD3 B:PRO207 3.8 133.2 1.0 CG B:ASN206 3.8 107.1 1.0 H5'' B:GDP401 3.8 128.8 0.5 CA B:ASN206 3.9 102.4 1.0 CG B:ASP220 3.9 98.0 1.0 PA B:GDP401 3.9 105.4 0.5 CB B:ASP220 4.0 100.4 1.0 PB B:GDP401 4.0 104.4 0.5 C5' B:GDP401 4.0 106.3 0.5 HZ2 B:LYS222 4.0 125.1 1.0 O5' B:GDP401 4.0 107.2 0.5 O2B B:GDP401 4.1 105.8 0.5 O2B B:GDP401 4.1 108.9 0.5 HB2 B:ASP220 4.1 121.7 1.0 H B:ASN206 4.1 108.8 1.0 N B:PRO207 4.1 110.4 1.0 O1B B:GDP401 4.2 103.0 0.5 HD21 B:ASN206 4.2 136.5 1.0 CD B:PRO207 4.3 110.0 1.0 HD2 B:PRO207 4.3 133.2 1.0 O5' B:GDP401 4.4 108.2 0.5 HB2 B:ASN206 4.4 134.6 1.0 N B:ASN206 4.5 89.6 1.0 HOA2 B:GDP401 4.5 127.4 0.5 O1A B:GDP401 4.5 105.0 0.5 HOB2 B:GDP401 4.5 128.1 0.5 HH21 B:ARG54 4.6 125.4 1.0 NE2 A:HIS259 4.6 109.2 1.0 HD2 A:HIS259 4.6 134.2 1.0 HA B:ASN206 4.7 124.1 1.0 OD1 B:ASN206 4.7 99.9 1.0 H B:VAL138 4.8 140.5 1.0 HE2 B:LYS222 4.9 119.3 1.0 CE B:LYS222 4.9 98.4 1.0 CD2 A:HIS259 5.0 110.9 1.0 HD2 B:LYS222 5.0 115.4 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