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Magnesium in PDB 7jfp: Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site

Enzymatic activity of Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site

All present enzymatic activity of Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site:
6.2.1.4; 6.2.1.5;

Protein crystallography data

The structure of Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site, PDB code: 7jfp 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) 52.99 / 2.55
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.645, 99.645, 134.262, 90, 90, 120
R / Rfree (%) 24 / 29.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site (pdb code 7jfp). 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, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site, PDB code: 7jfp:

Magnesium binding site 1 out of 1 in 7jfp

Go back to Magnesium Binding Sites List in 7jfp
Magnesium binding site 1 out of 1 in the Gtp-Specific Succinyl-Coa Synthetase Complexed with Mg-Gdp, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site


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, Phosphohistidine Loop Pointing Towards Nucleotide Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:102.2
occ:1.00
 O1B B:GDP401 1.8 108.4 0.5
O1B B:GDP401 1.9 103.2 0.5
O3B B:GDP401 2.0 106.5 0.5
PB B:GDP401 2.1 105.4 0.5
HOB3 B:GDP401 2.3 129.2 0.5
O2A B:GDP401 2.5 112.1 0.5
HZ1 B:LYS222 2.5 130.9 1.0
PB B:GDP401 2.6 112.5 0.5
HOA2 B:GDP401 2.6 136.0 0.5
O3A B:GDP401 2.8 113.6 0.5
OD2 B:ASP220 2.8 100.8 1.0
HOB2 B:GDP401 2.8 137.3 0.5
O3A B:GDP401 2.8 113.6 0.5
HD22 B:ASN206 2.9 117.7 1.0
HB3 B:ASN206 2.9 109.3 1.0
O2B B:GDP401 3.0 113.2 0.5
NZ B:LYS222 3.2 107.9 1.0
O B:ASN206 3.2 96.2 1.0
PA B:GDP401 3.2 114.2 0.5
HZ3 B:LYS222 3.2 130.9 1.0
HE3 B:LYS222 3.2 123.7 1.0
ND2 B:ASN206 3.5 96.8 1.0
O2B B:GDP401 3.6 106.0 0.5
NE2 A:HIS259 3.6 93.9 1.0
CE B:LYS222 3.7 101.8 1.0
CB B:ASN206 3.8 89.8 1.0
HZ2 B:LYS222 3.9 130.9 1.0
CG B:ASP220 3.9 95.5 1.0
HD2 A:HIS259 4.0 118.5 1.0
H5'' B:GDP401 4.0 145.8 0.5
O3B B:GDP401 4.0 115.7 0.5
HD21 B:ASN206 4.0 117.7 1.0
CG B:ASN206 4.1 93.3 1.0
O1A B:GDP401 4.1 107.1 0.5
HOB2 B:GDP401 4.1 128.6 0.5
C B:ASN206 4.1 93.8 1.0
CD2 A:HIS259 4.2 97.5 1.0
HB3 B:ASP220 4.2 112.7 1.0
PA B:GDP401 4.2 110.7 0.5
HD2 B:LYS222 4.3 106.2 1.0
HB2 B:ASP220 4.3 112.7 1.0
O5' B:GDP401 4.4 118.3 0.5
H B:GLY53 4.4 135.6 1.0
O2A B:GDP401 4.4 111.4 0.5
HE2 B:LYS222 4.4 123.7 1.0
CB B:ASP220 4.4 92.7 1.0
HB2 B:ASN206 4.5 109.3 1.0
HOB3 B:GDP401 4.5 140.3 0.5
HG12 B:VAL138 4.5 132.6 1.0
CA B:ASN206 4.5 87.8 1.0
C5' B:GDP401 4.6 120.3 0.5
H B:ASN206 4.6 101.3 1.0
CD B:LYS222 4.7 87.2 1.0
HA B:VAL138 4.7 121.3 1.0
H5' B:GDP401 4.7 150.1 0.5
H5' B:GDP401 4.7 145.8 0.5
CE1 A:HIS259 4.8 96.5 1.0
HH11 B:ARG54 4.8 118.6 1.0
OD1 B:ASP220 4.9 91.4 1.0

Reference:

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
Page generated: Wed Oct 2 21:50:45 2024

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