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Magnesium in PDB 7msr: Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A

Enzymatic activity of Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A

All present enzymatic activity of Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A:
6.2.1.4; 6.2.1.5;

Protein crystallography data

The structure of Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A, PDB code: 7msr 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) 39.13 / 1.58
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.436, 81.452, 54.331, 90, 103.37, 90
R / Rfree (%) 19.9 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A (pdb code 7msr). 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 Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A, PDB code: 7msr:

Magnesium binding site 1 out of 1 in 7msr

Go back to Magnesium Binding Sites List in 7msr
Magnesium binding site 1 out of 1 in the Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human E105QA Gtp-Specific Succinyl-Coa Synthetase Complexed with Succinyl-Phosphate, Magnesium Ion and Desulfo-Coenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:43.5
occ:1.00
 O B:HOH764 1.9 49.8 1.0
O5 B:ZNS602 2.1 41.7 0.8
O A:HOH567 2.2 41.1 1.0
O B:HOH719 2.4 37.8 1.0
O2 B:ZNS602 2.4 35.4 1.0
O B:HOH701 3.0 40.5 1.0
HA2 B:GLY272 3.1 42.7 1.0
OE1 A:GLN105 3.1 46.5 1.0
P B:ZNS602 3.3 40.2 0.8
C3 B:ZNS602 3.4 47.7 1.0
H B:ALA273 3.4 36.7 1.0
H32 A:DCA401 3.5 30.3 1.0
O3 B:ZNS602 3.6 31.6 1.0
O6 B:ZNS602 3.8 35.0 0.8
NE2 A:HIS259 4.0 37.0 1.0
HD2 A:HIS259 4.0 44.3 1.0
CA B:GLY272 4.1 35.5 1.0
OD2 B:ASP295 4.1 39.9 1.0
N B:ALA273 4.2 30.5 1.0
CD A:GLN105 4.2 46.7 1.0
OD1 B:ASP295 4.3 38.2 1.0
HE22 A:GLN105 4.3 63.9 1.0
HA2 B:GLY297 4.3 65.5 1.0
CD2 A:HIS259 4.4 36.8 1.0
HZ2 B:LYS258 4.4 79.6 1.0
OD1 A:ASN131 4.5 24.5 1.0
HA3 B:GLY272 4.5 42.7 1.0
H B:GLY298 4.5 47.7 0.5
H B:GLY298 4.5 47.7 0.5
C3P A:DCA401 4.5 25.1 1.0
H23 A:DCA401 4.5 37.0 1.0
O A:HOH610 4.5 47.1 1.0
H B:ZNS602 4.6 38.4 1.0
H B:GLY272 4.6 42.3 1.0
O4 B:ZNS602 4.6 31.5 0.8
CG B:ASP295 4.6 41.5 1.0
NE2 A:GLN105 4.7 53.1 1.0
C B:GLY272 4.7 34.6 1.0
HD21 A:ASN131 4.7 37.2 1.0
C2 B:ZNS602 4.7 44.0 1.0
HB3 B:ALA273 4.8 45.9 1.0
HZ1 B:LYS258 4.8 79.6 1.0
O5P A:DCA401 4.8 31.0 1.0
N B:GLY272 4.8 35.1 1.0
H31 A:DCA401 4.8 30.3 1.0
C2P A:DCA401 4.9 30.7 1.0
HB2 B:ALA273 4.9 45.9 1.0
H22 A:DCA401 4.9 37.0 1.0

Reference:

J.Huang, M.E.Fraser. The Structure of Succinyl-Coa Synthetase Bound to the Succinyl-Phosphate Intermediate Clarifies the Catalytic Mechanism of Atp-Citrate Lyase Acta Crystallogr.,Sect.F V. 78 363 2022.
ISSN: ESSN 2053-230X
DOI: 10.1107/S2053230X22008810
Page generated: Thu Oct 3 01:07:55 2024

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