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Magnesium in PDB 4q2e: Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)

Enzymatic activity of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)

All present enzymatic activity of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant):
2.7.7.41;

Protein crystallography data

The structure of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant), PDB code: 4q2e was solved by X.Liu, Y.Yin, J.Wu, Z.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 3.40
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 142.080, 142.080, 198.373, 90.00, 90.00, 120.00
R / Rfree (%) 29.9 / 33.8

Other elements in 4q2e:

The structure of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) also contains other interesting chemical elements:

Mercury (Hg) 6 atoms
Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) (pdb code 4q2e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant), PDB code: 4q2e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4q2e

Go back to Magnesium Binding Sites List in 4q2e
Magnesium binding site 1 out of 2 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)


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 An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:0.3
occ:1.00
OD1 A:ASP269 2.1 99.6 1.0
OD1 A:ASP239 2.1 0.7 1.0
CG A:ASP239 3.2 0.2 1.0
CG A:ASP269 3.2 97.2 1.0
N A:GLY270 3.5 92.1 1.0
OD1 A:ASP164 3.6 0.5 1.0
OD2 A:ASP269 3.7 97.3 1.0
OD2 A:ASP239 3.8 0.5 1.0
OD2 A:ASP235 3.9 95.4 1.0
CA A:GLY270 4.0 88.1 1.0
OD1 A:ASP235 4.0 95.2 1.0
O A:ASP266 4.1 0.8 1.0
O A:ARG267 4.1 0.6 1.0
CG A:ASP235 4.3 94.9 1.0
CB A:ASP239 4.3 0.7 1.0
CB A:ASP269 4.5 96.3 1.0
CG A:ASP164 4.5 0.1 1.0
C A:ASP269 4.5 93.9 1.0
OD2 A:ASP164 4.6 0.1 1.0
N A:ASP269 4.6 98.2 1.0
CA A:ASP269 4.7 95.6 1.0
C A:ARG267 5.0 0.9 1.0

Magnesium binding site 2 out of 2 in 4q2e

Go back to Magnesium Binding Sites List in 4q2e
Magnesium binding site 2 out of 2 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)


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 An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:0.2
occ:1.00
OD1 B:ASP269 2.1 0.7 1.0
OD1 B:ASP239 2.1 0.3 1.0
CG B:ASP239 3.2 0.6 1.0
CG B:ASP269 3.2 0.1 1.0
N B:GLY270 3.5 89.3 1.0
OD1 B:ASP164 3.6 0.2 1.0
OD2 B:ASP269 3.7 0.3 1.0
OD2 B:ASP239 3.7 0.1 1.0
CA B:GLY270 4.0 85.0 1.0
OD2 B:ASP235 4.0 90.4 1.0
OD1 B:ASP235 4.0 91.4 1.0
O B:ASP266 4.1 0.4 1.0
O B:ARG267 4.2 0.4 1.0
CB B:ASP239 4.3 98.4 1.0
CG B:ASP235 4.4 91.2 1.0
CB B:ASP269 4.5 98.6 1.0
C B:ASP269 4.5 93.1 1.0
CG B:ASP164 4.6 0.2 1.0
N B:ASP269 4.6 98.9 1.0
OD2 B:ASP164 4.6 0.5 1.0
CA B:ASP269 4.7 96.3 1.0
NZ B:LYS187 4.9 0.7 1.0
CA B:ASP239 5.0 94.9 1.0
C B:ARG267 5.0 0.2 1.0

Reference:

X.Liu, Y.Yin, J.Wu, Z.Liu. Structure and Mechanism of An Intramembrane Liponucleotide Synthetase Central For Phospholipid Biosynthesis Nat Commun V. 5 4244 2014.
ISSN: ESSN 2041-1723
PubMed: 24968740
DOI: 10.1038/NCOMMS5244
Page generated: Mon Dec 14 19:21:24 2020

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