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Mercury 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:

Magnesium (Mg) 2 atoms
Potassium (K) 2 atoms

Mercury Binding Sites:

The binding sites of Mercury 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 Mercury atom.
In total 6 binding sites of Mercury 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 Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 4q2e

Go back to Mercury Binding Sites List in 4q2e
Mercury binding site 1 out of 6 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 Mercury with other atoms in the Hg 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:Hg301

b:0.3
occ:1.00
 SG A:CYS220 2.1 0.3 1.0
CB A:CYS220 3.2 0.1 1.0
CA A:CYS220 3.9 0.8 1.0
NH2 A:ARG207 4.2 0.0 1.0
CE2 A:PHE221 4.5 0.3 1.0
CD2 A:PHE221 4.6 0.7 1.0
N A:PHE221 4.7 0.5 1.0
C A:CYS220 4.8 0.5 1.0
N A:CYS220 4.9 0.4 1.0
OE2 A:GLU286 5.0 0.1 1.0

Mercury binding site 2 out of 6 in 4q2e

Go back to Mercury Binding Sites List in 4q2e
Mercury binding site 2 out of 6 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 Mercury with other atoms in the Hg 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
A:Hg302

b:0.7
occ:1.00
 SG A:CYS41 2.1 0.7 1.0
O A:PHE37 2.7 0.3 1.0
CB A:CYS41 3.3 0.7 1.0
N A:CYS41 3.4 0.1 1.0
CA A:CYS41 3.6 0.5 1.0
C A:PHE37 3.6 0.3 1.0
CE2 A:PHE37 3.7 0.6 1.0
CD2 A:PHE37 3.7 0.8 1.0
CZ A:PHE37 3.8 0.2 1.0
C A:LEU40 3.9 0.7 1.0
CG A:PHE37 3.9 0.6 1.0
CE1 A:PHE37 3.9 0.1 1.0
CD1 A:PHE37 4.0 0.0 1.0
CB A:LEU40 4.2 0.1 1.0
CA A:PHE37 4.3 0.7 1.0
O A:LEU40 4.4 0.3 1.0
CA A:LEU40 4.5 0.3 1.0
N A:VAL38 4.6 0.9 1.0
CG A:LEU40 4.7 0.4 1.0
CB A:PHE37 4.7 0.8 1.0
O A:VAL38 4.7 0.9 1.0
N A:LEU40 4.8 0.9 1.0
CA A:VAL38 5.0 0.8 1.0
C A:VAL38 5.0 0.7 1.0

Mercury binding site 3 out of 6 in 4q2e

Go back to Mercury Binding Sites List in 4q2e
Mercury binding site 3 out of 6 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 Mercury with other atoms in the Hg binding site number 3 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:Hg303

b:0.2
occ:1.00
 SG A:CYS243 2.1 0.6 1.0
CB A:CYS243 3.0 0.9 1.0
O A:TYR183 3.3 0.0 1.0
CA A:CYS243 3.4 0.6 1.0
O A:CYS243 3.5 0.2 1.0
CE A:LYS246 3.5 0.3 1.0
CG A:ARG247 3.6 0.4 1.0
NE A:ARG247 3.8 0.8 1.0
C A:CYS243 3.8 0.4 1.0
NZ A:LYS246 3.9 0.2 1.0
CZ A:ARG247 3.9 0.6 1.0
NH2 A:ARG247 4.2 0.8 1.0
CD A:ARG247 4.2 0.6 1.0
C A:TYR183 4.3 0.7 1.0
NH1 A:ARG247 4.4 0.8 1.0
CA A:SER184 4.4 0.2 1.0
CB A:LYS246 4.4 0.1 1.0
N A:ARG247 4.7 0.8 1.0
N A:CYS243 4.8 98.5 1.0
CD A:LYS246 4.8 0.6 1.0
C A:SER184 4.8 0.2 1.0
CB A:ARG247 4.8 0.4 1.0
CD A:PRO185 4.8 0.9 1.0
N A:SER184 4.8 0.8 1.0
N A:PRO185 4.9 0.5 1.0

Mercury binding site 4 out of 6 in 4q2e

Go back to Mercury Binding Sites List in 4q2e
Mercury binding site 4 out of 6 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 Mercury with other atoms in the Hg binding site number 4 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:Hg301

b:1.0
occ:1.00
 SG B:CYS220 2.1 0.7 1.0
CB B:CYS220 3.1 0.2 1.0
CA B:CYS220 3.6 0.7 1.0
NH2 B:ARG207 3.9 0.7 1.0
CD2 B:PHE221 4.4 0.5 1.0
CE2 B:PHE221 4.4 0.7 1.0
N B:PHE221 4.5 0.6 1.0
C B:CYS220 4.6 0.6 1.0
N B:CYS220 4.7 0.9 1.0
CZ B:ARG207 4.8 0.9 1.0
OE2 B:GLU286 5.0 0.7 1.0

Mercury binding site 5 out of 6 in 4q2e

Go back to Mercury Binding Sites List in 4q2e
Mercury binding site 5 out of 6 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 Mercury with other atoms in the Hg binding site number 5 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:Hg302

b:0.6
occ:1.00
 SG B:CYS41 2.1 0.5 1.0
O B:PHE37 2.7 0.6 1.0
CE2 B:PHE37 3.4 0.6 1.0
CD2 B:PHE37 3.4 0.2 1.0
CZ B:PHE37 3.5 0.9 1.0
CB B:CYS41 3.5 0.5 1.0
C B:PHE37 3.6 0.3 1.0
CG B:PHE37 3.6 0.7 1.0
N B:CYS41 3.6 0.2 1.0
CE1 B:PHE37 3.7 0.8 1.0
CD1 B:PHE37 3.7 0.3 1.0
CA B:CYS41 3.8 0.2 1.0
CA B:PHE37 4.1 0.5 1.0
C B:LEU40 4.2 0.0 1.0
CB B:LEU40 4.3 0.6 1.0
CB B:PHE37 4.5 0.9 1.0
N B:VAL38 4.6 0.7 1.0
CA B:LEU40 4.7 0.3 1.0
O B:LEU40 4.7 0.9 1.0
CG B:LEU40 4.8 0.8 1.0
O B:VAL38 4.8 0.8 1.0
CA B:VAL38 5.0 0.1 1.0
N B:LEU40 5.0 1.0 1.0

Mercury binding site 6 out of 6 in 4q2e

Go back to Mercury Binding Sites List in 4q2e
Mercury binding site 6 out of 6 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 Mercury with other atoms in the Hg binding site number 6 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:Hg303

b:0.8
occ:1.00
 SG B:CYS243 2.1 0.6 1.0
O B:TYR183 3.0 0.9 1.0
CE B:LYS246 3.1 0.0 1.0
CB B:CYS243 3.2 0.3 1.0
NZ B:LYS246 3.4 0.2 1.0
CA B:CYS243 3.5 0.5 1.0
O B:CYS243 3.7 0.7 1.0
CZ B:ARG247 4.0 0.3 1.0
CG B:ARG247 4.0 0.5 1.0
C B:CYS243 4.1 0.5 1.0
NE B:ARG247 4.1 0.3 1.0
C B:TYR183 4.1 0.1 1.0
CB B:LYS246 4.2 0.0 1.0
NH2 B:ARG247 4.3 0.1 1.0
NH1 B:ARG247 4.3 0.6 1.0
CD B:LYS246 4.4 0.6 1.0
CA B:SER184 4.5 0.3 1.0
O B:LYS252 4.5 0.6 1.0
CD B:ARG247 4.6 0.5 1.0
N B:SER184 4.7 0.9 1.0
N B:CYS243 4.8 99.7 1.0
N B:ARG247 4.8 0.3 1.0
O B:VAL251 4.9 0.2 1.0
CG B:LYS246 4.9 0.2 1.0
C B:SER184 4.9 0.8 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: Sun Aug 11 05:07:49 2024

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