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Chlorine in PDB 7b1k: Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.

Enzymatic activity of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.

All present enzymatic activity of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.:
2.7.8.8;

Protein crystallography data

The structure of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate., PDB code: 7b1k was solved by O.Yildiz, M.Centola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.00 / 2.20
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.314, 70.758, 95.545, 90, 90, 90
R / Rfree (%) 25.4 / 30.7

Other elements in 7b1k:

The structure of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. (pdb code 7b1k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate., PDB code: 7b1k:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7b1k

Go back to Chlorine Binding Sites List in 7b1k
Chlorine binding site 1 out of 4 in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:40.0
occ:1.00
 O A:HOH415 2.7 44.7 1.0
NE A:ARG101 3.4 46.1 1.0
CG2 A:ILE118 3.5 42.8 1.0
N A:ILE118 3.5 39.8 1.0
NH2 A:ARG101 3.6 24.7 1.0
CD2 A:LEU102 3.6 33.3 1.0
CZ A:ARG101 3.9 41.5 1.0
CB A:ILE118 4.0 40.1 1.0
CA A:PRO117 4.2 41.3 1.0
CD A:PRO119 4.2 43.4 1.0
O A:HOH414 4.3 52.5 1.0
CB A:PRO117 4.3 44.4 1.0
OD2 A:ASP66 4.3 63.9 1.0
CA A:ILE118 4.4 33.4 1.0
C A:PRO117 4.4 26.0 1.0
CD A:ARG101 4.4 38.9 1.0
CG A:LEU102 4.6 46.3 1.0
CG A:PHE105 4.7 37.0 1.0
CB A:PHE105 4.7 32.3 1.0
CE1 A:PHE113 4.8 25.5 1.0
CD1 A:PHE105 4.9 45.3 1.0
CD1 A:PHE113 4.9 42.3 1.0

Chlorine binding site 2 out of 4 in 7b1k

Go back to Chlorine Binding Sites List in 7b1k
Chlorine binding site 2 out of 4 in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:46.2
occ:1.00
 O A:HOH406 2.9 54.8 1.0
NH2 A:ARG101 3.1 24.7 1.0
N A:ILE114 3.3 56.3 1.0
CB A:PHE105 3.6 32.3 1.0
CA A:PHE105 3.8 35.2 1.0
CD1 A:PHE105 3.9 45.3 1.0
O A:ILE114 4.0 35.4 1.0
CA A:PHE113 4.0 31.0 1.0
CZ A:ARG101 4.2 41.5 1.0
C A:PHE113 4.2 48.5 1.0
CA A:ILE114 4.2 35.6 1.0
CB A:ILE114 4.2 38.1 1.0
CG A:PHE105 4.3 37.0 1.0
N A:PHE105 4.3 47.9 1.0
CD1 A:PHE113 4.3 42.3 1.0
CB A:PHE113 4.3 25.6 1.0
CG1 A:ILE114 4.3 48.3 1.0
C A:ILE114 4.5 37.1 1.0
NH1 A:ARG101 4.6 38.0 1.0
O A:ARG101 4.7 48.1 1.0
CD1 A:LEU108 4.7 44.2 1.0
CG A:PHE113 4.8 43.7 1.0
O A:GLY112 4.9 60.0 1.0

Chlorine binding site 3 out of 4 in 7b1k

Go back to Chlorine Binding Sites List in 7b1k
Chlorine binding site 3 out of 4 in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:47.6
occ:1.00
 NE B:ARG101 3.2 41.0 1.0
NH2 B:ARG101 3.3 31.5 1.0
O B:HOH409 3.3 57.4 1.0
CG2 B:ILE118 3.4 42.5 1.0
O B:HOH408 3.4 48.9 1.0
N B:ILE118 3.6 35.8 1.0
CZ B:ARG101 3.7 30.0 1.0
CD2 B:LEU102 4.0 39.4 1.0
CB B:ILE118 4.1 41.1 1.0
CA B:PRO117 4.2 34.8 1.0
CE1 B:PHE113 4.3 42.6 1.0
CD B:ARG101 4.3 40.8 1.0
C B:PRO117 4.4 37.1 1.0
CA B:ILE118 4.5 36.0 1.0
CD1 B:PHE113 4.5 46.2 1.0
CD B:PRO119 4.5 42.5 1.0
CB B:PRO117 4.5 42.4 1.0
CG B:LEU102 4.6 36.4 1.0
CG B:PHE105 4.6 46.8 1.0
CB B:PHE105 4.6 40.5 1.0
CD1 B:PHE105 4.7 58.9 1.0
OD2 B:ASP66 4.8 56.9 1.0
O B:ARG101 4.9 46.8 1.0
NH1 B:ARG101 5.0 37.6 1.0

Chlorine binding site 4 out of 4 in 7b1k

Go back to Chlorine Binding Sites List in 7b1k
Chlorine binding site 4 out of 4 in the Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Phosphatidyl Serine Synthase (Pss) in the Closed Conformation with Bound Citrate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:54.5
occ:1.00
 O B:HOH406 3.0 86.8 1.0
N B:ILE114 3.1 47.2 1.0
NH2 B:ARG101 3.4 31.5 1.0
O B:ILE114 3.7 42.7 1.0
CA B:PHE113 3.9 40.4 1.0
CA B:ILE114 3.9 37.1 1.0
CB B:ILE114 3.9 47.7 1.0
C B:PHE113 4.0 49.7 1.0
O B:HOH412 4.0 63.6 1.0
CD1 B:PHE105 4.1 58.9 1.0
CB B:PHE105 4.1 40.5 1.0
CA B:PHE105 4.1 37.9 1.0
CD1 B:PHE113 4.2 46.2 1.0
C B:ILE114 4.2 41.3 1.0
CZ B:ARG101 4.4 30.0 1.0
CG1 B:ILE114 4.4 59.9 1.0
CB B:PHE113 4.5 37.7 1.0
N B:PHE105 4.6 43.2 1.0
CG B:PHE105 4.6 46.8 1.0
NH1 B:ARG101 4.7 37.6 1.0
O B:GLY112 4.8 62.0 1.0
CG B:PHE113 4.8 38.8 1.0
NE B:ARG104 4.9 35.2 1.0
O B:ARG101 4.9 46.8 1.0
CD1 B:LEU108 5.0 60.5 1.0

Reference:

M.Centola, H.Betz, O.Yildiz. Crystal Structures of Phosphatidyl Serine Synthase Pss Reveal the Catalytic Mechanism of Cdp-Dag Alcohol O-Phosphatidyl Transferases Nat Commun V. 12 6982 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-27281-W
Page generated: Mon Jul 29 18:53:48 2024

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