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Sodium in PDB 3qvq: The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate

Enzymatic activity of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate

All present enzymatic activity of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate:
3.1.4.2;

Protein crystallography data

The structure of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate, PDB code: 3qvq was solved by A.U.Singer, O.Kagan, E.Evdokimova, M.E.Cuff, A.M.Edwards, A.Joachimiak, A.F.Yakunin, A.Savchenko, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.26 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.861, 92.717, 125.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Other elements in 3qvq:

The structure of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 13 atoms
Chlorine (Cl) 18 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate (pdb code 3qvq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate, PDB code: 3qvq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3qvq

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Sodium binding site 1 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na253

b:48.1
occ:1.00
 O D:HOH349 3.2 31.5 1.0
O A:PHE197 3.5 14.8 1.0
NZ D:LYS72 3.6 19.6 1.0
O A:SER195 3.8 13.3 1.0
C A:PHE196 3.9 10.8 1.0
CA A:PHE196 4.0 9.7 1.0
O A:PHE196 4.0 10.7 1.0
C A:PHE197 4.2 14.4 1.0
N A:PHE197 4.5 9.2 1.0
CB A:ASP198 4.5 13.0 1.0
C A:SER195 4.7 12.6 1.0
CA A:ASP198 4.7 11.7 1.0
N A:ASP198 4.7 12.3 1.0
O A:HOH316 4.8 15.1 1.0
N A:PHE196 4.8 9.0 1.0
CD1 A:PHE196 4.9 20.1 1.0
CB A:PHE196 5.0 9.4 1.0

Sodium binding site 2 out of 7 in 3qvq

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Sodium binding site 2 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na254

b:45.5
occ:1.00
 NE2 A:GLN194 3.8 19.2 1.0
O A:HOH357 4.2 23.8 1.0
CL A:CL260 4.2 18.4 1.0
CD A:GLN194 4.3 19.1 1.0
O A:HOH573 4.4 27.3 1.0
OE1 A:GLN194 4.6 22.5 1.0
O A:THR216 4.6 12.2 1.0

Sodium binding site 3 out of 7 in 3qvq

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Sodium binding site 3 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na255

b:39.3
occ:1.00
 C1 A:EDO263 2.4 34.3 1.0
O1 A:EDO263 3.3 40.5 1.0
C2 A:EDO263 3.5 33.5 1.0
CB A:GLU90 3.5 20.6 1.0
O2 A:EDO263 3.7 36.3 1.0
CG A:GLU90 3.9 22.9 1.0
CD A:GLU90 4.6 22.6 1.0
CA A:GLU90 4.9 21.9 1.0

Sodium binding site 4 out of 7 in 3qvq

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Sodium binding site 4 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na256

b:37.3
occ:1.00
 CD A:PRO74 3.6 22.1 1.0
C A:GLY48 3.6 18.9 1.0
CA A:GLY48 3.6 17.4 1.0
N A:PRO74 3.7 15.4 1.0
O A:GLY48 3.8 19.1 1.0
O A:LYS72 3.8 23.6 1.0
CB A:PRO74 3.9 19.7 1.0
CA A:PRO74 4.0 16.8 1.0
N A:ASP49 4.1 14.9 1.0
CG A:PRO74 4.1 21.9 1.0
C A:THR73 4.1 20.6 1.0
C A:LYS72 4.2 20.6 1.0
N A:THR73 4.4 17.4 1.0
CA A:THR73 4.5 19.3 1.0
N A:GLY48 4.7 15.3 1.0
O A:THR73 4.8 14.6 1.0
CA A:ASP49 4.8 15.7 1.0
CB A:ASP49 4.9 21.2 1.0

Sodium binding site 5 out of 7 in 3qvq

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Sodium binding site 5 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na254

b:18.0
occ:1.00
 O B:ILE165 2.8 11.8 1.0
O B:TRP162 2.8 13.2 1.0
NH1 B:ARG167 2.9 9.8 1.0
O B:ALA158 3.2 10.7 1.0
CG B:ARG167 3.4 8.3 1.0
CD B:ARG167 3.5 9.1 1.0
C B:ALA158 3.5 12.1 1.0
CD2 B:PHE147 3.6 8.8 1.0
C B:ILE165 3.7 11.7 1.0
C B:TRP162 3.8 11.7 1.0
CB B:ALA158 3.9 12.1 1.0
CB B:ILE165 3.9 11.8 1.0
N B:LYS159 3.9 11.6 0.4
N B:LYS159 4.0 11.6 0.6
CZ B:ARG167 4.0 11.2 1.0
CA B:LYS159 4.1 10.8 0.6
CA B:ILE165 4.1 11.3 1.0
CA B:LYS159 4.1 10.9 0.4
CE2 B:PHE147 4.1 9.8 1.0
N B:ILE165 4.1 10.7 1.0
NE B:ARG167 4.2 10.3 1.0
CA B:ALA158 4.2 9.8 1.0
CA B:PRO163 4.4 14.2 1.0
O B:PRO163 4.4 12.2 1.0
C B:PRO163 4.5 13.8 1.0
N B:PRO163 4.5 12.9 1.0
CG2 B:ILE165 4.6 10.3 1.0
CG B:PHE147 4.7 9.3 1.0
O B:ALA166 4.7 8.9 1.0
CA B:TRP162 4.8 11.0 1.0
CB B:TRP162 4.8 13.5 1.0
CB B:ARG167 4.8 9.0 1.0
CB B:PHE147 4.8 8.1 1.0
C B:ALA166 4.9 11.1 1.0
N B:ALA166 4.9 8.0 1.0
CB B:LYS159 5.0 13.9 0.6
CG1 B:ILE165 5.0 12.9 1.0

Sodium binding site 6 out of 7 in 3qvq

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Sodium binding site 6 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na252

b:32.9
occ:1.00
 O C:HOH723 2.3 23.8 1.0
O C:HOH790 2.3 26.7 1.0
O C:HOH360 2.4 33.6 1.0
O C:HOH834 4.1 30.5 1.0
OE1 C:GLN80 4.4 32.9 1.0
O C:HOH810 4.4 25.8 1.0
O C:LYS79 4.6 14.9 1.0
O C:GLN80 4.6 18.5 1.0
NE2 C:GLN80 4.7 39.0 1.0
O C:HOH882 4.7 37.1 1.0
CD C:GLN80 4.8 30.2 1.0
CA C:GLN80 4.8 16.0 1.0

Sodium binding site 7 out of 7 in 3qvq

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Sodium binding site 7 out of 7 in the The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na254

b:26.7
occ:1.00
 O D:HOH351 2.5 32.8 1.0
N D:ARG167 3.2 13.2 1.0
N D:ALA188 3.3 11.9 1.0
O D:HOH678 3.3 29.9 1.0
O D:ASP186 3.4 17.2 1.0
CB D:ALA188 3.5 19.1 1.0
CA D:ALA166 3.7 10.2 1.0
O D:ARG167 3.7 12.9 1.0
O D:HOH331 3.7 23.1 1.0
C D:ALA166 3.9 13.6 1.0
C D:CYS187 4.0 16.4 1.0
CA D:CYS187 4.0 12.1 1.0
CA D:ALA188 4.0 12.4 1.0
CB D:ALA166 4.1 13.6 1.0
CA D:ARG167 4.1 13.7 1.0
NH1 D:ARG167 4.2 16.4 1.0
CB D:ARG167 4.3 10.4 1.0
C D:ASP186 4.3 15.6 1.0
C D:ARG167 4.3 14.0 1.0
CZ D:ARG167 4.5 18.5 1.0
O D:HOH584 4.6 23.8 1.0
N D:CYS187 4.6 13.7 1.0
NE D:ARG167 4.6 13.4 1.0
CE2 D:TYR5 4.8 13.4 1.0
OD1 D:ASP186 4.9 25.6 1.0
N D:ALA166 4.9 11.2 1.0
O D:ILE165 5.0 13.0 1.0

Reference:

A.U.Singer, O.Kagan, E.Evdokimova, M.E.Cuff, A.M.Edwards, A.Joachimiak, A.F.Yakunin, A.Savchenko. The Structure of An Oleispira Antarctica Phosphodiesterase OLEI02445 in Complex with the Product Sn-Glycerol-3-Phosphate To Be Published.
Page generated: Mon Oct 7 12:42:47 2024

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