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Sodium in PDB 5eqv: 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site

Enzymatic activity of 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site

All present enzymatic activity of 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site:
3.1.4.16;

Protein crystallography data

The structure of 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site, PDB code: 5eqv was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, O.Kiryukhina, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.91 / 1.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.282, 107.282, 63.357, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 15.3

Other elements in 5eqv:

The structure of 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site (pdb code 5eqv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site, PDB code: 5eqv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5eqv

Go back to Sodium Binding Sites List in 5eqv
Sodium binding site 1 out of 2 in the 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:21.3
occ:0.50
 O A:HOH617 2.3 36.6 1.0
O A:HOH802 2.3 35.7 1.0
O A:HOH955 2.4 28.7 1.0
O A:HOH893 2.4 54.4 1.0
O A:HOH1031 2.5 27.8 1.0
O A:HOH1114 2.6 30.6 0.5
O A:HOH721 4.2 30.0 1.0
O A:HOH916 4.3 32.9 1.0
O A:HOH627 4.3 20.8 1.0
N A:ALA322 4.5 18.0 1.0
O A:GLY290 4.6 18.6 1.0
O A:HOH623 4.7 32.0 1.0
CA A:ASP321 4.8 20.5 0.5
CA A:ASP321 4.8 19.3 0.5
OD1 A:ASP321 4.8 20.9 0.5
O A:ALA322 4.8 21.1 1.0
O A:ILE320 4.9 22.5 1.0

Sodium binding site 2 out of 2 in 5eqv

Go back to Sodium Binding Sites List in 5eqv
Sodium binding site 2 out of 2 in the 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:31.1
occ:1.00
 O A:HOH900 2.2 35.0 1.0
O A:HOH997 2.3 41.3 1.0
O A:SER77 2.4 13.3 0.5
O A:HOH852 2.4 18.1 0.5
O A:HOH878 2.5 16.8 0.5
O A:HOH625 2.5 28.0 1.0
O A:SER77 2.6 13.7 0.5
O A:HOH878 2.6 18.6 0.5
O A:HOH705 3.4 19.1 0.5
C A:SER77 3.6 13.5 0.5
C A:SER77 3.7 13.8 0.5
O A:HOH705 3.9 17.9 0.5
O A:HOH537 4.0 33.9 1.0
OG A:SER77 4.0 14.8 0.5
N A:SER77 4.1 13.9 0.5
N A:SER77 4.1 13.5 0.5
O A:HOH630 4.3 32.0 1.0
CA A:SER77 4.3 14.1 0.5
CA A:SER77 4.4 13.6 0.5
O A:HOH614 4.4 31.9 0.5
CB A:SER77 4.4 15.7 0.5
OD2 A:ASP116 4.4 19.9 1.0
O A:HOH1072 4.5 23.4 1.0
O A:HOH1126 4.6 51.1 1.0
N A:VAL78 4.7 12.8 1.0
O A:HOH923 4.7 36.7 1.0
O A:HOH599 4.7 28.6 1.0
O A:HOH914 4.8 46.3 1.0
O A:HOH715 4.8 20.5 1.0
CB A:SER77 4.8 14.3 0.5
O A:HOH999 4.8 49.1 1.0
O A:HOH660 4.9 14.6 1.0
CA A:VAL78 4.9 12.5 1.0

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, O.Kiryukhina, I.Dubrovska, S.Grimshaw, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.45 Angstrom Crystal Structure of Bifunctional 2',3'-Cyclic Nucleotide 2'-Phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein From Yersinia Pestis with Phosphate Bound to the Active Site. To Be Published.
Page generated: Mon Oct 7 20:50:46 2024

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