Sodium in PDB 7apu: Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution.

All present enzymatic activity of Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution.:
2.7.4.3;

The structure of Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution., PDB code: 7apu was solved by C.Grundstom, M.Wolf-Watz, K.Nam, U.H.Sauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.81 / 1.36
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.754, 82.226, 78.783, 90, 90, 90
R / Rfree (%)	18.4 / 20.6

The binding sites of Sodium atom in the Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution. (pdb code 7apu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution., PDB code: 7apu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:19.2 occ:1.00 O A:HOH531 2.3 23.3 1.0 O A:HOH606 2.3 24.9 1.0 O A:ASN190 2.4 16.1 1.0 O A:VAL103 2.4 17.2 1.0 C A:ASN190 3.4 14.9 1.0 C A:VAL103 3.5 16.0 1.0 O A:HOH435 3.6 20.6 1.0 N A:VAL103 4.0 15.8 1.0 O A:HOH461 4.1 15.8 1.0 N A:THR191 4.1 14.9 1.0 CB A:ASN102 4.1 25.2 1.0 CA A:THR191 4.2 14.8 1.0 CA A:ASN190 4.3 17.1 1.0 N A:ASP104 4.3 13.6 1.0 CA A:ASP104 4.4 13.9 1.0 CA A:VAL103 4.4 14.9 1.0 OD1 A:ASP104 4.4 15.2 1.0 CB A:THR191 4.6 14.2 1.0 C A:ASN102 4.6 19.3 1.0 O A:HOH545 4.7 35.5 1.0 CG A:ASN102 4.8 50.3 1.0 CA A:ASN102 4.9 22.5 1.0 ND2 A:ASN102 5.0 50.3 1.0

Sodium binding site 2 out of 2 in the Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Adenylate Kinase From Escherichia Coli in Complex with Two Adp Molecules Refined at 1.36 A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:36.3 occ:1.00 O B:HOH472 2.3 28.7 1.0 O B:ASN190 2.6 19.7 1.0 O B:HOH568 2.6 27.9 1.0 O B:HOH589 2.9 33.8 1.0 C B:ASN190 3.4 17.9 1.0 CA B:ASN190 3.7 18.6 1.0 O B:HOH575 4.1 22.7 1.0 O B:HOH407 4.2 31.0 1.0 CB B:ASN190 4.3 17.9 1.0 O B:HOH627 4.5 31.5 1.0 CB B:ASN102 4.5 22.3 1.0 O B:GLY189 4.5 22.2 1.0 ND2 B:ASN102 4.5 31.6 1.0 N B:THR191 4.5 18.6 1.0 O B:VAL103 4.6 18.5 1.0 N B:ASN190 4.9 17.1 1.0 CG B:ASN102 5.0 24.8 1.0 OD1 B:ASN190 5.0 23.1 1.0

P.Ojeda-May, A.U.Mushtaq, P.Rogne, A.Verma, V.Ovchinnikov, C.Grundstrom, B.Dulko-Smith, U.H.Sauer, M.Wolf-Watz, K.Nam. Dynamic Connection Between Enzymatic Catalysis and Collective Protein Motions. Biochemistry V. 60 2246 2021.
ISSN: ISSN 0006-2960
PubMed: 34250801
DOI: 10.1021/ACS.BIOCHEM.1C00221