Chlorine in PDB 8rj4: E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis

Enzymatic activity of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis

All present enzymatic activity of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis:
2.7.4.3;

Protein crystallography data

The structure of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis, PDB code: 8rj4 was solved by S.Tischlik, P.Ronge, M.Wolf-Watz, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.71 / 2.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.385, 76.29, 93.391, 90, 110.76, 90
R / Rfree (%) 19.1 / 25.3

Other elements in 8rj4:

The structure of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis (pdb code 8rj4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis, PDB code: 8rj4:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8rj4

Go back to Chlorine Binding Sites List in 8rj4
Chlorine binding site 1 out of 2 in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:70.0
occ:1.00
NZ C:LYS47 3.3 65.7 1.0
N C:GLY46 3.3 51.2 1.0
CG C:GLN48 3.4 60.7 1.0
CB C:GLN48 3.6 56.2 1.0
N C:GLN48 3.6 48.1 1.0
OE1 C:GLN48 3.7 58.3 1.0
N C:LYS47 3.7 41.6 1.0
CG C:LYS47 3.8 56.3 1.0
CD C:GLN48 4.0 63.4 1.0
CA C:GLY46 4.0 47.9 1.0
C C:GLY46 4.1 46.7 1.0
O C:GLU44 4.2 63.4 1.0
CA C:LEU45 4.2 52.7 1.0
C C:LEU45 4.2 50.8 1.0
CA C:GLN48 4.3 53.6 1.0
CD1 C:LEU63 4.3 54.6 1.0
CE C:LYS47 4.4 59.8 1.0
C C:LYS47 4.5 51.6 1.0
CA C:LYS47 4.5 55.2 1.0
CD C:LYS47 4.5 64.6 1.0
CB C:LYS47 4.6 60.8 1.0
O C:GLY46 5.0 44.2 1.0
C C:GLU44 5.0 65.8 1.0

Chlorine binding site 2 out of 2 in 8rj4

Go back to Chlorine Binding Sites List in 8rj4
Chlorine binding site 2 out of 2 in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl303

b:46.9
occ:1.00
O D:HOH443 2.6 48.1 1.0
NZ D:LYS47 3.2 50.6 1.0
NE2 D:GLN48 3.3 43.0 1.0
N D:GLY46 3.4 37.3 1.0
CG D:GLN48 3.5 40.3 1.0
CG D:LYS47 3.7 40.1 1.0
N D:LYS47 3.7 36.4 1.0
CD D:GLN48 3.9 45.6 1.0
N D:GLN48 4.0 35.8 1.0
CA D:GLY46 4.1 35.8 1.0
C D:GLY46 4.2 37.0 1.0
CB D:GLN48 4.2 41.9 1.0
CA D:LEU45 4.3 46.9 1.0
C D:LEU45 4.3 44.0 1.0
CE D:LYS47 4.4 46.7 1.0
O D:GLU44 4.4 44.0 1.0
CD1 D:LEU63 4.4 51.5 1.0
CA D:LYS47 4.6 37.2 1.0
CD D:LYS47 4.6 48.8 1.0
CB D:LYS47 4.7 40.2 1.0
CA D:GLN48 4.7 35.5 1.0
C D:LYS47 4.8 42.2 1.0

Reference:

A.T.Abdul Raafik, S.Tischlik, T.M.Nagy, C.Phoeurk, L.Schierholtz, J.Aden, P.Rogne, M.Drescher, K.Nam, A.E.Sauer-Eriksson, M.Wolf-Watz. Magnesium Induced Structural Preorganization in the Active Site of Adenylate Kinase. Sci Adv 2024.
ISSN: ESSN 2375-2548
Page generated: Tue Jul 30 12:15:22 2024

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