Magnesium in PDB 7cnp: Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)

The structure of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form), PDB code: 7cnp was solved by Y.Murase, Y.Watanabe, S.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.06 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.131, 73.15, 133.603, 90, 101.39, 90
R / Rfree (%)	17.6 / 20.5

The structure of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) (pdb code 7cnp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form), PDB code: 7cnp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:11.2 occ:1.00 O A:HOH1076 2.9 8.6 1.0 OH A:TYR534 3.0 10.2 1.0 OG A:SER293 3.2 11.9 0.4 C A:GLY69 3.4 10.3 1.0 CA A:GLY69 3.4 10.7 1.0 O A:GLY393 3.6 17.5 1.0 CA A:THR394 3.6 11.7 1.0 CE2 A:TYR534 3.6 10.0 1.0 O A:HOH837 3.6 12.2 1.0 C A:GLY393 3.6 13.3 1.0 N A:SER70 3.7 9.9 1.0 N A:THR394 3.7 11.2 1.0 CZ A:TYR534 3.8 10.3 1.0 O A:GLY69 3.8 12.1 1.0 CE A:LYS530 3.9 12.1 1.0 CA A:SER70 4.0 8.7 1.0 CG2 A:THR394 4.0 9.4 1.0 NZ A:LYS530 4.1 11.2 1.0 OG A:SER293 4.1 13.4 0.6 CB A:SER293 4.1 11.1 0.6 CB A:SER293 4.2 11.1 0.4 CB A:THR394 4.3 11.1 1.0 CB A:SER70 4.4 10.8 1.0 CA A:GLY393 4.4 11.7 1.0 CD A:LYS530 4.7 9.8 1.0 N A:GLY69 4.8 10.4 1.0 C A:THR394 4.8 12.0 1.0 CD2 A:TYR534 4.9 8.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:9.5 occ:1.00 O B:HOH1155 2.9 7.5 1.0 OH B:TYR534 3.0 9.0 1.0 OG B:SER293 3.3 11.2 0.6 C B:GLY69 3.3 8.3 1.0 CA B:GLY69 3.4 8.6 1.0 CE2 B:TYR534 3.6 8.3 1.0 N B:SER70 3.6 8.6 1.0 CA B:THR394 3.6 8.1 1.0 O B:HOH755 3.6 9.5 1.0 C B:GLY393 3.7 14.3 1.0 O B:GLY393 3.7 15.7 1.0 N B:THR394 3.7 9.2 1.0 CZ B:TYR534 3.7 8.4 1.0 O B:GLY69 3.8 10.5 1.0 CE B:LYS530 3.9 9.8 1.0 CA B:SER70 3.9 7.3 1.0 CG2 B:THR394 4.0 9.4 1.0 NZ B:LYS530 4.1 9.7 1.0 CB B:SER293 4.2 10.5 0.4 OG B:SER293 4.2 10.3 0.4 CB B:SER293 4.2 10.5 0.6 CB B:THR394 4.3 12.8 1.0 CB B:SER70 4.3 10.1 1.0 CA B:GLY393 4.5 10.0 1.0 N B:GLY69 4.7 9.5 1.0 CD B:LYS530 4.8 6.5 1.0 C B:THR394 4.8 9.9 1.0 CD2 B:TYR534 4.9 10.2 1.0 O B:ALA390 4.9 9.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Agrobacterium Tumefaciens Aconitase X (Apo-Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:12.6 occ:1.00 O C:HOH982 2.9 10.1 1.0 OH C:TYR534 3.0 12.6 1.0 OG C:SER293 3.1 14.6 0.6 C C:GLY69 3.4 11.9 1.0 CA C:GLY69 3.5 10.1 1.0 O C:HOH853 3.5 10.9 1.0 O C:GLY393 3.6 19.5 1.0 CA C:THR394 3.6 12.9 1.0 N C:SER70 3.6 11.2 1.0 CE2 C:TYR534 3.6 11.4 1.0 C C:GLY393 3.6 17.0 1.0 N C:THR394 3.7 10.9 1.0 CZ C:TYR534 3.8 14.6 1.0 O C:GLY69 3.8 13.3 1.0 CE C:LYS530 3.9 12.5 1.0 CA C:SER70 3.9 10.2 1.0 CG2 C:THR394 4.0 12.9 1.0 CB C:SER293 4.1 13.3 0.5 CB C:SER293 4.1 13.3 0.6 OG C:SER293 4.1 11.2 0.5 NZ C:LYS530 4.1 11.3 1.0 CB C:SER70 4.3 12.9 1.0 CB C:THR394 4.3 15.2 1.0 CA C:GLY393 4.4 10.4 1.0 CD C:LYS530 4.7 11.5 1.0 C C:THR394 4.8 13.3 1.0 N C:GLY69 4.8 12.3 1.0 CD2 C:TYR534 4.9 13.3 1.0 O C:ALA390 4.9 10.7 1.0

Y.Murase, S.Watanabe, Y.Watanabe. Crystal Structure of Aconitase X To Be Published.