Magnesium in PDB 4fkx: Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp

All present enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp:
2.7.4.6;

The structure of Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp, PDB code: 4fkx was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.33 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.630, 121.370, 112.870, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.2

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp (pdb code 4fkx). 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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp, PDB code: 4fkx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp


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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:23.6 occ:1.00 O3B A:CDP201 2.0 20.4 1.0 O A:HOH392 2.0 22.5 1.0 O A:HOH395 2.1 34.6 1.0 O A:HOH394 2.1 32.6 1.0 O A:HOH393 2.1 33.1 1.0 O1A A:CDP201 2.1 19.5 1.0 PB A:CDP201 3.2 19.8 1.0 PA A:CDP201 3.4 18.9 1.0 O3A A:CDP201 3.7 19.5 1.0 O1B A:CDP201 3.8 19.4 1.0 O A:HOH312 4.1 15.9 1.0 O A:HOH448 4.2 38.7 1.0 NH1 A:ARG87 4.2 21.8 1.0 CE1 A:HIS117 4.3 12.2 1.0 O A:HOH321 4.4 19.1 1.0 C5' A:CDP201 4.4 17.6 1.0 OD2 A:ASP120 4.4 24.8 1.0 O5' A:CDP201 4.5 17.7 1.0 O2A A:CDP201 4.5 19.4 1.0 O2B A:CDP201 4.5 22.6 1.0 ND1 A:HIS117 4.6 11.7 1.0 O A:GLY118 4.6 12.3 1.0 O A:HOH340 4.6 24.4 1.0 CB A:ASP120 4.7 19.8 1.0 CG A:ASP120 4.8 21.4 1.0 O A:HOH409 4.8 26.7 1.0 O A:HOH396 4.9 17.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp


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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.8 occ:1.00 O1B B:CDP201 1.9 17.4 1.0 O B:HOH397 2.0 16.0 1.0 O2A B:CDP201 2.1 16.9 1.0 O B:HOH399 2.1 20.8 1.0 O B:HOH398 2.1 21.9 1.0 O B:HOH364 2.1 17.0 1.0 PB B:CDP201 3.2 17.4 1.0 PA B:CDP201 3.3 16.7 1.0 O3A B:CDP201 3.6 17.1 1.0 O3B B:CDP201 3.8 16.2 1.0 NH1 B:ARG87 4.1 19.1 1.0 O B:HOH322 4.2 13.9 1.0 O B:HOH444 4.2 29.5 1.0 O B:HOH458 4.3 31.2 1.0 CE1 B:HIS117 4.3 12.0 1.0 C5' B:CDP201 4.3 16.3 1.0 O5' B:CDP201 4.3 16.3 1.0 O2B B:CDP201 4.4 18.1 1.0 OD2 B:ASP120 4.4 18.8 1.0 ND1 B:HIS117 4.4 11.6 1.0 O1A B:CDP201 4.4 17.8 1.0 O B:HOH372 4.5 15.2 1.0 O B:GLY118 4.6 11.1 1.0 O B:HOH327 4.8 16.1 1.0 CB B:ASP120 4.8 15.4 1.0 O B:HOH350 4.9 23.7 1.0 CG B:ASP120 4.9 17.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp


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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:12.5 occ:1.00 O3B C:CDP201 2.0 13.8 1.0 O C:HOH414 2.0 16.1 1.0 O C:HOH415 2.0 11.6 1.0 O1A C:CDP201 2.1 13.4 1.0 O C:HOH416 2.1 19.1 1.0 O C:HOH417 2.2 15.1 1.0 PB C:CDP201 3.2 14.0 1.0 PA C:CDP201 3.3 12.9 1.0 O3A C:CDP201 3.6 13.5 1.0 O1B C:CDP201 3.7 12.7 1.0 O C:HOH419 4.1 20.1 1.0 O C:HOH397 4.1 20.1 1.0 NH1 C:ARG87 4.2 13.1 1.0 O C:HOH306 4.3 11.0 1.0 CE1 C:HIS117 4.3 9.5 1.0 OD2 C:ASP120 4.3 16.8 1.0 C5' C:CDP201 4.3 13.4 1.0 O5' C:CDP201 4.4 13.2 1.0 O2A C:CDP201 4.4 14.4 1.0 O2B C:CDP201 4.4 14.1 1.0 O C:HOH329 4.5 12.8 1.0 ND1 C:HIS117 4.5 9.5 1.0 O C:GLY118 4.6 9.1 1.0 CB C:ASP120 4.7 13.2 1.0 CG C:ASP120 4.8 14.3 1.0 O C:HOH324 4.9 9.3 1.0 O C:HOH420 5.0 28.2 1.0 CE1 C:TYR51 5.0 12.2 1.0

A.S.Gardberg, T.E.Edwards, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Cdp To Be Published.