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

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

The structure of Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Gtp, PDB code: 4fky 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)	41.65 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.680, 121.490, 112.830, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 18.8

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei Bound to Gtp (pdb code 4fky). 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 Gtp, PDB code: 4fky:
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 Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:25.9 occ:1.00 O A:HOH434 2.1 33.9 1.0 O3B A:GDP201 2.1 17.9 1.0 O A:HOH324 2.1 27.4 1.0 O1A A:GDP201 2.1 16.9 1.0 O A:HOH433 2.1 35.6 1.0 O A:HOH345 2.2 23.4 1.0 PB A:GDP201 3.3 17.8 1.0 PA A:GDP201 3.4 17.4 1.0 O3A A:GDP201 3.6 17.4 1.0 O1B A:GDP201 3.9 16.9 1.0 NH1 A:ARG87 4.1 21.7 1.0 O A:HOH316 4.2 16.9 1.0 O A:HOH341 4.2 16.7 1.0 OD2 A:ASP120 4.3 24.0 1.0 CE1 A:HIS117 4.3 11.0 1.0 O2A A:GDP201 4.3 18.2 1.0 C5' A:GDP201 4.4 15.4 1.0 O5' A:GDP201 4.5 16.3 1.0 O2B A:GDP201 4.5 18.7 1.0 ND1 A:HIS117 4.6 10.5 1.0 CG A:ASP120 4.7 19.5 1.0 O A:GLY118 4.7 11.7 1.0 CB A:ASP120 4.8 18.4 1.0 O A:HOH432 4.8 20.2 1.0 O A:HOH384 4.9 18.7 1.0 O A:HOH399 4.9 30.7 1.0

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


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:17.0 occ:1.00 O1B B:GDP201 1.9 17.4 1.0 O B:HOH403 2.0 12.1 1.0 O B:HOH401 2.0 20.2 1.0 O B:HOH402 2.1 17.9 1.0 O2A B:GDP201 2.1 15.8 1.0 O B:HOH399 2.2 14.2 1.0 PB B:GDP201 3.1 16.9 1.0 PA B:GDP201 3.4 16.1 1.0 O3A B:GDP201 3.6 16.4 1.0 O3B B:GDP201 3.8 17.2 1.0 NH1 B:ARG87 4.0 16.4 1.0 O B:HOH420 4.2 32.8 1.0 O B:HOH352 4.2 12.4 1.0 OD2 B:ASP120 4.3 18.3 1.0 O2B B:GDP201 4.3 18.1 1.0 CE1 B:HIS117 4.4 9.8 1.0 O1A B:GDP201 4.4 16.6 1.0 O5' B:GDP201 4.4 15.4 1.0 C5' B:GDP201 4.5 14.6 1.0 ND1 B:HIS117 4.5 9.6 1.0 O B:GLY118 4.6 10.3 1.0 O B:HOH391 4.6 12.8 1.0 CB B:ASP120 4.7 14.6 1.0 O B:HOH335 4.8 14.7 1.0 CG B:ASP120 4.8 16.2 1.0 CZ B:ARG87 5.0 16.8 1.0 O B:HOH400 5.0 23.4 1.0

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


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:12.6 occ:1.00 O3B C:GDP201 2.0 13.3 1.0 O C:HOH412 2.0 14.7 1.0 O1A C:GDP201 2.1 12.7 1.0 O C:HOH415 2.1 11.9 1.0 O C:HOH414 2.1 14.1 1.0 O C:HOH413 2.2 13.9 1.0 PB C:GDP201 3.1 12.9 1.0 PA C:GDP201 3.3 12.6 1.0 O3A C:GDP201 3.6 12.6 1.0 O1B C:GDP201 3.6 12.3 1.0 NH1 C:ARG87 4.2 13.1 1.0 O C:HOH370 4.2 17.2 1.0 O C:HOH374 4.3 22.8 1.0 O C:HOH310 4.3 8.9 1.0 CE1 C:HIS117 4.3 7.9 1.0 C5' C:GDP201 4.3 11.9 1.0 OD2 C:ASP120 4.3 13.3 1.0 O5' C:GDP201 4.3 12.3 1.0 O2A C:GDP201 4.4 13.3 1.0 O C:HOH360 4.4 11.0 1.0 O2B C:GDP201 4.4 13.0 1.0 ND1 C:HIS117 4.4 7.8 1.0 O C:GLY118 4.6 8.5 1.0 CB C:ASP120 4.8 11.5 1.0 CG C:ASP120 4.9 12.2 1.0 O C:HOH416 4.9 7.6 1.0 CE1 C:TYR51 5.0 11.3 1.0 O C:HOH417 5.0 22.1 1.0 O C:HOH388 5.0 18.4 1.0

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