Magnesium in PDB 4f4a: Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form

All present enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form:
2.7.4.6;

The structure of Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form, PDB code: 4f4a 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)	41.74 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.830, 121.510, 113.170, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.5

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form (pdb code 4f4a). 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, Udp-Bound Form, PDB code: 4f4a:
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, Udp-Bound 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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:36.5 occ:1.00 O2A A:UDP201 2.2 24.0 1.0 O3B A:UDP201 2.2 24.9 1.0 O A:HOH385 2.3 23.3 1.0 O A:HOH384 2.6 35.3 1.0 PB A:UDP201 3.5 24.8 1.0 PA A:UDP201 3.6 24.4 1.0 O A:HOH338 3.7 18.2 1.0 CE1 A:HIS117 3.9 12.0 1.0 O3A A:UDP201 3.9 24.0 1.0 O A:HOH331 3.9 14.8 1.0 O1B A:UDP201 4.0 23.6 1.0 O A:HOH330 4.2 28.0 1.0 C5' A:UDP201 4.3 21.3 1.0 ND1 A:HIS117 4.3 11.7 1.0 NH1 A:ARG87 4.5 18.9 1.0 O5' A:UDP201 4.5 22.6 1.0 OD1 A:ASP120 4.6 22.0 1.0 O A:HOH430 4.7 29.7 1.0 CE1 A:TYR51 4.7 22.1 1.0 O1A A:UDP201 4.7 24.6 1.0 O2B A:UDP201 4.8 24.9 1.0 O A:GLY118 4.8 12.2 1.0 CG A:ASP120 4.9 19.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound 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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:32.1 occ:1.00 O3B B:UDP201 1.9 34.7 1.0 O B:HOH356 2.1 30.7 1.0 O B:HOH406 2.2 22.2 1.0 O2A B:UDP201 2.2 29.3 1.0 PB B:UDP201 3.2 34.9 1.0 PA B:UDP201 3.5 30.7 1.0 O3A B:UDP201 3.7 31.6 1.0 O1B B:UDP201 3.7 31.1 1.0 O B:HOH320 3.9 12.5 1.0 CE1 B:HIS117 4.0 15.0 1.0 NH1 B:ARG87 4.1 18.8 1.0 ND1 B:HIS117 4.3 14.2 1.0 C5' B:UDP201 4.3 28.7 1.0 OD2 B:ASP120 4.4 19.6 1.0 O B:HOH405 4.4 24.1 1.0 O2B B:UDP201 4.5 33.6 1.0 O5' B:UDP201 4.5 29.6 1.0 O B:GLY118 4.6 12.7 1.0 O1A B:UDP201 4.6 31.3 1.0 CB B:ASP120 4.8 16.7 1.0 O B:HOH428 4.8 26.1 1.0 CG B:ASP120 4.8 18.3 1.0 O B:HOH302 5.0 12.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound 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 Nucleoside Diphosphate Kinase B From Trypanosoma Brucei, Udp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:25.6 occ:1.00 O3B C:UDP201 2.0 24.1 1.0 O C:HOH382 2.0 25.4 1.0 O C:HOH383 2.0 36.4 1.0 O2A C:UDP201 2.1 21.2 1.0 O C:HOH381 2.2 18.6 1.0 PB C:UDP201 3.2 23.2 1.0 PA C:UDP201 3.3 20.8 1.0 O3A C:UDP201 3.6 24.0 1.0 O1B C:UDP201 3.8 21.1 1.0 NH1 C:ARG87 4.1 15.8 1.0 O C:HOH311 4.2 10.7 1.0 O C:HOH435 4.2 38.0 1.0 O C:HOH384 4.3 18.9 1.0 CE1 C:HIS117 4.3 12.6 1.0 C5' C:UDP201 4.3 21.4 1.0 OD2 C:ASP120 4.4 18.4 1.0 O5' C:UDP201 4.4 21.8 1.0 O C:HOH386 4.4 29.0 1.0 O2B C:UDP201 4.4 23.8 1.0 O1A C:UDP201 4.5 21.7 1.0 ND1 C:HIS117 4.6 12.5 1.0 O C:GLY118 4.7 10.9 1.0 CB C:ASP120 4.7 15.1 1.0 CG C:ASP120 4.8 16.0 1.0

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