Magnesium in PDB 8qw1: Human Ndpk-C in Complex with Adp and MG2+

The structure of Human Ndpk-C in Complex with Adp and MG2+, PDB code: 8qw1 was solved by S.Werten, R.Amjadi, K.Scheffzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.01 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.46, 116.31, 84.07, 90, 93.05, 90
R / Rfree (%)	17.2 / 20.5

The binding sites of Magnesium atom in the Human Ndpk-C in Complex with Adp and MG2+ (pdb code 8qw1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Ndpk-C in Complex with Adp and MG2+, PDB code: 8qw1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Human Ndpk-C in Complex with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Ndpk-C in Complex with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:61.6 occ:1.00 O A:HOH312 2.1 52.7 1.0 O1B A:ADP201 2.1 61.4 1.0 O1A A:ADP201 2.2 57.1 1.0 O A:HOH327 2.3 52.9 1.0 O A:HOH346 2.4 49.0 1.0 O A:HOH302 2.4 57.0 1.0 PB A:ADP201 3.1 56.4 1.0 O3B A:ADP201 3.3 53.9 1.0 PA A:ADP201 3.4 64.7 1.0 O3A A:ADP201 3.6 54.6 1.0 C5' A:ADP201 4.0 59.5 1.0 O A:HOH325 4.1 49.2 1.0 NH1 A:ARG105 4.2 45.7 1.0 CE1 A:HIS135 4.2 45.9 1.0 O5' A:ADP201 4.3 62.3 1.0 ND1 A:HIS135 4.3 40.8 1.0 O2B A:ADP201 4.5 58.0 1.0 OD2 A:ASP138 4.5 48.4 1.0 O2A A:ADP201 4.6 71.2 1.0 O A:GLY136 4.7 39.4 1.0 O A:HOH308 4.8 44.7 1.0 CB A:ASP138 4.9 41.0 1.0 O A:HOH332 4.9 33.0 1.0 CG A:ASP138 5.0 43.0 1.0

Magnesium binding site 2 out of 6 in the Human Ndpk-C in Complex with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Ndpk-C in Complex with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:51.7 occ:1.00 O B:HOH311 2.1 52.0 1.0 O1A B:ADP201 2.3 52.4 1.0 O1B B:ADP201 2.3 54.1 1.0 O B:HOH362 2.3 43.0 1.0 O B:HOH339 2.3 47.6 1.0 O B:HOH305 2.6 54.1 1.0 PB B:ADP201 3.3 53.9 1.0 PA B:ADP201 3.5 55.9 1.0 O3B B:ADP201 3.5 46.9 1.0 O3A B:ADP201 3.6 56.3 1.0 C5' B:ADP201 4.1 46.6 1.0 NH1 B:ARG105 4.2 41.5 1.0 O B:HOH309 4.2 33.0 1.0 CE1 B:HIS135 4.2 41.9 1.0 O B:HOH322 4.4 37.0 1.0 O5' B:ADP201 4.4 49.5 1.0 ND1 B:HIS135 4.4 40.2 1.0 OD2 B:ASP138 4.5 48.0 1.0 O2A B:ADP201 4.6 59.0 1.0 O2B B:ADP201 4.7 55.4 1.0 O B:GLY136 4.8 28.9 1.0 CB B:ASP138 5.0 38.6 1.0 O B:HOH325 5.0 30.7 1.0

Magnesium binding site 3 out of 6 in the Human Ndpk-C in Complex with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Ndpk-C in Complex with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:60.1 occ:1.00 O C:HOH344 2.1 54.0 1.0 O C:HOH306 2.1 55.6 1.0 O1B C:ADP201 2.1 60.6 1.0 O C:HOH350 2.2 49.5 1.0 O C:HOH315 2.2 47.6 1.0 O1A C:ADP201 2.2 54.7 1.0 PB C:ADP201 3.2 55.5 1.0 PA C:ADP201 3.5 58.9 1.0 O3B C:ADP201 3.6 55.7 1.0 O3A C:ADP201 3.6 56.0 1.0 O C:HOH329 4.0 42.6 1.0 NH1 C:ARG105 4.2 48.2 1.0 CE1 C:HIS135 4.2 44.7 1.0 C5' C:ADP201 4.3 53.7 1.0 OD2 C:ASP138 4.3 55.5 1.0 O C:HOH336 4.4 48.2 1.0 ND1 C:HIS135 4.4 46.3 1.0 O5' C:ADP201 4.5 53.5 1.0 O2A C:ADP201 4.5 71.1 1.0 O2B C:ADP201 4.6 52.1 1.0 O C:GLY136 4.8 43.4 1.0 CB C:ASP138 4.9 45.9 1.0 CG C:ASP138 4.9 51.3 1.0 O C:HOH322 4.9 39.5 1.0

Magnesium binding site 4 out of 6 in the Human Ndpk-C in Complex with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Ndpk-C in Complex with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:61.5 occ:1.00 O D:HOH311 2.0 62.7 1.0 O1A D:ADP201 2.2 58.4 1.0 O D:HOH351 2.2 52.5 1.0 O D:HOH377 2.2 50.0 1.0 O1B D:ADP201 2.4 60.0 1.0 O D:HOH301 2.8 49.8 1.0 PB D:ADP201 3.3 66.2 1.0 PA D:ADP201 3.4 62.1 1.0 O3A D:ADP201 3.5 62.7 1.0 O3B D:ADP201 3.6 57.2 1.0 C5' D:ADP201 4.0 54.6 1.0 O D:HOH310 4.1 25.7 1.0 CE1 D:HIS135 4.2 33.6 1.0 NH1 D:ARG105 4.3 45.2 1.0 O5' D:ADP201 4.3 53.0 1.0 ND1 D:HIS135 4.4 34.0 1.0 OD2 D:ASP138 4.4 43.0 1.0 O2A D:ADP201 4.5 60.5 1.0 O D:HOH336 4.5 36.7 1.0 O2B D:ADP201 4.7 59.8 1.0 O D:HOH321 4.8 27.7 1.0 O D:GLY136 4.8 26.6 1.0 O D:HOH330 4.8 43.7 1.0 O D:HOH323 4.9 45.5 1.0 CB D:ASP138 4.9 35.5 1.0 CG D:ASP138 5.0 36.9 1.0

Magnesium binding site 5 out of 6 in the Human Ndpk-C in Complex with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Ndpk-C in Complex with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:49.9 occ:1.00 O E:HOH324 2.0 42.5 1.0 O1A E:ADP201 2.1 45.7 1.0 O E:HOH369 2.1 47.8 1.0 O E:HOH352 2.2 44.2 1.0 O1B E:ADP201 2.3 44.7 1.0 O E:HOH301 2.6 46.0 1.0 PB E:ADP201 3.3 49.2 1.0 PA E:ADP201 3.3 46.8 1.0 O3B E:ADP201 3.5 40.1 1.0 O3A E:ADP201 3.6 42.7 1.0 C5' E:ADP201 4.0 39.1 1.0 NH1 E:ARG105 4.2 43.2 1.0 O E:HOH305 4.2 34.0 1.0 O5' E:ADP201 4.3 45.2 1.0 CE1 E:HIS135 4.3 32.4 1.0 O2A E:ADP201 4.4 59.3 1.0 O E:HOH336 4.4 34.7 1.0 OD2 E:ASP138 4.4 43.5 1.0 ND1 E:HIS135 4.5 31.8 1.0 O2B E:ADP201 4.7 41.9 1.0 O E:GLY136 4.8 32.8 1.0 O E:HOH332 4.8 32.5 1.0 CB E:ASP138 4.9 33.7 1.0 CG E:ASP138 5.0 37.2 1.0 NH2 E:ARG105 5.0 44.4 1.0

Magnesium binding site 6 out of 6 in the Human Ndpk-C in Complex with Adp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Ndpk-C in Complex with Adp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:53.1 occ:1.00 O F:HOH337 1.9 48.7 1.0 O1B F:ADP201 2.1 45.5 1.0 O F:HOH340 2.1 43.6 1.0 O1A F:ADP201 2.2 48.9 1.0 O F:HOH365 2.2 43.8 1.0 O F:HOH304 2.4 46.0 1.0 PB F:ADP201 3.2 43.6 1.0 PA F:ADP201 3.5 47.8 1.0 O3B F:ADP201 3.6 41.3 1.0 O3A F:ADP201 3.6 43.4 1.0 NH1 F:ARG105 4.0 37.3 1.0 O F:HOH324 4.0 31.0 1.0 C5' F:ADP201 4.1 43.0 1.0 CE1 F:HIS135 4.2 34.6 1.0 ND1 F:HIS135 4.4 32.0 1.0 O5' F:ADP201 4.4 43.4 1.0 O F:HOH317 4.5 41.7 1.0 OD2 F:ASP138 4.5 43.0 1.0 O2B F:ADP201 4.6 41.9 1.0 O F:HOH349 4.6 57.3 1.0 O F:GLY136 4.6 31.2 1.0 O2A F:ADP201 4.6 50.3 1.0 O F:HOH323 4.7 36.2 1.0 CB F:ASP138 4.8 33.9 1.0 CG F:ASP138 4.9 40.1 1.0 CZ F:ARG105 4.9 40.7 1.0 NH2 F:ARG105 5.0 44.3 1.0

R.Amjadi, S.Werten, S.K.Lomada, C.Baldin, K.Scheffzek, T.Dunzendorfer-Matt, T.Wieland. Mechanistic Insights Into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes Int J Mol Sci V. 25 2024.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS25189768