Magnesium in PDB 8qw2: Human Ndpk-C in Complex with Udp and MG2+

The structure of Human Ndpk-C in Complex with Udp and MG2+, PDB code: 8qw2 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)	47.72 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.532, 115.991, 83.842, 90, 93.28, 90
R / Rfree (%)	17 / 20.3

The binding sites of Magnesium atom in the Human Ndpk-C in Complex with Udp and MG2+ (pdb code 8qw2). 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 Udp and MG2+, PDB code: 8qw2:
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 Udp 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 Udp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:96.2 occ:1.00 O A:HOH323 2.2 63.2 1.0 O2A A:UDP201 2.2 95.7 1.0 O1B A:UDP201 2.7 102.6 1.0 O3B A:UDP201 3.2 114.6 1.0 PB A:UDP201 3.4 106.7 1.0 PA A:UDP201 3.5 101.9 1.0 O3A A:UDP201 3.7 99.7 1.0 CE1 A:HIS135 3.9 66.9 1.0 C5' A:UDP201 4.0 83.8 1.0 ND1 A:HIS135 4.2 63.2 1.0 O5' A:UDP201 4.2 89.7 1.0 NH1 A:ARG105 4.6 70.0 1.0 OD2 A:ASP138 4.7 73.9 1.0 O1A A:UDP201 4.8 115.2 1.0 O2B A:UDP201 4.8 109.0 1.0 O A:GLY136 4.9 56.1 1.0 O A:HOH305 4.9 52.6 1.0 CD1 A:LEU72 5.0 77.4 1.0

Magnesium binding site 2 out of 6 in the Human Ndpk-C in Complex with Udp 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 Udp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:81.2 occ:1.00 O B:HOH325 2.0 76.1 1.0 O2A B:UDP201 2.2 75.0 1.0 O1B B:UDP201 2.3 86.2 1.0 O B:HOH342 2.3 62.6 1.0 O B:HOH351 2.6 66.9 1.0 O B:HOH305 2.7 78.9 1.0 PB B:UDP201 3.3 76.6 1.0 PA B:UDP201 3.4 84.9 1.0 O3B B:UDP201 3.5 69.6 1.0 O3A B:UDP201 3.5 77.8 1.0 C5' B:UDP201 4.1 64.4 1.0 NH1 B:ARG105 4.2 61.6 1.0 O B:HOH308 4.3 56.0 1.0 CE1 B:HIS135 4.3 61.6 1.0 O5' B:UDP201 4.4 71.3 1.0 O B:HOH328 4.5 56.3 1.0 OD2 B:ASP138 4.5 72.1 1.0 O1A B:UDP201 4.5 80.3 1.0 ND1 B:HIS135 4.6 54.4 1.0 O2B B:UDP201 4.7 86.0 1.0 O B:HOH304 4.9 50.5 1.0 NH2 B:ARG105 4.9 73.9 1.0 O B:GLY136 4.9 48.0 1.0 CB B:ASP138 4.9 54.6 1.0

Magnesium binding site 3 out of 6 in the Human Ndpk-C in Complex with Udp 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 Udp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:97.5 occ:1.00 O2A C:UDP201 2.3 111.0 1.0 O C:HOH306 2.5 86.0 1.0 O1B C:UDP201 2.5 108.9 1.0 O C:HOH322 2.6 86.9 1.0 PB C:UDP201 3.4 104.5 1.0 PA C:UDP201 3.5 105.8 1.0 O3B C:UDP201 3.5 113.3 1.0 O3A C:UDP201 3.6 118.2 1.0 CE1 C:HIS135 3.7 69.5 1.0 C5' C:UDP201 3.8 93.1 1.0 ND1 C:HIS135 3.8 69.3 1.0 O5' C:UDP201 4.1 100.1 1.0 O C:HOH312 4.1 68.9 1.0 CE1 C:TYR69 4.6 75.9 1.0 O C:HOH301 4.6 65.0 1.0 CD1 C:LEU72 4.7 85.8 1.0 O1A C:UDP201 4.8 104.8 1.0 NH1 C:ARG105 4.8 76.0 1.0 O2B C:UDP201 4.8 92.7 1.0 CD1 C:TYR69 4.9 74.2 1.0 NE2 C:HIS135 4.9 65.0 1.0 O C:GLY136 4.9 63.4 1.0

Magnesium binding site 4 out of 6 in the Human Ndpk-C in Complex with Udp 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 Udp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:68.8 occ:1.00 O D:HOH305 2.1 62.2 1.0 O2A D:UDP201 2.2 67.2 1.0 O D:HOH344 2.3 49.9 1.0 O1B D:UDP201 2.3 65.3 1.0 O D:HOH367 2.4 59.1 1.0 PB D:UDP201 3.1 65.2 1.0 O3B D:UDP201 3.1 68.9 1.0 PA D:UDP201 3.4 71.6 1.0 O3A D:UDP201 3.5 69.9 1.0 C5' D:UDP201 3.7 61.4 1.0 CE1 D:HIS135 3.8 47.7 1.0 ND1 D:HIS135 3.9 48.2 1.0 O D:HOH351 4.1 64.0 1.0 O5' D:UDP201 4.1 64.2 1.0 O D:HOH311 4.4 42.7 1.0 O D:HOH323 4.4 45.4 1.0 NH1 D:ARG105 4.4 57.2 1.0 O D:HOH334 4.5 44.7 1.0 O2B D:UDP201 4.6 68.7 1.0 O1A D:UDP201 4.7 67.8 1.0 CE1 D:TYR69 4.7 49.3 1.0 O D:GLY136 4.7 43.9 1.0 C4' D:UDP201 4.9 64.9 1.0 CD1 D:LEU72 4.9 51.5 1.0

Magnesium binding site 5 out of 6 in the Human Ndpk-C in Complex with Udp 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 Udp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:72.4 occ:1.00 O2A E:UDP201 2.0 70.0 1.0 O E:HOH328 2.1 66.5 1.0 O E:HOH348 2.2 53.7 1.0 O E:HOH352 2.2 69.2 1.0 O1B E:UDP201 2.3 67.9 1.0 O E:HOH312 2.4 69.7 1.0 PA E:UDP201 3.2 68.0 1.0 PB E:UDP201 3.3 66.3 1.0 O3A E:UDP201 3.5 63.2 1.0 O3B E:UDP201 3.7 60.5 1.0 C5' E:UDP201 4.1 58.2 1.0 O E:HOH313 4.1 46.7 1.0 NH1 E:ARG105 4.3 58.4 1.0 O5' E:UDP201 4.3 63.2 1.0 CE1 E:HIS135 4.3 50.3 1.0 O1A E:UDP201 4.3 74.5 1.0 OD2 E:ASP138 4.5 68.5 1.0 O E:HOH333 4.5 53.9 1.0 ND1 E:HIS135 4.6 46.0 1.0 O2B E:UDP201 4.7 62.8 1.0 O E:HOH305 4.8 49.7 1.0 CB E:ASP138 4.9 56.1 1.0 O E:GLY136 4.9 44.7 1.0 CG E:ASP138 4.9 58.9 1.0 CD1 E:LEU72 5.0 61.1 1.0

Magnesium binding site 6 out of 6 in the Human Ndpk-C in Complex with Udp 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 Udp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:78.8 occ:1.00 O F:HOH334 1.9 68.9 1.0 O F:HOH340 2.1 61.9 1.0 O1B F:UDP201 2.2 72.7 1.0 O2A F:UDP201 2.2 72.3 1.0 O F:HOH353 2.2 68.9 1.0 O F:HOH310 2.4 64.2 1.0 PB F:UDP201 3.2 72.1 1.0 PA F:UDP201 3.4 70.5 1.0 O3B F:UDP201 3.5 68.7 1.0 O3A F:UDP201 3.6 68.3 1.0 NH1 F:ARG105 4.0 53.1 1.0 O F:HOH312 4.1 52.0 1.0 CE1 F:HIS135 4.2 56.5 1.0 C5' F:UDP201 4.2 59.4 1.0 O5' F:UDP201 4.5 64.9 1.0 OD2 F:ASP138 4.5 65.8 1.0 ND1 F:HIS135 4.5 55.4 1.0 O1A F:UDP201 4.5 69.1 1.0 CB F:ASP138 4.6 52.3 1.0 O F:GLY136 4.6 46.8 1.0 O2B F:UDP201 4.7 68.6 1.0 O F:HOH330 4.7 57.8 1.0 O F:HOH308 4.7 53.2 1.0 CG F:ASP138 4.8 61.6 1.0 NH2 F:ARG105 4.9 63.8 1.0 CZ F:ARG105 4.9 59.1 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