Magnesium in PDB 5hci: Gpn-Loop Gtpase NPA3 in Complex with Gdp

The structure of Gpn-Loop Gtpase NPA3 in Complex with Gdp, PDB code: 5hci was solved by J.Niesser, F.R.Wagner, D.Kostrewa, W.Muehlbacher, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.25 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.990, 119.180, 347.670, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 27.6

The binding sites of Magnesium atom in the Gpn-Loop Gtpase NPA3 in Complex with Gdp (pdb code 5hci). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Gpn-Loop Gtpase NPA3 in Complex with Gdp, PDB code: 5hci:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Gpn-Loop Gtpase NPA3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gpn-Loop Gtpase NPA3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:55.6 occ:1.00 O A:HOH403 1.9 53.3 1.0 O A:HOH402 2.2 44.0 1.0 O A:HOH419 2.2 42.6 1.0 O3B A:GDP301 2.3 65.5 1.0 OG1 A:THR17 2.3 48.3 1.0 O A:HOH410 2.3 44.1 1.0 CB A:THR17 3.1 55.9 1.0 PB A:GDP301 3.3 63.6 1.0 O1A A:GDP301 3.3 58.3 1.0 O2B A:GDP301 3.4 59.2 1.0 PA A:GDP301 4.0 63.4 1.0 O3A A:GDP301 4.0 58.3 1.0 CG2 A:THR17 4.1 45.4 1.0 N A:THR17 4.1 54.3 1.0 O A:HOH408 4.2 44.3 1.0 CA A:THR17 4.3 54.0 1.0 O2A A:GDP301 4.3 66.5 1.0 OD2 A:ASP40 4.4 66.0 1.0 O A:HOH413 4.5 45.3 1.0 O1B A:GDP301 4.6 63.0 1.0 OD2 A:ASP106 4.7 47.9 1.0 CG2 A:VAL43 4.8 46.1 1.0

Magnesium binding site 2 out of 6 in the Gpn-Loop Gtpase NPA3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gpn-Loop Gtpase NPA3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:52.0 occ:1.00 O B:HOH403 2.0 44.0 1.0 OG1 B:THR17 2.1 59.9 1.0 O B:HOH405 2.2 48.8 1.0 O1B B:GDP301 2.2 52.0 1.0 O B:HOH411 2.2 43.5 1.0 O B:HOH409 2.4 40.9 1.0 CB B:THR17 3.3 46.2 1.0 PB B:GDP301 3.4 58.9 1.0 O3B B:GDP301 3.5 65.4 1.0 N B:THR17 3.7 50.2 1.0 OD1 B:ASP106 3.8 53.7 1.0 OD2 B:ASP106 4.0 53.1 1.0 CA B:THR17 4.0 60.0 1.0 O B:THR107 4.1 43.7 1.0 O B:HOH407 4.2 58.5 1.0 CB B:LYS16 4.3 48.6 1.0 O2B B:GDP301 4.3 65.2 1.0 OD2 B:ASP40 4.3 48.2 1.0 CG B:ASP106 4.3 61.5 1.0 CE B:LYS16 4.3 43.9 1.0 CG2 B:THR17 4.4 39.0 1.0 C B:LYS16 4.6 56.2 1.0 O2A B:GDP301 4.6 52.2 1.0 NZ B:LYS16 4.6 54.4 1.0 O3A B:GDP301 4.7 52.4 1.0 O1A B:GDP301 4.7 51.5 1.0 PA B:GDP301 4.9 56.5 1.0 CA B:LYS16 4.9 52.7 1.0 CA B:GLY109 4.9 40.5 1.0

Magnesium binding site 3 out of 6 in the Gpn-Loop Gtpase NPA3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gpn-Loop Gtpase NPA3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:63.9 occ:1.00 O C:HOH404 2.4 65.3 1.0 OG1 C:THR17 2.5 44.8 1.0 O C:HOH405 2.5 52.3 1.0 O C:HOH410 2.7 47.6 1.0 O C:HOH401 2.8 50.3 1.0 OD2 C:ASP40 2.9 56.3 1.0 O1B C:GDP301 3.5 45.1 1.0 CB C:THR17 3.8 58.6 1.0 CG C:ASP40 4.0 64.6 1.0 CG2 C:VAL43 4.0 56.9 1.0 CB C:ASP40 4.2 45.6 1.0 CB C:VAL43 4.2 60.4 1.0 OD2 C:ASP106 4.2 52.0 1.0 CG2 C:THR17 4.3 44.7 1.0 O C:THR107 4.4 54.2 1.0 OD1 C:ASP106 4.6 42.0 1.0 CG C:ASP106 4.7 59.4 1.0 PB C:GDP301 4.8 66.7 1.0 CA C:THR17 5.0 58.4 1.0

Magnesium binding site 4 out of 6 in the Gpn-Loop Gtpase NPA3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gpn-Loop Gtpase NPA3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:66.0 occ:1.00 O D:HOH408 2.0 52.7 1.0 OG1 D:THR17 2.1 63.9 1.0 O1B D:GDP301 2.2 55.3 1.0 O D:HOH406 2.2 55.8 1.0 O D:HOH402 2.5 61.1 1.0 CB D:THR17 3.2 69.6 1.0 PB D:GDP301 3.3 67.9 1.0 O2B D:GDP301 3.4 60.7 1.0 O2A D:GDP301 3.7 58.4 1.0 N D:THR17 3.9 76.8 1.0 CA D:THR17 4.1 63.5 1.0 OD2 D:ASP40 4.2 80.6 1.0 CG2 D:THR17 4.3 74.8 1.0 O3A D:GDP301 4.3 0.0 1.0 OD2 D:ASP106 4.3 83.3 1.0 O3B D:GDP301 4.3 92.5 1.0 PA D:GDP301 4.4 76.1 1.0 OD1 D:ASP106 4.5 69.5 1.0 O1A D:GDP301 4.5 72.4 1.0 O D:THR107 4.8 72.1 1.0 CB D:LYS16 4.8 70.1 1.0 CG D:ASP106 4.8 69.8 1.0 CE D:LYS16 4.9 78.2 1.0 C D:LYS16 5.0 76.2 1.0

Magnesium binding site 5 out of 6 in the Gpn-Loop Gtpase NPA3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Gpn-Loop Gtpase NPA3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:61.6 occ:1.00 O E:HOH414 1.9 57.3 1.0 OG1 E:THR17 2.2 65.1 1.0 O2B E:GDP301 2.2 57.7 1.0 O E:HOH408 2.2 44.3 1.0 O E:HOH404 2.3 66.4 1.0 O E:HOH402 2.6 62.1 1.0 PB E:GDP301 3.2 61.5 1.0 O3B E:GDP301 3.3 56.4 1.0 CB E:THR17 3.3 62.3 1.0 O1A E:GDP301 4.0 83.0 1.0 N E:THR17 4.0 57.1 1.0 OD2 E:ASP40 4.1 61.6 1.0 O1B E:GDP301 4.1 56.5 1.0 CA E:THR17 4.2 56.4 1.0 O3A E:GDP301 4.3 0.0 1.0 CG2 E:THR17 4.3 45.5 1.0 OD2 E:ASP106 4.4 73.5 1.0 PA E:GDP301 4.4 56.8 1.0 OD1 E:ASP106 4.5 70.3 1.0 O2A E:GDP301 4.6 61.7 1.0 O E:THR107 4.8 66.9 1.0 CB E:LYS16 4.8 49.9 1.0 CG E:ASP106 4.9 72.4 1.0 CE E:LYS16 4.9 69.4 1.0

Magnesium binding site 6 out of 6 in the Gpn-Loop Gtpase NPA3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Gpn-Loop Gtpase NPA3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg302 b:85.8 occ:1.00 OG1 F:THR17 1.9 0.8 1.0 O F:HOH405 1.9 77.7 1.0 O1B F:GDP301 2.4 84.7 1.0 O F:HOH402 2.8 92.4 1.0 CB F:THR17 3.1 0.7 1.0 O F:HOH401 3.1 87.3 1.0 O2A F:GDP301 3.7 0.3 1.0 PB F:GDP301 3.7 93.2 1.0 OD2 F:ASP40 3.8 94.1 1.0 CG2 F:THR17 3.8 0.3 1.0 O3B F:GDP301 3.9 99.8 1.0 OD2 F:ASP106 4.1 0.6 1.0 CA F:THR17 4.2 0.7 1.0 N F:THR17 4.3 0.4 1.0 CG2 F:VAL43 4.4 91.1 1.0 OD1 F:ASP106 4.6 0.6 1.0 PA F:GDP301 4.6 93.6 1.0 O3A F:GDP301 4.7 71.3 1.0 CG F:ASP106 4.7 0.4 1.0 O2B F:GDP301 4.8 96.3 1.0 CG F:ASP40 4.9 94.0 1.0 O F:THR107 4.9 93.8 1.0 CB F:VAL43 5.0 0.1 1.0

J.Niesser, F.R.Wagner, D.Kostrewa, W.Muhlbacher, P.Cramer. Structure of Gpn-Loop Gtpase NPA3 and Implications For Rna Polymerase II Assembly. Mol.Cell.Biol. V. 36 820 2015.
ISSN: ESSN 1098-5549
PubMed: 26711263
DOI: 10.1128/MCB.01009-15