Magnesium in PDB 9g8j: Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate

The structure of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate, PDB code: 9g8j was solved by K.Vidilaseris, J.Liu, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 3.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.185, 147.362, 252.335, 90, 90, 90
R / Rfree (%)	26.6 / 30.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate (pdb code 9g8j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate, PDB code: 9g8j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:92.3 occ:1.00 OD1 A:ASP465 2.5 110.0 1.0 OD2 A:ASP232 2.5 110.5 1.0 O11 A:ZOL801 2.5 112.8 1.0 O13 A:ZOL801 2.7 125.5 1.0 OD1 A:ASP232 2.8 111.1 1.0 OD2 A:ASP465 2.8 113.7 1.0 CG A:ASP232 2.9 110.0 1.0 CG A:ASP465 2.9 114.3 1.0 H13 A:ZOL801 3.0 146.3 1.0 O15 A:ZOL801 3.0 112.0 1.0 C8 A:ZOL801 3.2 119.0 1.0 P9 A:ZOL801 3.3 117.1 1.0 MG A:MG805 3.3 115.5 1.0 O A:HOH902 3.4 104.2 1.0 P14 A:ZOL801 3.5 117.3 1.0 O12 A:ZOL801 3.6 111.6 1.0 O17 A:ZOL801 3.7 123.1 1.0 OD1 A:ASP228 3.8 114.4 1.0 OD2 A:ASP228 4.1 117.7 1.0 OD2 A:ASP202 4.1 115.9 1.0 CG A:ASP228 4.2 114.3 1.0 CB A:ASP232 4.2 102.9 1.0 CB A:ASP465 4.2 119.0 1.0 O10 A:ZOL801 4.7 101.2 1.0 C7 A:ZOL801 4.7 119.4 1.0 O A:ASP228 4.8 104.8 1.0 CG A:ASP202 5.0 107.8 1.0 O16 A:ZOL801 5.0 110.3 1.0

Magnesium binding site 2 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:101.1 occ:1.00 OD1 A:ASP692 2.0 101.6 1.0 O10 A:ZOL801 2.4 101.2 1.0 O12 A:ZOL801 2.5 111.6 1.0 H71 A:ZOL801 2.8 138.9 1.0 P9 A:ZOL801 2.8 117.1 1.0 MG A:MG804 2.9 86.7 1.0 H72 A:ZOL801 3.0 138.9 1.0 CG A:ASP692 3.0 100.0 1.0 OD1 A:ASP688 3.1 114.5 1.0 C7 A:ZOL801 3.1 119.4 1.0 OD1 A:ASP202 3.2 106.0 1.0 C8 A:ZOL801 3.3 119.0 1.0 OD1 A:ASP660 3.4 107.9 1.0 NZ A:LYS695 3.4 101.3 1.0 CE A:LYS695 3.4 101.8 1.0 OD2 A:ASP692 3.4 102.3 1.0 OD2 A:ASP688 3.6 140.5 1.0 CG A:ASP688 3.7 117.0 1.0 O16 A:ZOL801 4.0 110.3 1.0 CG A:ASP660 4.2 114.7 1.0 P14 A:ZOL801 4.2 117.3 1.0 CG A:ASP202 4.2 107.8 1.0 O11 A:ZOL801 4.3 112.8 1.0 CB A:ASP692 4.4 93.0 1.0 N15 A:ZOL801 4.5 121.8 1.0 O15 A:ZOL801 4.5 112.0 1.0 O A:ASP688 4.5 109.7 1.0 O13 A:ZOL801 4.6 125.5 1.0 OD2 A:ASP202 4.6 115.9 1.0 NZ A:LYS199 4.7 123.1 1.0 CA A:ASP692 4.7 99.3 1.0 CB A:ASP660 4.8 113.0 1.0 OD2 A:ASP660 4.9 126.8 1.0 CD A:LYS695 4.9 105.1 1.0

Magnesium binding site 3 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:86.7 occ:1.00 O16 A:ZOL801 2.3 110.3 1.0 OD1 A:ASP202 2.7 106.0 1.0 OD2 A:ASP206 2.7 103.2 1.0 OD2 A:ASP688 2.9 140.5 1.0 MG A:MG803 2.9 101.1 1.0 P14 A:ZOL801 3.1 117.3 1.0 O15 A:ZOL801 3.2 112.0 1.0 CG A:ASP206 3.3 104.2 1.0 H71 A:ZOL801 3.4 138.9 1.0 CG A:ASP202 3.5 107.8 1.0 O12 A:ZOL801 3.5 111.6 1.0 OD2 A:ASP202 3.5 115.9 1.0 OD2 A:ASP692 3.7 102.3 1.0 OD1 A:ASP206 3.7 111.1 1.0 CG A:ASP688 3.8 117.0 1.0 C8 A:ZOL801 3.8 119.0 1.0 OD1 A:ASP692 4.0 101.6 1.0 C7 A:ZOL801 4.0 119.4 1.0 OD1 A:ASP688 4.1 114.5 1.0 CG A:ASP692 4.3 100.0 1.0 P9 A:ZOL801 4.3 117.1 1.0 CB A:ASP206 4.3 98.5 1.0 O17 A:ZOL801 4.5 123.1 1.0 H72 A:ZOL801 4.6 138.9 1.0 OD1 A:ASP660 4.6 107.9 1.0 O10 A:ZOL801 4.8 101.2 1.0 H19 A:ZOL801 4.8 150.1 1.0 CB A:ASP202 4.9 102.5 1.0

Magnesium binding site 4 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:115.5 occ:1.00 O A:HOH902 1.9 104.2 1.0 OD2 A:ASP218 2.6 123.6 1.0 OD1 A:ASP218 2.8 138.7 1.0 O15 A:ZOL801 2.9 112.0 1.0 OD2 A:ASP228 2.9 117.7 1.0 O17 A:ZOL801 3.0 123.1 1.0 CG A:ASP218 3.1 127.5 1.0 MG A:MG802 3.3 92.3 1.0 OD1 A:ASP465 3.5 110.0 1.0 P14 A:ZOL801 3.6 117.3 1.0 CG A:ASP228 3.6 114.3 1.0 OD1 A:ASN229 3.9 109.5 1.0 OD2 A:ASP232 4.1 110.5 1.0 CG A:ASP465 4.2 114.3 1.0 OD2 A:ASP465 4.2 113.7 1.0 OD1 A:ASP228 4.2 114.4 1.0 H13 A:ZOL801 4.3 146.3 1.0 OE2 A:GLU217 4.4 108.6 1.0 CB A:ASP228 4.4 104.8 1.0 OD2 A:ASP202 4.5 115.9 1.0 CB A:ASP218 4.6 121.2 1.0 O13 A:ZOL801 4.6 125.5 1.0 O16 A:ZOL801 4.7 110.3 1.0 C8 A:ZOL801 4.8 119.0 1.0 O A:ASP465 4.9 121.6 1.0

Magnesium binding site 5 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:110.2 occ:1.00 O15 B:ZOL801 2.4 130.1 1.0 MG B:MG804 2.7 98.7 1.0 OD2 B:ASP465 2.7 129.4 1.0 OD1 B:ASP465 3.0 142.2 1.0 H13 B:ZOL801 3.0 139.5 1.0 CG B:ASP465 3.2 136.8 1.0 OD2 B:ASP228 3.2 128.9 1.0 P14 B:ZOL801 3.4 137.4 1.0 OD2 B:ASP232 3.5 126.5 1.0 O16 B:ZOL801 3.6 118.1 1.0 O13 B:ZOL801 3.6 118.0 1.0 CG B:ASP228 3.7 122.1 1.0 OD1 B:ASP228 3.8 123.5 1.0 OD2 B:ASP218 4.0 140.5 1.0 C8 B:ZOL801 4.1 115.6 1.0 OD1 B:ASP218 4.2 143.7 1.0 CG B:ASP232 4.4 129.3 1.0 O10 B:ZOL801 4.5 115.5 1.0 OD1 B:ASN229 4.5 109.1 1.0 CG B:ASP218 4.5 140.7 1.0 CB B:ASP465 4.5 125.3 1.0 OD1 B:ASP232 4.6 134.5 1.0 O B:ASP465 4.6 114.6 1.0 OE2 B:GLU217 4.6 121.0 1.0 CB B:ASP228 4.7 116.9 1.0 O17 B:ZOL801 4.7 129.8 1.0 OD2 B:ASP202 4.8 116.7 1.0 P9 B:ZOL801 5.0 108.6 1.0 O B:HOH906 5.0 127.0 1.0 H19 B:ZOL801 5.0 157.5 1.0

Magnesium binding site 6 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:111.7 occ:1.00 OD2 B:ASP202 2.2 116.7 1.0 O12 B:ZOL801 2.2 110.3 1.0 MG B:MG805 2.5 122.8 1.0 O10 B:ZOL801 2.7 115.5 1.0 OD1 B:ASP692 2.7 128.8 1.0 P9 B:ZOL801 2.9 108.6 1.0 CG B:ASP692 3.0 123.4 1.0 NZ B:LYS199 3.0 131.2 1.0 CG B:ASP202 3.1 121.4 1.0 OD2 B:ASP692 3.2 124.3 1.0 O16 B:ZOL801 3.7 118.1 1.0 CB B:ASP692 3.8 108.8 1.0 OD1 B:ASP202 3.9 124.8 1.0 CB B:ASP202 3.9 118.5 1.0 C8 B:ZOL801 4.0 115.6 1.0 CE B:LYS199 4.2 114.8 1.0 O11 B:ZOL801 4.2 113.9 1.0 CD B:LYS199 4.3 101.0 1.0 CE B:LYS695 4.4 107.0 1.0 CA B:ASP692 4.5 102.1 1.0 P14 B:ZOL801 4.5 137.4 1.0 H71 B:ZOL801 4.5 140.4 1.0 NZ B:LYS695 4.7 109.5 1.0 C7 B:ZOL801 4.7 118.8 1.0 H72 B:ZOL801 4.7 140.4 1.0 OD1 B:ASP688 4.8 113.4 1.0 OD2 B:ASP688 4.8 116.3 1.0

Magnesium binding site 7 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:98.7 occ:1.00 OD2 B:ASP465 2.0 129.4 1.0 OD2 B:ASP232 2.5 126.5 1.0 OD1 B:ASP232 2.6 134.5 1.0 CG B:ASP232 2.7 129.3 1.0 MG B:MG802 2.7 110.2 1.0 O10 B:ZOL801 2.8 115.5 1.0 CG B:ASP465 3.2 136.8 1.0 O13 B:ZOL801 3.4 118.0 1.0 H13 B:ZOL801 3.5 139.5 1.0 P9 B:ZOL801 3.6 108.6 1.0 OD1 B:ASP228 3.7 123.5 1.0 C8 B:ZOL801 3.9 115.6 1.0 CB B:ASP232 3.9 115.6 1.0 O11 B:ZOL801 3.9 113.9 1.0 OD1 B:ASP465 3.9 142.2 1.0 OD2 B:ASP202 4.2 116.7 1.0 O15 B:ZOL801 4.2 130.1 1.0 CB B:ASP465 4.2 125.3 1.0 O16 B:ZOL801 4.2 118.1 1.0 P14 B:ZOL801 4.3 137.4 1.0 O B:HOH901 4.4 119.7 1.0 CG B:ASP228 4.4 122.1 1.0 OD2 B:ASP228 4.5 128.9 1.0 O B:ASP228 4.7 122.4 1.0 CA B:ASP232 4.9 111.5 1.0 CG B:ASP202 5.0 121.4 1.0

Magnesium binding site 8 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg805 b:122.8 occ:1.00 O16 B:ZOL801 2.4 118.1 1.0 MG B:MG803 2.5 111.7 1.0 OD2 B:ASP202 2.8 116.7 1.0 OD1 B:ASP202 3.0 124.8 1.0 O17 B:ZOL801 3.1 129.8 1.0 P14 B:ZOL801 3.1 137.4 1.0 OD2 B:ASP688 3.2 116.3 1.0 CG B:ASP202 3.2 121.4 1.0 OD2 B:ASP692 3.3 124.3 1.0 O12 B:ZOL801 3.3 110.3 1.0 OD2 B:ASP206 3.4 126.3 1.0 H71 B:ZOL801 3.5 140.4 1.0 OD1 B:ASP692 3.5 128.8 1.0 C8 B:ZOL801 3.7 115.6 1.0 CG B:ASP692 3.7 123.4 1.0 O B:HOH906 3.8 127.0 1.0 P9 B:ZOL801 3.9 108.6 1.0 O10 B:ZOL801 3.9 115.5 1.0 C7 B:ZOL801 4.0 118.8 1.0 CG B:ASP688 4.0 113.4 1.0 CG B:ASP206 4.2 121.8 1.0 OD1 B:ASP688 4.2 113.4 1.0 OD1 B:ASP660 4.3 116.2 1.0 H72 B:ZOL801 4.5 140.4 1.0 CB B:ASP202 4.5 118.5 1.0 OD1 B:ASP206 4.6 118.2 1.0 O15 B:ZOL801 4.6 130.1 1.0

Magnesium binding site 9 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:104.5 occ:1.00 O10 C:ZOL801 2.4 107.2 1.0 OD2 C:ASP202 2.5 120.4 1.0 O11 C:ZOL801 2.6 120.8 1.0 P9 C:ZOL801 2.8 123.0 1.0 OD2 C:ASP692 2.8 102.5 1.0 OD1 C:ASP692 2.9 114.4 1.0 MG C:MG803 2.9 116.9 1.0 CG C:ASP692 3.1 102.3 1.0 O15 C:ZOL801 3.2 135.3 1.0 CG C:ASP202 3.3 116.8 1.0 OD1 C:ASP202 3.4 115.3 1.0 C8 C:ZOL801 3.5 136.6 1.0 O16 C:ZOL801 3.5 135.2 1.0 P14 C:ZOL801 3.5 153.9 1.0 H71 C:ZOL801 4.0 179.2 1.0 OD2 C:ASP688 4.1 126.8 1.0 O12 C:ZOL801 4.3 130.1 1.0 C7 C:ZOL801 4.3 146.3 1.0 NZ C:LYS199 4.3 135.2 1.0 CB C:ASP692 4.4 93.1 1.0 CE C:LYS695 4.6 115.7 1.0 OD1 C:ASP688 4.7 99.0 1.0 O13 C:ZOL801 4.7 129.4 1.0 CG C:ASP688 4.7 108.7 1.0 H72 C:ZOL801 4.7 179.2 1.0 CB C:ASP202 4.8 110.8 1.0 NZ C:LYS695 4.8 108.4 1.0 H13 C:ZOL801 4.8 158.9 1.0 OD2 C:ASP206 4.9 115.9 1.0

Magnesium binding site 10 out of 16 in the Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of K+-Dependent Na+-Ppase From Thermotoga Maritima in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg803 b:116.9 occ:1.00 OD2 C:ASP206 2.4 115.9 1.0 O15 C:ZOL801 2.5 135.3 1.0 CG C:ASP206 2.8 112.0 1.0 OD1 C:ASP206 2.9 126.6 1.0 O16 C:ZOL801 2.9 135.2 1.0 MG C:MG802 2.9 104.5 1.0 OD1 C:ASP202 3.1 115.3 1.0 P14 C:ZOL801 3.2 153.9 1.0 OE2 C:GLU217 3.3 136.6 1.0 OD2 C:ASP202 3.4 120.4 1.0 CG C:ASP202 3.5 116.8 1.0 CB C:ASP206 3.8 99.8 1.0 OD2 C:ASP692 4.1 102.5 1.0 O17 C:ZOL801 4.3 139.1 1.0 OD2 C:ASP688 4.4 126.8 1.0 CD C:GLU217 4.5 126.7 1.0 C8 C:ZOL801 4.6 136.6 1.0 OD2 C:ASP228 4.6 129.5 1.0 NZ C:LYS210 4.6 142.1 1.0 O11 C:ZOL801 4.6 120.8 1.0 O C:ASP202 4.7 117.3 1.0 CB C:ASP202 4.9 110.8 1.0 P9 C:ZOL801 5.0 123.0 1.0

J.Liu, A.Shah, Y.Ma, K.Hardman, N.G.Johansson, O.Ribeiro, A.Brookfield, A.Bowen, J.Yli-Kauhaluoma, H.Xhaard, L.J.Jeuken, A.Goldman, C.Pliotas, K.Vidilaseris. Conformational Dynamics and Asymmetry in Multimodal Inhibition of Membrane-Bound Pyrophosphatases Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.102288.1