Magnesium in PDB 6rke: Molybdenum Storage Protein - P212121, Adp, Molybdate

The structure of Molybdenum Storage Protein - P212121, Adp, Molybdate, PDB code: 6rke was solved by U.Ermler, S.Bruenle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.060, 148.860, 183.170, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.4

The structure of Molybdenum Storage Protein - P212121, Adp, Molybdate also contains other interesting chemical elements:

Molybdenum

(Mo)

144 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Molybdenum Storage Protein - P212121, Adp, Molybdate (pdb code 6rke). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Molybdenum Storage Protein - P212121, Adp, Molybdate, PDB code: 6rke:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:16.9 occ:1.00 O2A B:ADP301 2.0 20.0 1.0 O B:HOH405 2.1 24.9 0.6 O3B B:ADP301 2.1 18.0 1.0 O B:HOH421 2.1 16.1 1.0 O B:HOH429 2.2 16.9 1.0 O4 B:PO4305 2.2 27.1 0.4 O A:HOH426 2.2 20.6 1.0 PB B:ADP301 3.3 17.8 1.0 PA B:ADP301 3.3 18.8 1.0 P B:PO4305 3.5 15.1 0.4 O3A B:ADP301 3.6 20.8 1.0 O2B B:ADP301 3.6 21.1 1.0 O3 B:PO4305 3.8 16.6 0.4 NH2 B:ARG83 3.8 21.7 1.0 NZ B:LYS189 3.9 17.9 1.0 O5' B:ADP301 3.9 17.8 1.0 O4 B:MOO304 4.0 27.6 0.6 NZ B:LYS42 4.0 19.0 1.0 O1 B:PO4305 4.0 18.4 0.4 O B:HOH427 4.1 17.8 1.0 O1 B:MOO304 4.1 22.0 0.6 O B:HOH401 4.1 20.8 0.6 OD2 B:ASP170 4.1 18.4 1.0 NE2 A:GLN21 4.2 34.3 1.0 O A:THR19 4.4 20.5 1.0 OE1 B:GLU227 4.6 18.4 1.0 O1A B:ADP301 4.6 18.1 1.0 O1B B:ADP301 4.6 19.8 1.0 MO B:MOO304 4.6 23.4 0.6 O2 B:PO4305 4.6 16.5 0.4 CG B:ASP170 4.7 18.6 1.0 OD1 B:ASP170 4.7 18.0 1.0 OG1 B:THR169 4.8 15.7 1.0 NH1 B:ARG168 4.9 25.3 1.0

Magnesium binding site 2 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:15.2 occ:1.00 O2A A:ATP301 1.9 17.3 1.0 O1B A:ATP301 2.0 15.0 1.0 O A:PRO227 2.0 15.5 1.0 OE2 A:GLU190 2.0 17.6 1.0 O A:HOH408 2.1 15.3 1.0 O A:HOH407 2.1 15.0 1.0 CD A:GLU190 3.0 24.4 1.0 PA A:ATP301 3.2 17.5 1.0 C A:PRO227 3.2 16.4 1.0 PB A:ATP301 3.3 17.1 1.0 OE1 A:GLU190 3.3 23.5 1.0 O3A A:ATP301 3.6 19.5 1.0 OD2 A:ASP171 3.8 18.2 1.0 O A:HOH440 4.0 18.6 1.0 O3G A:ATP301 4.0 16.3 1.0 O A:HOH444 4.1 16.3 1.0 CA A:PRO227 4.1 17.5 1.0 NZ A:LYS45 4.1 15.6 1.0 N A:VAL228 4.2 15.9 1.0 O A:HOH431 4.2 17.5 1.0 O5' A:ATP301 4.2 19.2 1.0 C5' A:ATP301 4.3 17.0 1.0 O1A A:ATP301 4.3 19.9 1.0 O2B A:ATP301 4.3 18.0 1.0 OD1 A:ASP171 4.3 17.2 1.0 CA A:VAL228 4.3 15.4 1.0 O3B A:ATP301 4.4 18.2 1.0 CG A:GLU190 4.4 20.7 1.0 CB A:PRO227 4.4 18.6 1.0 CG A:ASP171 4.5 18.2 1.0 PG A:ATP301 4.8 16.6 1.0 O A:HOH416 4.9 16.6 1.0 CG1 A:VAL228 4.9 19.5 1.0

Magnesium binding site 3 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:21.7 occ:1.00 O2A D:ADP301 2.1 22.8 1.0 O1B D:ADP301 2.1 25.3 1.0 O C:HOH428 2.2 25.8 1.0 O D:HOH436 2.2 32.5 0.7 O D:HOH416 2.2 19.9 1.0 O1 D:PO4304 2.3 33.0 0.3 O D:HOH413 2.3 21.4 1.0 PB D:ADP301 3.3 24.8 1.0 PA D:ADP301 3.4 23.2 1.0 P D:PO4304 3.6 23.5 0.3 O3B D:ADP301 3.7 30.3 1.0 O3A D:ADP301 3.8 21.6 1.0 NH2 D:ARG83 3.8 25.7 1.0 NE2 C:GLN21 3.9 45.2 1.0 O2 D:MOO303 3.9 19.4 0.7 NZ D:LYS189 4.0 20.9 1.0 O5' D:ADP301 4.0 23.1 1.0 O4 D:PO4304 4.0 22.4 0.3 NZ D:LYS42 4.0 20.4 1.0 O D:HOH410 4.1 20.8 0.7 O D:HOH440 4.1 19.1 1.0 OD2 D:ASP170 4.2 23.9 1.0 O3 D:PO4304 4.2 24.0 0.3 O1 D:MOO303 4.3 24.3 0.7 O C:THR19 4.3 25.4 1.0 OE1 D:GLU227 4.5 18.9 1.0 O2B D:ADP301 4.6 28.1 1.0 MO D:MOO303 4.6 23.7 0.7 O1A D:ADP301 4.6 23.0 1.0 CG D:ASP170 4.7 19.1 1.0 O2 D:PO4304 4.7 21.9 0.3 OD1 D:ASP170 4.7 19.5 1.0 OG1 D:THR169 4.8 22.1 1.0 NH2 D:ARG168 4.8 24.3 1.0 O3 D:MOO303 4.8 22.3 0.7 CZ D:ARG83 5.0 30.7 1.0

Magnesium binding site 4 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:14.6 occ:1.00 O2A C:ATP302 1.9 15.4 1.0 O1B C:ATP302 1.9 18.8 1.0 OE2 C:GLU190 2.0 16.5 1.0 O C:PRO227 2.0 16.3 1.0 O C:HOH405 2.1 17.3 1.0 O C:HOH408 2.1 15.3 1.0 CD C:GLU190 3.0 19.1 1.0 PA C:ATP302 3.2 17.2 1.0 PB C:ATP302 3.2 17.3 1.0 C C:PRO227 3.2 16.9 1.0 OE1 C:GLU190 3.3 21.4 1.0 O3A C:ATP302 3.6 21.9 1.0 OD2 C:ASP171 3.9 17.6 1.0 O C:HOH439 4.0 18.9 1.0 O C:HOH463 4.0 17.0 1.0 O3G C:ATP302 4.1 15.5 1.0 CA C:PRO227 4.1 18.3 1.0 NZ C:LYS45 4.1 14.3 1.0 O C:HOH423 4.2 19.1 1.0 N C:VAL228 4.2 16.4 1.0 O2B C:ATP302 4.2 19.0 1.0 O5' C:ATP302 4.2 23.4 1.0 C5' C:ATP302 4.3 22.7 1.0 OD1 C:ASP171 4.3 16.5 1.0 O1A C:ATP302 4.3 24.9 1.0 CG C:GLU190 4.3 18.6 1.0 CA C:VAL228 4.4 17.7 1.0 O3B C:ATP302 4.4 17.5 1.0 CB C:PRO227 4.4 16.7 1.0 CG C:ASP171 4.5 15.0 1.0 PG C:ATP302 4.8 16.6 1.0 O C:HOH419 4.9 17.6 1.0 CG1 C:VAL228 5.0 18.7 1.0

Magnesium binding site 5 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg302 b:17.6 occ:1.00 O2A F:ADP301 2.0 21.4 1.0 O3B F:ADP301 2.1 20.3 1.0 O E:HOH414 2.2 20.6 1.0 O3 F:PO4305 2.2 16.1 0.4 O F:HOH413 2.2 19.3 1.0 O F:HOH410 2.2 18.9 1.0 PB F:ADP301 3.3 21.3 1.0 PA F:ADP301 3.3 21.2 1.0 P F:PO4305 3.5 20.2 0.4 O2B F:ADP301 3.7 25.0 1.0 O3A F:ADP301 3.7 20.1 1.0 O2 F:PO4305 3.8 18.8 0.4 NH2 F:ARG83 3.9 26.4 1.0 O5' F:ADP301 3.9 19.2 1.0 NZ F:LYS189 4.0 19.4 1.0 O F:HOH407 4.0 30.9 1.0 NZ F:LYS42 4.0 19.5 1.0 O F:HOH449 4.1 18.8 1.0 O3 F:MOO304 4.1 20.8 0.6 O1 F:PO4305 4.1 27.4 0.4 NE2 E:GLN21 4.2 30.4 1.0 OD2 F:ASP170 4.2 19.7 1.0 O E:THR19 4.3 21.4 1.0 O1 F:MOO304 4.4 19.9 0.6 OE1 F:GLU227 4.5 19.8 1.0 O4 F:PO4305 4.6 20.3 0.4 O1A F:ADP301 4.6 21.0 1.0 O1B F:ADP301 4.6 25.1 1.0 MO F:MOO304 4.7 20.7 0.6 CG F:ASP170 4.7 16.6 1.0 OD1 F:ASP170 4.7 17.0 1.0 OG1 F:THR169 4.8 21.3 1.0 NH2 F:ARG168 4.9 25.7 1.0 O4 F:MOO304 5.0 19.0 0.6

Magnesium binding site 6 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg302 b:19.5 occ:1.00 O2A E:ATP301 1.9 20.4 1.0 O1B E:ATP301 1.9 18.7 1.0 OE2 E:GLU190 2.0 21.7 1.0 O E:PRO227 2.1 20.6 1.0 O E:HOH409 2.1 20.1 1.0 O E:HOH410 2.1 19.0 1.0 CD E:GLU190 3.0 22.5 1.0 PA E:ATP301 3.2 18.0 1.0 PB E:ATP301 3.2 19.3 1.0 C E:PRO227 3.3 20.1 1.0 OE1 E:GLU190 3.3 25.2 1.0 O3A E:ATP301 3.6 22.1 1.0 OD2 E:ASP171 3.8 19.3 1.0 O F:HOH435 3.9 17.7 1.0 NZ E:LYS45 4.1 15.5 1.0 O E:HOH443 4.1 18.9 1.0 O3G E:ATP301 4.1 15.3 1.0 CA E:PRO227 4.1 19.6 1.0 O E:HOH447 4.2 25.5 1.0 N E:VAL228 4.2 20.6 1.0 O2B E:ATP301 4.3 20.0 1.0 O5' E:ATP301 4.3 24.8 1.0 O1A E:ATP301 4.3 25.4 1.0 OD1 E:ASP171 4.3 21.3 1.0 C5' E:ATP301 4.3 24.4 1.0 O3B E:ATP301 4.3 18.0 1.0 CG E:GLU190 4.4 23.2 1.0 CA E:VAL228 4.4 20.9 1.0 CB E:PRO227 4.5 19.0 1.0 CG E:ASP171 4.5 21.5 1.0 PG E:ATP301 4.8 20.3 1.0 CG1 E:VAL228 4.9 23.1 1.0 O2G E:ATP301 4.9 14.3 1.0 O E:HOH408 5.0 19.4 1.0

Magnesium binding site 7 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg302 b:24.1 occ:1.00 O2A H:ADP301 2.1 26.1 1.0 O G:HOH437 2.1 28.9 1.0 O H:HOH410 2.2 25.6 1.0 O4 H:PO4305 2.2 31.1 0.3 O H:HOH427 2.2 33.1 0.7 O H:HOH409 2.2 25.5 1.0 O3B H:ADP301 2.2 27.6 1.0 PB H:ADP301 3.3 29.8 1.0 P H:PO4305 3.4 26.7 0.3 PA H:ADP301 3.4 28.2 1.0 O2B H:ADP301 3.6 35.3 1.0 O1 H:PO4305 3.6 28.3 0.3 O3A H:ADP301 3.7 32.1 1.0 O2 H:MOO304 3.8 31.8 0.7 NZ H:LYS189 3.9 29.4 1.0 NH2 H:ARG83 3.9 29.8 1.0 O2 H:PO4305 4.0 26.3 0.3 O5' H:ADP301 4.0 29.3 1.0 NZ H:LYS42 4.0 29.3 1.0 O H:HOH403 4.0 27.6 0.7 O H:HOH429 4.0 29.4 1.0 NE2 G:GLN21 4.0 42.4 1.0 OD2 H:ASP170 4.1 25.5 1.0 O3 H:MOO304 4.2 27.2 0.7 O G:THR19 4.4 30.0 1.0 OE1 H:GLU227 4.5 24.7 1.0 O3 H:PO4305 4.6 27.4 0.3 MO H:MOO304 4.6 30.0 0.7 CG H:ASP170 4.6 23.5 1.0 O1A H:ADP301 4.6 26.6 1.0 O1B H:ADP301 4.7 35.5 1.0 OG1 H:THR169 4.7 28.1 1.0 OD1 H:ASP170 4.7 25.3 1.0 O4 H:MOO304 4.8 27.7 0.7 NH2 H:ARG168 5.0 32.6 1.0

Magnesium binding site 8 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:19.8 occ:1.00 O2A G:ATP301 1.9 21.6 1.0 O1B G:ATP301 1.9 25.0 1.0 O G:HOH414 2.0 17.6 1.0 OE2 G:GLU190 2.0 22.9 1.0 O G:PRO227 2.1 22.2 1.0 O G:HOH411 2.1 18.9 1.0 CD G:GLU190 3.0 23.1 1.0 PB G:ATP301 3.2 18.9 1.0 PA G:ATP301 3.2 22.9 1.0 OE1 G:GLU190 3.3 23.8 1.0 C G:PRO227 3.3 22.2 1.0 O3A G:ATP301 3.6 24.2 1.0 OD2 G:ASP171 3.9 22.6 1.0 O H:HOH428 4.0 19.5 1.0 O3G G:ATP301 4.0 20.3 1.0 O G:HOH444 4.0 21.2 1.0 NZ G:LYS45 4.1 18.1 1.0 CA G:PRO227 4.1 20.1 1.0 O2B G:ATP301 4.2 19.3 1.0 O G:HOH423 4.2 19.7 1.0 N G:VAL228 4.2 23.1 1.0 O5' G:ATP301 4.3 23.5 1.0 OD1 G:ASP171 4.3 20.8 1.0 C5' G:ATP301 4.3 24.8 1.0 O1A G:ATP301 4.3 27.3 1.0 CG G:GLU190 4.4 22.7 1.0 O3B G:ATP301 4.4 17.4 1.0 CA G:VAL228 4.4 20.9 1.0 CB G:PRO227 4.5 24.2 1.0 CG G:ASP171 4.5 17.6 1.0 PG G:ATP301 4.7 20.7 1.0 CG1 G:VAL228 4.9 25.2 1.0 O G:HOH420 4.9 20.9 1.0 O2G G:ATP301 5.0 20.2 1.0

Magnesium binding site 9 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg303 b:12.0 occ:0.50 O2A J:ADP301 2.0 26.6 1.0 O1B J:ADP301 2.1 23.0 1.0 O J:HOH426 2.1 31.1 1.0 O J:HOH423 2.2 21.9 1.0 O J:HOH408 2.2 24.9 1.0 O J:HOH427 2.3 26.6 1.0 PB J:ADP301 3.3 26.7 1.0 PA J:ADP301 3.3 26.0 1.0 O3A J:ADP301 3.8 25.7 1.0 O3B J:ADP301 3.8 33.6 1.0 NZ J:LYS189 3.9 22.6 1.0 O5' J:ADP301 3.9 27.3 1.0 O1 J:PO4305 4.0 29.1 0.5 NH2 J:ARG83 4.0 32.4 1.0 NZ J:LYS42 4.0 25.9 1.0 O4 J:MOO304 4.0 29.5 0.5 O J:HOH424 4.0 25.8 1.0 O J:HOH457 4.0 25.1 1.0 OD2 J:ASP170 4.1 25.4 1.0 O2 J:MOO304 4.2 25.5 0.5 O4 J:PO4305 4.2 30.8 0.5 NE2 I:GLN21 4.3 42.0 1.0 O I:THR19 4.4 29.3 1.0 OE1 J:GLU227 4.5 32.4 1.0 O2B J:ADP301 4.6 29.8 1.0 CG J:ASP170 4.6 20.3 1.0 P J:PO4305 4.6 26.6 0.5 O1A J:ADP301 4.6 23.1 1.0 MO J:MOO304 4.6 24.9 0.5 OD1 J:ASP170 4.7 22.3 1.0 OG1 J:THR169 4.7 24.1 1.0 NH2 J:ARG168 4.8 28.3 1.0 O3 J:PO4305 4.8 22.6 0.5 O3 J:MOO304 4.9 21.7 0.5

Magnesium binding site 10 out of 12 in the Molybdenum Storage Protein - P212121, Adp, Molybdate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Molybdenum Storage Protein - P212121, Adp, Molybdate within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg302 b:20.0 occ:1.00 O1B I:ATP301 1.9 22.9 1.0 O2A I:ATP301 1.9 23.4 1.0 OE2 I:GLU190 2.0 25.3 1.0 O I:PRO227 2.0 24.0 1.0 O I:HOH410 2.1 22.4 1.0 O I:HOH403 2.1 18.8 1.0 CD I:GLU190 3.0 26.9 1.0 PB I:ATP301 3.2 24.1 1.0 PA I:ATP301 3.2 25.1 1.0 C I:PRO227 3.2 20.6 1.0 OE1 I:GLU190 3.3 28.9 1.0 O3A I:ATP301 3.6 27.9 1.0 OD2 I:ASP171 3.8 25.2 1.0 O I:HOH440 3.9 19.1 1.0 NZ I:LYS45 4.0 22.2 1.0 CA I:PRO227 4.1 24.5 1.0 O3G I:ATP301 4.1 20.0 1.0 O J:HOH442 4.1 24.7 1.0 O2B I:ATP301 4.2 22.9 1.0 N I:VAL228 4.2 25.4 1.0 O I:HOH411 4.2 25.6 1.0 O5' I:ATP301 4.2 28.2 1.0 OD1 I:ASP171 4.3 20.9 1.0 O1A I:ATP301 4.3 33.0 1.0 C5' I:ATP301 4.3 26.3 1.0 CA I:VAL228 4.3 24.5 1.0 CG I:GLU190 4.3 26.2 1.0 O3B I:ATP301 4.4 24.0 1.0 CB I:PRO227 4.4 26.3 1.0 CG I:ASP171 4.5 25.1 1.0 PG I:ATP301 4.8 22.3 1.0 CG1 I:VAL228 4.8 20.0 1.0 O I:HOH406 5.0 22.8 1.0

S.Brunle, M.L.Eisinger, J.Poppe, D.J.Mills, J.D.Langer, J.Vonck, U.Ermler. Molybdate Pumping Into the Molybdenum Storage Protein Via An Atp-Powered Piercing Mechanism. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31811022
DOI: 10.1073/PNAS.1913031116