Magnesium in PDB 4dmz: Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form

The structure of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form, PDB code: 4dmz was solved by J.C.Whitney, K.M.Colvin, L.S.Marmont, H.Robinson, M.R.Parsek, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.73 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.511, 113.346, 61.846, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Magnesium atom in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form (pdb code 4dmz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form, PDB code: 4dmz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:69.4 occ:1.00 O A:GLN215 2.7 72.3 1.0 N A:ARG205 2.9 52.1 1.0 O A:GLU213 3.2 77.5 1.0 CB A:GLU213 3.3 69.5 1.0 CA A:TYR204 3.5 52.0 1.0 C A:TYR204 3.6 53.2 1.0 C A:GLN215 3.7 74.4 1.0 OE1 A:GLU213 3.7 89.1 1.0 CB A:TYR204 3.8 53.1 1.0 C A:GLU213 3.8 80.0 1.0 CA A:ARG205 3.8 56.8 1.0 CB A:ARG205 3.8 60.6 1.0 O A:ARG205 3.9 53.5 1.0 CA A:GLU213 4.0 70.1 1.0 CD2 A:LEU217 4.0 56.0 1.0 CG A:LEU217 4.0 61.0 1.0 CA A:PRO216 4.2 68.8 1.0 CD2 A:TYR204 4.2 65.3 1.0 N A:LEU217 4.2 52.7 1.0 N A:GLU213 4.2 68.6 1.0 C A:ARG205 4.3 55.8 1.0 N A:PRO216 4.3 73.7 1.0 CG A:GLU213 4.4 85.1 1.0 C A:PRO216 4.4 65.1 1.0 CG A:TYR204 4.5 60.6 1.0 CD A:GLU213 4.5 92.9 1.0 N A:GLN215 4.6 82.3 1.0 O A:LEU203 4.7 53.4 1.0 CD1 A:LEU217 4.7 64.9 1.0 CA A:GLN215 4.7 76.6 1.0 N A:PRO214 4.8 85.3 1.0 N A:TYR204 4.8 53.4 1.0 O A:TYR204 4.8 52.5 1.0 C A:PRO214 4.8 81.9 1.0

Magnesium binding site 2 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:67.4 occ:1.00 O A:HOH604 2.6 34.3 1.0 O A:LEU390 2.6 44.9 1.0 OE1 A:GLN158 2.8 73.1 1.0 CD A:GLN158 3.2 71.7 1.0 NE2 A:GLN158 3.4 78.5 1.0 CD A:ARG161 3.6 48.9 0.6 C A:LEU390 3.8 38.1 1.0 MG A:MG509 3.8 61.5 1.0 CA A:GLN158 3.8 42.5 1.0 MG A:MG512 3.9 68.0 1.0 CD A:ARG161 3.9 48.5 0.5 NE A:ARG161 3.9 51.5 0.6 O A:ASP157 3.9 46.3 1.0 CB A:LEU390 4.0 36.1 1.0 CB A:ARG161 4.0 41.9 0.5 CB A:ARG161 4.0 42.3 0.6 CB A:GLN158 4.1 44.9 1.0 CG A:GLN158 4.2 62.2 1.0 CG A:ARG161 4.3 50.2 0.6 CA A:LEU390 4.5 39.9 1.0 CG A:ARG161 4.6 48.2 0.5 N A:GLN158 4.6 38.4 1.0 C A:ASP157 4.6 38.5 1.0 C A:GLN158 4.7 41.5 1.0 N A:THR391 4.8 41.9 1.0 N A:ARG161 4.9 37.1 0.5 N A:ARG161 4.9 36.9 0.6 OG1 A:THR391 5.0 40.3 1.0 O A:GLN158 5.0 37.7 1.0

Magnesium binding site 3 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:47.6 occ:1.00 OH A:TYR399 2.7 42.9 1.0 OE1 A:GLN372 2.7 43.4 1.0 O A:LEU362 2.7 44.0 1.0 N A:GLN366 3.5 55.5 1.0 CE2 A:TYR399 3.5 43.6 1.0 CZ A:TYR399 3.5 46.5 1.0 C A:LEU362 3.7 37.9 1.0 CG2 A:VAL386 3.7 27.9 1.0 CG1 A:VAL386 3.7 27.8 1.0 CB A:SER365 3.8 48.7 1.0 O A:GLU363 3.8 49.5 1.0 CA A:GLN366 3.8 52.1 1.0 C A:SER365 3.8 53.7 1.0 CD A:GLN372 3.9 45.3 1.0 CA A:GLU363 3.9 38.3 1.0 C A:GLU363 4.1 53.0 1.0 CB A:GLN366 4.1 45.5 1.0 N A:SER365 4.1 43.9 1.0 CA A:SER365 4.1 50.5 1.0 N A:GLU363 4.2 34.4 1.0 CB A:VAL386 4.4 30.6 1.0 NE2 A:GLN372 4.4 37.2 1.0 O A:SER365 4.5 48.5 1.0 CD2 A:LEU384 4.5 28.4 1.0 OG A:SER365 4.6 57.1 1.0 CD2 A:TYR399 4.8 46.9 1.0 CE1 A:TYR399 4.9 46.9 1.0 CA A:LEU362 4.9 33.0 1.0 N A:GLY364 5.0 50.8 1.0

Magnesium binding site 4 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:84.1 occ:1.00 N A:ALA179 3.5 80.7 1.0 C A:GLU178 3.5 85.7 1.0 O A:GLY176 3.5 0.3 1.0 O A:GLU178 3.6 86.3 1.0 CA A:ALA179 3.7 72.7 1.0 O A:ASP177 3.8 0.5 1.0 C A:ASP177 3.9 0.2 1.0 N A:GLU178 4.0 0.8 1.0 CA A:GLU178 4.1 93.0 1.0 C A:GLY176 4.3 0.9 1.0 CB A:ALA179 4.4 77.2 1.0 CA A:ASP177 4.5 0.5 1.0 N A:ASP177 4.7 0.3 1.0

Magnesium binding site 5 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:90.6 occ:1.00 N A:THR219 2.8 54.9 1.0 OE2 A:GLU186 3.1 96.1 1.0 O A:THR219 3.2 53.5 1.0 OG1 A:THR219 3.3 56.6 1.0 CA A:THR219 3.6 57.6 1.0 CA A:ALA218 3.7 51.8 1.0 C A:ALA218 3.7 51.9 1.0 C A:THR219 3.8 58.0 1.0 OE1 A:GLU186 3.8 88.2 1.0 CD A:GLU186 3.9 86.6 1.0 CB A:THR219 4.0 52.6 1.0 CB A:ALA218 4.1 49.8 1.0 CG2 A:THR219 4.5 57.6 1.0 O A:HOH634 4.8 56.0 1.0 O A:ALA218 4.9 53.4 1.0 N A:ALA218 5.0 56.1 1.0

Magnesium binding site 6 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:40.3 occ:1.00 OH A:TYR427 2.9 44.1 1.0 ND2 A:ASN433 3.4 76.0 1.0 CE2 A:TYR427 3.6 33.4 1.0 CZ A:TYR427 3.7 39.9 1.0 O A:HOH641 3.7 40.8 1.0 CD2 A:LEU332 3.8 41.0 1.0 CB A:ASN433 3.8 72.0 1.0 CG A:ASN433 4.0 76.0 1.0 O A:ASP430 4.3 67.4 1.0 CB A:LEU438 4.4 34.8 1.0 CA A:LEU429 4.4 46.9 1.0 CG A:LEU429 4.4 39.9 1.0 N A:ASP430 4.6 44.6 1.0 CB A:LEU429 4.7 41.2 1.0 CD2 A:TYR427 4.9 40.6 1.0 O A:GLU428 5.0 41.2 1.0 CD2 A:LEU438 5.0 40.1 1.0

Magnesium binding site 7 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:81.0 occ:1.00 O A:SER365 2.5 48.5 1.0 NE A:ARG402 2.8 66.7 1.0 O A:TYR399 2.9 53.5 1.0 CB A:ARG402 2.9 61.6 1.0 CD A:ARG402 3.1 75.7 1.0 CD2 A:TYR399 3.2 46.9 1.0 CA A:TYR399 3.2 46.1 1.0 C A:TYR399 3.4 53.8 1.0 C A:SER365 3.5 53.7 1.0 CG A:ARG402 3.6 66.0 1.0 CB A:SER365 3.6 48.7 1.0 CG A:TYR399 3.7 49.4 1.0 CA A:SER365 3.8 50.5 1.0 CB A:TYR399 3.8 43.7 1.0 CE2 A:TYR399 3.9 43.6 1.0 CZ A:ARG402 4.0 64.8 1.0 CG A:ARG367 4.1 55.0 1.0 CA A:ARG402 4.2 61.1 1.0 N A:LEU403 4.3 50.6 1.0 O A:GLY398 4.3 58.6 1.0 NH2 A:ARG402 4.3 64.1 1.0 N A:TYR399 4.4 45.1 1.0 C A:ARG402 4.5 53.1 1.0 N A:ARG402 4.6 55.1 1.0 CD A:ARG367 4.6 48.9 1.0 OG A:SER365 4.7 57.1 1.0 CD1 A:TYR399 4.7 46.3 1.0 N A:GLN366 4.7 55.5 1.0 C A:GLY398 4.8 46.0 1.0 N A:LEU400 4.8 48.8 1.0 CZ A:TYR399 4.8 46.5 1.0

Magnesium binding site 8 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:85.0 occ:1.00 O A:GLN366 2.7 43.8 1.0 O A:GLY364 3.0 57.3 1.0 NH2 A:ARG402 3.7 64.1 1.0 C A:GLY364 3.8 48.3 1.0 C A:GLN366 3.8 47.9 1.0 N A:GLN366 3.9 55.5 1.0 CA A:GLN366 4.2 52.1 1.0 CB A:GLN366 4.3 45.5 1.0 CA A:GLY364 4.3 48.2 1.0 C A:SER365 4.4 53.7 1.0 N A:SER365 4.6 43.9 1.0 O A:GLU363 4.7 49.5 1.0 CA A:SER365 4.9 50.5 1.0 O A:SER365 4.9 48.5 1.0 N A:ARG367 4.9 45.5 1.0 CZ A:ARG402 5.0 64.8 1.0

Magnesium binding site 9 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:61.5 occ:1.00 OE1 A:GLN158 2.7 73.1 1.0 OG1 A:THR391 2.8 40.3 1.0 NH1 A:ARG367 2.9 47.4 1.0 NE A:ARG161 3.3 51.5 0.6 NH2 A:ARG367 3.5 41.8 1.0 CD A:GLN158 3.5 71.7 1.0 CZ A:ARG367 3.6 45.2 1.0 O A:LEU390 3.6 44.9 1.0 CD A:ARG161 3.7 48.9 0.6 CB A:THR391 3.7 42.3 1.0 NE2 A:GLN158 3.7 78.5 1.0 CD A:ARG161 3.7 48.5 0.5 CG2 A:THR391 3.7 37.7 1.0 MG A:MG502 3.8 67.4 1.0 CZ A:ARG161 3.8 41.0 0.6 NE A:ARG161 3.8 42.3 0.5 CA A:THR391 4.0 48.7 1.0 NH2 A:ARG161 4.1 41.1 0.6 O A:GLY395 4.4 67.5 1.0 C A:LEU390 4.5 38.1 1.0 CZ A:ARG161 4.5 55.9 0.5 NH1 A:ARG161 4.6 41.8 0.6 N A:THR391 4.7 41.9 1.0 O A:PRO389 4.7 31.7 1.0 NE A:ARG367 4.9 48.2 1.0 O A:HOH645 4.9 51.7 1.0 CG A:GLN158 4.9 62.2 1.0

Magnesium binding site 10 out of 20 in the Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Peld 156-455 From Pseudomonas Aeruginosa PA14, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:82.3 occ:1.00 OE2 A:GLU356 3.0 82.5 1.0 O A:HOH629 3.2 49.7 1.0 NH1 A:ARG360 3.3 64.1 1.0 CG A:GLU356 3.6 51.2 1.0 CD A:ARG360 3.7 58.8 1.0 CD A:GLU356 3.8 65.1 1.0 NH2 A:ARG374 3.8 47.2 1.0 CG A:ARG360 3.8 58.7 1.0 NH1 A:ARG374 3.9 39.1 1.0 CZ A:ARG374 4.3 43.3 1.0 CZ A:ARG360 4.3 64.2 1.0 NE A:ARG360 4.5 54.8 1.0 O A:GLU356 4.9 37.6 1.0 OE1 A:GLU356 5.0 55.8 1.0

J.C.Whitney, K.M.Colvin, L.S.Marmont, H.Robinson, M.R.Parsek, P.L.Howell. Structure of the Cytoplasmic Region of Peld, A Degenerate Diguanylate Cyclase Receptor That Regulates Exopolysaccharide Production in Pseudomonas Aeruginosa. J.Biol.Chem. V. 287 23582 2012.
ISSN: ISSN 0021-9258
PubMed: 22605337
DOI: 10.1074/JBC.M112.375378