Magnesium in PDB 3t7d: Vall From Streptomyces Hygroscopicus in Complex with Trehalose

The structure of Vall From Streptomyces Hygroscopicus in Complex with Trehalose, PDB code: 3t7d was solved by H.Zhang, L.Zheng, H.Qian, J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.78 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.661, 45.820, 115.030, 90.00, 107.36, 90.00
R / Rfree (%)	16.2 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose (pdb code 3t7d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose, PDB code: 3t7d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg499 b:29.2 occ:1.00 OG1 A:THR100 3.1 29.2 1.0 O A:HOH745 3.2 41.7 1.0 NE2 A:GLN160 3.3 21.8 1.0 NH2 A:ARG326 3.3 30.0 1.0 CE A:LYS11 3.7 31.3 1.0 CD A:LYS11 3.8 25.9 1.0 CB A:THR100 3.9 26.9 1.0 OH A:TYR159 4.1 18.1 1.0 O A:HOH711 4.2 28.5 1.0 CG A:GLN160 4.2 19.1 1.0 CD A:GLN160 4.2 19.1 1.0 CG A:GLN96 4.3 37.3 1.0 CZ A:ARG326 4.3 35.1 1.0 NE A:ARG326 4.5 29.6 1.0 C A:THR100 4.6 27.9 1.0 N A:ALA101 4.6 28.6 1.0 O A:THR100 4.8 26.8 1.0 CA A:THR100 4.9 24.6 1.0 NE2 A:GLN96 4.9 43.4 1.0 CG A:LYS11 4.9 26.2 1.0 CA A:ALA101 4.9 28.7 1.0 CZ A:TYR159 5.0 17.7 1.0 CG2 A:THR100 5.0 23.8 1.0

Magnesium binding site 2 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:47.8 occ:1.00 OG A:SER260 2.7 33.6 1.0 OE2 A:GLU461 2.7 55.0 1.0 NH1 A:ARG78 3.2 38.7 1.0 N A:LEU262 3.4 30.9 1.0 CD A:GLU461 3.4 44.2 1.0 CB A:SER260 3.5 34.1 1.0 CD A:PRO261 3.5 29.9 1.0 OE1 A:GLU461 3.5 37.5 1.0 N A:PRO261 3.5 28.4 1.0 C A:SER260 3.6 30.3 1.0 CA A:SER260 3.6 28.8 1.0 CB A:LEU262 3.6 34.0 1.0 NH2 A:ARG78 3.8 39.6 1.0 CG A:LEU262 3.8 34.9 1.0 CG A:PRO261 3.9 39.7 1.0 CZ A:ARG78 4.0 42.2 1.0 CA A:LEU262 4.1 35.5 1.0 O A:SER260 4.3 31.1 1.0 C A:PRO261 4.4 34.0 1.0 CA A:PRO261 4.4 32.4 1.0 CD1 A:LEU262 4.4 32.8 1.0 CG A:GLU41 4.6 29.8 1.0 CB A:LEU460 4.6 26.5 1.0 CB A:PRO261 4.7 38.3 1.0 CG A:GLU461 4.8 37.1 1.0 CD2 A:LEU460 5.0 32.5 1.0 C A:LEU262 5.0 40.0 1.0 N A:THR263 5.0 40.4 1.0

Magnesium binding site 3 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:48.3 occ:1.00 NH1 A:ARG249 2.2 51.8 1.0 O A:HOH629 2.5 28.4 1.0 O A:ASP474 2.8 26.8 1.0 CZ A:ARG249 3.4 52.3 1.0 C A:ASP474 3.5 24.4 1.0 O A:ALA477 3.5 55.0 1.0 CB A:ASP474 3.6 26.8 1.0 CA A:ASP474 3.6 25.1 1.0 CD A:ARG249 3.6 45.6 1.0 NE A:ARG249 3.9 48.2 1.0 CB A:ALA477 4.1 34.7 1.0 C A:ALA477 4.3 48.3 1.0 O A:ARG249 4.4 27.8 1.0 CG A:ASP474 4.4 29.7 1.0 NH2 A:ARG249 4.4 38.1 1.0 O A:THR210 4.4 19.7 1.0 CB A:ARG251 4.5 23.1 1.0 CG A:ARG249 4.5 40.1 1.0 OD1 A:ASP474 4.5 26.9 1.0 N A:HIS475 4.7 24.3 1.0 CA A:ALA477 4.7 40.4 1.0 CG2 A:THR210 4.8 19.4 1.0 N A:ARG251 4.8 17.5 1.0 C A:ARG249 5.0 30.9 1.0

Magnesium binding site 4 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.4 occ:1.00 O A:HOH813 3.1 36.1 1.0 NE1 A:TRP245 3.3 30.2 1.0 OD2 A:ASP233 3.4 44.6 1.0 CB A:ASP233 3.5 35.6 1.0 N A:ASP233 3.5 33.5 1.0 CG A:ASP233 3.6 43.2 1.0 CD A:PRO232 3.6 33.1 1.0 NH2 A:ARG246 3.7 44.7 1.0 N A:PRO232 3.8 30.0 1.0 CA A:LEU231 3.8 21.3 1.0 C A:LEU231 3.9 24.6 1.0 CB A:LEU231 3.9 20.8 1.0 CA A:ASP233 4.1 33.2 1.0 CD1 A:TRP245 4.1 28.2 1.0 CD2 A:LEU231 4.1 24.0 1.0 CG A:PRO232 4.2 39.3 1.0 NE A:ARG246 4.3 48.5 1.0 O A:HOH789 4.3 42.4 1.0 CZ A:ARG246 4.3 45.6 1.0 CE2 A:TRP245 4.3 28.5 1.0 OD1 A:ASP233 4.4 40.3 1.0 CG A:LEU231 4.5 20.4 1.0 C A:PRO232 4.6 34.1 1.0 O A:LEU231 4.6 25.6 1.0 CA A:PRO232 4.7 34.0 1.0 CZ2 A:TRP245 4.7 25.9 1.0 NE2 A:HIS204 4.8 23.8 1.0 N A:ALA234 5.0 29.2 1.0 C A:ASP233 5.0 40.4 1.0

Magnesium binding site 5 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:33.9 occ:1.00 N A:ARG267 3.2 33.4 1.0 NH1 A:ARG267 3.2 40.6 1.0 CB A:ARG267 3.6 33.6 1.0 CG A:ARG267 3.7 35.0 1.0 CA A:GLY266 3.9 36.0 1.0 CA A:ARG267 4.0 32.1 1.0 CD A:ARG267 4.0 34.5 1.0 C A:GLY266 4.0 36.5 1.0 CZ A:ARG267 4.3 41.8 1.0 NE A:ARG267 4.6 34.2 1.0

Magnesium binding site 6 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:39.5 occ:1.00 O A:HOH717 2.6 31.2 1.0 N A:GLU197 2.9 17.6 1.0 CB A:GLU197 3.3 24.6 1.0 CZ A:ARG125 3.4 35.3 1.0 NH2 A:ARG125 3.4 32.1 1.0 CG A:GLU197 3.5 44.4 1.0 N A:LYS196 3.6 15.0 1.0 CA A:GLU197 3.6 21.4 1.0 NH1 A:ARG125 3.8 45.3 1.0 NE A:ARG125 3.9 36.6 1.0 C A:LYS196 3.9 17.0 1.0 CB A:LYS196 4.0 18.2 1.0 CA A:LYS196 4.0 15.2 1.0 O B:HOH519 4.0 23.6 1.0 OE1 A:GLU197 4.1 44.6 1.0 CD A:GLU197 4.1 45.0 1.0 C A:PRO195 4.2 15.5 1.0 CB A:PRO195 4.2 13.6 1.0 OD2 B:ASP425 4.5 20.4 1.0 O B:HOH650 4.5 41.5 1.0 CD A:ARG125 4.6 38.3 1.0 CA A:PRO195 4.7 14.1 1.0 O A:PRO195 4.8 15.4 1.0 C A:GLU197 4.8 20.5 1.0 N A:ILE198 4.9 17.9 1.0

Magnesium binding site 7 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:37.1 occ:1.00 OG A:SER119 2.9 19.2 1.0 O B:HOH747 3.1 57.1 1.0 O A:HOH542 3.5 35.7 1.0 CB A:SER119 3.5 18.0 1.0 CG B:ARG299 3.9 12.2 1.0 CG B:ARG302 3.9 27.5 1.0 O A:HOH716 3.9 37.1 1.0 CD1 B:LEU426 4.2 21.5 1.0 OE2 B:GLU298 4.4 38.3 1.0 CB B:ARG302 4.4 19.8 1.0 CA B:ARG299 4.4 14.8 1.0 CD2 B:LEU426 4.5 20.7 1.0 CD B:GLU298 4.6 35.0 1.0 CD B:ARG302 4.7 37.2 1.0 NE B:ARG302 4.7 47.2 1.0 CB B:ARG299 4.7 14.3 1.0 CD B:ARG299 4.7 12.4 1.0 NE B:ARG299 4.7 13.5 1.0 N B:ARG299 4.8 16.4 1.0 CG B:GLU298 4.8 24.9 1.0 CG B:LEU426 4.8 18.2 1.0

Magnesium binding site 8 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:51.3 occ:1.00 OD1 A:ASP55 2.1 60.1 1.0 OD2 A:ASP59 2.5 49.1 1.0 OD1 A:ASP59 2.6 49.5 1.0 CG A:ASP59 2.9 44.9 1.0 CG A:ASP55 3.0 59.3 1.0 O A:ILE15 3.1 55.3 1.0 OD2 A:ASP55 3.3 54.8 1.0 O A:ALA13 3.4 41.6 1.0 N A:ILE15 3.6 63.9 1.0 CB A:ILE15 3.9 55.3 1.0 C A:ILE15 3.9 61.2 1.0 CA A:ILE15 4.0 57.5 1.0 CB A:ASP55 4.3 43.3 1.0 CB A:ASP59 4.4 44.0 1.0 N A:ASP55 4.5 41.4 1.0 C A:ALA13 4.6 50.6 1.0 CD1 A:LEU84 4.6 37.3 1.0 O A:HOH715 4.7 35.7 1.0 C A:ALA14 4.7 57.2 1.0 CE2 A:TYR17 4.7 50.6 1.0 OH A:TYR17 4.8 41.3 1.0 CG2 A:ILE15 4.8 41.0 1.0 CA A:ALA14 4.8 58.2 1.0 CG1 A:ILE15 4.8 53.4 1.0 OG A:SER56 4.9 56.5 1.0 O A:SER53 4.9 28.4 1.0 CA A:ASP55 5.0 41.6 1.0

Magnesium binding site 9 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:32.2 occ:1.00 CE A:MSE104 2.2 24.6 1.0 MG A:MG508 3.2 35.0 1.0 CD1 A:ILE202 3.5 15.4 1.0 CG2 A:VAL162 3.7 13.4 1.0 O A:TYR159 3.9 16.1 1.0 SE A:MSE104 4.1 24.2 0.4 CG1 A:VAL162 4.1 14.5 1.0 CG2 A:ILE202 4.3 15.4 1.0 CG A:MSE104 4.3 26.9 0.8 CH2 A:TRP191 4.3 13.4 1.0 CD2 A:TYR159 4.4 14.8 1.0 CB A:TYR159 4.5 13.6 1.0 CB A:VAL162 4.5 12.6 1.0 CG1 A:ILE202 4.5 15.7 1.0 CB A:MSE104 4.6 28.4 1.0 C A:TYR159 4.7 15.4 1.0 OD1 A:ASN108 4.8 24.5 1.0 CZ3 A:TRP191 4.8 13.4 1.0 CG A:TYR159 5.0 13.6 1.0 CA A:TYR159 5.0 15.9 1.0

Magnesium binding site 10 out of 18 in the Vall From Streptomyces Hygroscopicus in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Vall From Streptomyces Hygroscopicus in Complex with Trehalose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:35.0 occ:1.00 CG A:MSE104 2.6 26.9 0.8 CB A:MSE104 2.6 28.4 1.0 CA A:MSE104 2.7 27.2 1.0 O A:MSE104 3.1 22.5 1.0 MG A:MG507 3.2 32.2 1.0 C A:MSE104 3.3 22.7 1.0 CE A:MSE104 3.4 24.6 1.0 OD1 A:ASN108 3.8 24.5 1.0 SE A:MSE104 3.9 24.2 0.4 CB A:ALA107 3.9 18.0 1.0 N A:MSE104 4.0 28.2 1.0 CZ3 A:TRP191 4.5 13.4 1.0 N A:TRP105 4.6 26.4 1.0 CD1 A:ILE202 4.6 15.4 1.0 CH2 A:TRP191 4.7 13.4 1.0 CD1 A:LEU194 4.7 13.3 1.0 CG A:ASN108 4.7 19.8 1.0 O A:LEU103 4.7 26.8 1.0 C A:LEU103 4.8 34.5 1.0 CD2 A:LEU103 4.8 22.0 1.0

H.Zhang, L.Zheng, H.Qian, J.Chen. Structural Basis For the Substrate Specificity of Vall To Be Published.