Magnesium in PDB 3t5t: Vall From Streptomyces Hygroscopicus in Apo Form

The structure of Vall From Streptomyces Hygroscopicus in Apo Form, PDB code: 3t5t was solved by H.Zhang, L.Zheng, H.Qian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.39 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.671, 46.693, 123.879, 90.00, 108.08, 90.00
R / Rfree (%)	17.9 / 20.9

The binding sites of Magnesium atom in the Vall From Streptomyces Hygroscopicus in Apo Form (pdb code 3t5t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Vall From Streptomyces Hygroscopicus in Apo Form, PDB code: 3t5t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:43.0 occ:1.00 O A:HOH682 2.3 27.1 1.0 OD1 A:ASP55 2.4 28.9 1.0 OD2 A:ASP59 2.5 24.6 1.0 CG A:ASP55 3.1 25.1 1.0 OD2 A:ASP55 3.2 28.9 1.0 CG A:ASP59 3.3 23.4 1.0 OD1 A:ASP59 3.3 25.6 1.0 O A:ALA13 3.5 17.0 1.0 N A:ILE15 3.7 19.2 1.0 O A:ILE15 3.8 20.4 1.0 OG A:SER56 4.1 28.2 1.0 CA A:ALA14 4.4 18.0 1.0 CA A:ILE15 4.5 20.2 1.0 C A:ALA14 4.5 18.8 1.0 CB A:ASP55 4.5 22.7 1.0 CB A:ILE15 4.6 20.4 1.0 C A:ILE15 4.6 21.0 1.0 C A:ALA13 4.6 16.4 1.0 CB A:SER56 4.6 26.1 1.0 CB A:ASP59 4.7 22.8 1.0 N A:SER56 4.8 24.9 1.0 N A:ASP55 4.8 20.1 1.0 CA A:ASP55 5.0 22.4 1.0 N A:ALA14 5.0 16.9 1.0

Magnesium binding site 2 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg498 b:30.0 occ:1.00 MG A:MG499 3.0 30.0 1.0 NH1 B:ARG114 3.1 5.9 1.0 OG A:SER187 3.1 6.0 1.0 NH2 B:ARG114 3.2 6.7 1.0 CE1 A:TYR110 3.4 7.1 1.0 CZ B:ARG114 3.6 6.8 1.0 CB A:SER187 3.8 5.6 1.0 CZ A:TYR110 3.8 7.1 1.0 OH A:TYR110 3.9 8.3 1.0 CB B:TYR190 3.9 5.0 1.0 CD2 B:TYR190 3.9 5.0 1.0 CB B:ASP189 4.0 5.7 1.0 N B:TYR190 4.0 5.3 1.0 CD1 A:TYR110 4.1 5.4 1.0 CB A:TYR190 4.1 4.7 1.0 CB B:SER187 4.3 5.2 1.0 CA B:TYR190 4.3 5.2 1.0 NH2 A:ARG114 4.4 6.7 1.0 CG B:TYR190 4.4 4.9 1.0 OG B:SER187 4.5 6.5 1.0 CD2 A:TYR190 4.5 4.7 1.0 C B:ASP189 4.5 5.5 1.0 CG A:TYR190 4.6 4.7 1.0 N A:SER187 4.7 4.8 1.0 CE2 A:TYR110 4.7 7.1 1.0 CA B:ASP189 4.8 6.0 1.0 CA A:SER187 4.9 5.5 1.0 NE B:ARG114 4.9 7.0 1.0 CG A:TYR110 5.0 6.6 1.0

Magnesium binding site 3 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg499 b:30.0 occ:1.00 OG B:SER187 2.8 6.5 1.0 MG A:MG498 3.0 30.0 1.0 NH1 A:ARG114 3.1 6.7 1.0 NH2 A:ARG114 3.2 6.7 1.0 CE1 B:TYR110 3.3 6.5 1.0 OH B:TYR110 3.6 5.6 1.0 CZ B:TYR110 3.6 5.8 1.0 CB B:SER187 3.6 5.2 1.0 CZ A:ARG114 3.6 7.0 1.0 CB A:ASP189 3.6 5.2 1.0 N A:TYR190 3.8 4.8 1.0 CB A:TYR190 3.9 4.7 1.0 CD1 B:TYR110 4.0 4.8 1.0 CB A:SER187 4.1 5.6 1.0 CA A:TYR190 4.2 4.7 1.0 C A:ASP189 4.2 4.9 1.0 CB B:TYR190 4.4 5.0 1.0 OG A:SER187 4.4 6.0 1.0 CA A:ASP189 4.4 5.0 1.0 N B:SER187 4.5 4.8 1.0 CD2 B:TYR190 4.5 5.0 1.0 CE2 B:TYR110 4.5 6.2 1.0 CD2 A:TYR190 4.6 4.7 1.0 CA B:SER187 4.7 5.8 1.0 CG B:TYR190 4.7 4.9 1.0 CG A:ASP189 4.7 5.1 1.0 CG A:TYR190 4.8 4.7 1.0 N A:ASP189 4.8 5.5 1.0 OD2 A:ASP189 4.8 6.4 1.0 O B:HOH517 4.9 3.8 1.0 CG B:TYR110 4.9 5.5 1.0 NE A:ARG114 5.0 6.7 1.0 NH2 B:ARG114 5.0 6.7 1.0 O A:ASP189 5.0 6.0 1.0

Magnesium binding site 4 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:30.0 occ:1.00 NZ A:LYS11 3.1 16.3 1.0 NE2 A:GLN160 3.2 11.4 1.0 NH2 A:ARG326 3.3 32.4 1.0 O A:HOH512 3.5 28.4 1.0 CD A:ARG12 3.6 20.0 1.0 CE A:LYS11 3.6 14.5 1.0 CB A:MET99 3.7 21.5 1.0 CD A:LYS11 3.7 12.4 1.0 CG A:ARG12 3.8 15.3 1.0 NH1 A:ARG326 3.8 33.1 1.0 CG A:GLN160 3.9 8.3 1.0 CZ A:ARG326 4.0 32.2 1.0 CD A:GLN160 4.1 9.8 1.0 OH A:TYR159 4.2 10.8 1.0 CG A:MET99 4.3 23.3 1.0 NE A:ARG12 4.4 22.6 1.0 CG A:GLN96 4.5 20.0 1.0 OE1 A:GLN96 4.6 22.6 1.0 CG A:LYS11 4.9 10.4 1.0 CA A:MET99 5.0 20.9 1.0 CZ A:TYR159 5.0 9.2 1.0 CD A:GLN96 5.0 22.6 1.0

Magnesium binding site 5 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.0 occ:1.00 NZ A:LYS295 2.2 23.4 1.0 N A:ARG290 3.0 15.0 1.0 O A:HOH549 3.1 19.7 1.0 CG A:ARG290 3.4 20.7 1.0 CE A:LYS295 3.6 17.5 1.0 CB A:ARG290 3.6 16.2 1.0 CA A:GLY289 3.7 15.3 1.0 C A:GLY289 3.8 14.7 1.0 NE A:ARG290 3.8 29.9 1.0 CA A:ARG290 3.9 15.6 1.0 CD A:ARG290 4.1 24.5 1.0 CD A:LYS295 4.3 14.2 1.0 O A:HOH662 4.4 23.1 1.0 ND2 A:ASN323 4.4 19.6 1.0 O A:HOH845 4.4 22.8 1.0 CZ A:ARG290 4.6 29.7 1.0 CG A:LYS295 4.7 10.0 1.0 O A:HOH527 4.7 32.7 1.0 NH2 A:ARG290 4.9 29.2 1.0 O A:GLY289 4.9 15.0 1.0

Magnesium binding site 6 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:20.4 occ:1.00 OD2 B:ASP59 1.9 19.2 1.0 OD1 B:ASP55 2.1 22.8 1.0 CG B:ASP59 2.9 20.9 1.0 CG B:ASP55 3.2 21.4 1.0 OD1 B:ASP59 3.3 22.1 1.0 OD2 B:ASP55 3.6 25.0 1.0 O B:ALA13 3.8 15.9 1.0 O B:HOH646 4.0 21.9 1.0 OG B:SER56 4.0 21.0 1.0 O B:HOH701 4.0 25.4 1.0 N B:ASP55 4.1 17.3 1.0 CB B:ASP59 4.2 21.5 1.0 CB B:ASP55 4.4 19.5 1.0 CB B:SER56 4.5 21.9 1.0 CA B:ASP55 4.6 19.2 1.0 N B:SER56 4.6 20.8 1.0 O B:HOH680 4.6 37.3 1.0 C B:ASP55 4.6 19.9 1.0 O B:ILE15 4.7 19.4 1.0 N B:ILE15 4.7 17.1 1.0 O B:HOH697 4.8 10.5 1.0 O B:SER53 4.8 11.0 1.0 C B:ALA13 5.0 14.8 1.0

Magnesium binding site 7 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg498 b:30.0 occ:1.00 OE2 B:GLU412 2.7 8.0 1.0 O B:HOH913 2.7 18.0 1.0 NE B:ARG218 3.0 6.3 1.0 CG B:GLU412 3.3 7.8 1.0 CD B:GLU412 3.4 8.2 1.0 CB B:ARG218 3.5 5.3 1.0 O B:HOH600 3.5 14.3 1.0 CD B:ARG218 3.8 4.7 1.0 CZ B:ARG218 3.9 8.8 1.0 NH2 B:ARG218 3.9 10.8 1.0 CG B:ARG218 4.2 5.5 1.0 O B:HOH700 4.5 11.9 1.0 N B:ARG218 4.5 6.0 1.0 O B:GLU406 4.6 6.1 1.0 CA B:ARG218 4.6 5.0 1.0 O B:HOH610 4.6 13.2 1.0 OE1 B:GLU412 4.6 8.5 1.0 CB B:GLU412 4.8 8.4 1.0 CB B:ALA216 4.8 6.3 1.0 O B:CYS408 4.9 6.6 1.0

Magnesium binding site 8 out of 8 in the Vall From Streptomyces Hygroscopicus in Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg499 b:30.0 occ:1.00 O B:ARG321 2.7 10.3 1.0 O B:HOH549 2.8 6.4 1.0 ND1 B:HIS287 2.8 8.1 1.0 CE1 B:HIS287 3.4 7.6 1.0 CG1 B:VAL320 3.5 11.1 1.0 C B:ARG321 3.6 11.6 1.0 N B:GLY289 3.6 9.4 1.0 CG B:MET322 3.7 14.3 1.0 O B:HIS287 3.8 9.5 1.0 CB B:ALA297 3.9 7.0 1.0 O B:GLY289 3.9 9.7 1.0 C B:SER288 3.9 9.8 1.0 CA B:SER288 4.0 9.9 1.0 CG B:HIS287 4.0 7.6 1.0 C B:HIS287 4.0 9.0 1.0 N B:ARG321 4.1 10.8 1.0 N B:SER288 4.1 9.1 1.0 CA B:MET322 4.2 12.4 1.0 N B:MET322 4.2 11.7 1.0 CA B:GLY289 4.4 9.0 1.0 CB B:MET322 4.4 12.7 1.0 CA B:ARG321 4.5 12.1 1.0 C B:VAL320 4.5 10.8 1.0 OH B:TYR335 4.5 7.1 1.0 C B:GLY289 4.5 9.4 1.0 CB B:HIS287 4.5 8.1 1.0 CE B:MET322 4.6 13.2 1.0 NE2 B:HIS287 4.7 6.6 1.0 O B:SER288 4.7 9.5 1.0 CA B:VAL320 4.7 10.5 1.0 CB B:VAL320 4.7 10.7 1.0 SD B:MET322 4.8 20.7 1.0 CA B:HIS287 5.0 8.7 1.0 CD2 B:HIS287 5.0 7.6 1.0

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