Magnesium in PDB 8wmy: Crystal Structure of Yqek in Complex with Mg and Adp.

All present enzymatic activity of Crystal Structure of Yqek in Complex with Mg and Adp.:
3.6.1.41;

The structure of Crystal Structure of Yqek in Complex with Mg and Adp., PDB code: 8wmy was solved by X.Mo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.04 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	159.944, 37.672, 76.301, 90, 92.7, 90
R / Rfree (%)	21.5 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Yqek in Complex with Mg and Adp. (pdb code 8wmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Yqek in Complex with Mg and Adp., PDB code: 8wmy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Yqek in Complex with Mg and Adp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Yqek in Complex with Mg and Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:7.8 occ:1.00 O1B A:ADP201 1.9 26.1 1.0 O2B A:ADP201 2.1 26.7 1.0 OD1 A:ASP59 2.2 25.5 1.0 O2A A:ADP201 2.2 30.3 1.0 NE2 A:HIS91 2.2 25.4 1.0 NE2 A:HIS117 2.3 24.7 1.0 PB A:ADP201 2.4 65.0 1.0 CG A:ASP59 3.1 27.9 1.0 CD2 A:HIS91 3.2 24.4 1.0 CE1 A:HIS91 3.2 22.9 1.0 CD2 A:HIS117 3.2 18.8 1.0 PA A:ADP201 3.3 30.5 1.0 O3A A:ADP201 3.3 41.2 1.0 CE1 A:HIS117 3.3 23.4 1.0 OD2 A:ASP59 3.4 29.5 1.0 MG A:MG203 3.6 9.7 1.0 O3B A:ADP201 3.7 31.3 1.0 CD2 A:HIS58 3.9 25.7 1.0 OG1 A:THR118 4.0 24.2 1.0 O1A A:ADP201 4.3 29.7 1.0 ND1 A:HIS91 4.3 19.6 1.0 NE2 A:HIS58 4.3 27.9 1.0 CG A:HIS91 4.3 16.6 1.0 CG A:HIS117 4.4 19.8 1.0 OD2 A:ASP135 4.4 37.1 1.0 O5' A:ADP201 4.4 31.4 1.0 ND1 A:HIS117 4.4 18.9 1.0 CB A:ASP59 4.5 21.2 1.0 CD A:LYS62 4.6 24.9 1.0 NZ A:LYS62 4.6 30.2 1.0 C5' A:ADP201 4.7 40.4 1.0 O A:HIS58 4.8 23.9 1.0 CA A:ASP59 4.8 19.4 1.0 OD1 A:ASP135 4.9 28.3 1.0 O A:HOH359 5.0 35.5 1.0 CG A:ASP135 5.0 36.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Yqek in Complex with Mg and Adp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Yqek in Complex with Mg and Adp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:9.7 occ:1.00 O3B A:ADP201 1.9 31.3 1.0 O1B A:ADP201 2.1 26.1 1.0 NE2 A:HIS58 2.1 27.9 1.0 OD1 A:ASP135 2.1 28.3 1.0 OD2 A:ASP59 2.1 29.5 1.0 NE2 A:HIS29 2.3 25.7 1.0 PB A:ADP201 2.4 65.0 1.0 CD2 A:HIS58 2.9 25.7 1.0 CG A:ASP135 3.1 36.2 1.0 CG A:ASP59 3.1 27.9 1.0 CE1 A:HIS58 3.2 19.9 1.0 CE1 A:HIS29 3.2 32.3 1.0 CD2 A:HIS29 3.2 26.3 1.0 OD2 A:ASP135 3.4 37.1 1.0 OD1 A:ASP59 3.5 25.5 1.0 O2B A:ADP201 3.5 26.7 1.0 MG A:MG202 3.6 7.8 1.0 O3A A:ADP201 3.8 41.2 1.0 O A:HOH359 3.9 35.5 1.0 CG A:HIS58 4.1 25.3 1.0 ND1 A:HIS58 4.2 23.0 1.0 CB A:ASP59 4.3 21.2 1.0 ND1 A:HIS29 4.3 28.4 1.0 CB A:ASP135 4.4 29.3 1.0 CG A:HIS29 4.4 32.5 1.0 CG2 A:VAL33 4.6 22.4 1.0 NE2 A:HIS117 4.7 24.7 1.0 CD2 A:HIS117 4.8 18.8 1.0 O2A A:ADP201 4.8 30.3 1.0 PA A:ADP201 4.9 30.5 1.0 CA A:ASP135 5.0 27.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Yqek in Complex with Mg and Adp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Yqek in Complex with Mg and Adp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:7.4 occ:1.00 O B:HOH335 1.9 26.3 1.0 O3B B:ADP201 1.9 29.2 1.0 OD1 B:ASP59 2.0 24.6 1.0 NE2 B:HIS91 2.2 26.6 1.0 O2A B:ADP201 2.2 30.5 1.0 NE2 B:HIS117 2.3 24.8 1.0 CG B:ASP59 3.1 29.8 1.0 PB B:ADP201 3.1 33.3 1.0 CD2 B:HIS91 3.1 26.5 1.0 CE1 B:HIS91 3.2 27.5 1.0 CD2 B:HIS117 3.2 22.2 1.0 CE1 B:HIS117 3.3 26.6 1.0 O3A B:ADP201 3.3 24.6 1.0 PA B:ADP201 3.3 29.7 1.0 OD2 B:ASP59 3.4 25.8 1.0 MG B:MG203 3.5 10.4 1.0 O1B B:ADP201 3.8 28.6 1.0 OG1 B:THR118 3.9 21.4 1.0 CD2 B:HIS58 4.1 23.6 1.0 O2B B:ADP201 4.1 59.9 1.0 NZ B:LYS62 4.1 50.0 1.0 ND1 B:HIS91 4.3 26.0 1.0 CG B:HIS91 4.3 25.9 1.0 CD B:LYS62 4.3 32.9 1.0 OD2 B:ASP135 4.3 28.7 1.0 ND1 B:HIS117 4.4 20.1 1.0 CG B:HIS117 4.4 23.5 1.0 O1A B:ADP201 4.4 30.1 1.0 CB B:ASP59 4.5 26.5 1.0 NE2 B:HIS58 4.5 30.5 1.0 O5' B:ADP201 4.5 33.0 1.0 CE B:LYS62 4.8 36.1 1.0 OD1 B:ASP135 4.8 27.5 1.0 O B:HIS58 4.8 21.1 1.0 CA B:ASP59 4.8 27.9 1.0 C5' B:ADP201 5.0 43.4 1.0 CG B:ASP135 5.0 24.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Yqek in Complex with Mg and Adp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Yqek in Complex with Mg and Adp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:10.4 occ:1.00 O B:HOH335 2.0 26.3 1.0 OD2 B:ASP59 2.1 25.8 1.0 NE2 B:HIS29 2.1 27.0 1.0 OD1 B:ASP135 2.2 27.5 1.0 NE2 B:HIS58 2.2 30.5 1.0 O1B B:ADP201 2.5 28.6 1.0 CG B:ASP59 3.0 29.8 1.0 CD2 B:HIS58 3.0 23.6 1.0 CE1 B:HIS29 3.1 27.3 1.0 CG B:ASP135 3.2 24.9 1.0 CD2 B:HIS29 3.2 31.4 1.0 OD1 B:ASP59 3.3 24.6 1.0 CE1 B:HIS58 3.4 21.2 1.0 O3B B:ADP201 3.4 29.2 1.0 PB B:ADP201 3.5 33.3 1.0 OD2 B:ASP135 3.5 28.7 1.0 MG B:MG202 3.5 7.4 1.0 O3A B:ADP201 3.9 24.6 1.0 ND1 B:HIS29 4.2 26.1 1.0 CG B:HIS58 4.2 22.0 1.0 CB B:ASP59 4.3 26.5 1.0 CG B:HIS29 4.3 33.8 1.0 ND1 B:HIS58 4.4 23.0 1.0 CB B:ASP135 4.4 24.1 1.0 O B:HOH316 4.5 47.8 1.0 NE2 B:HIS117 4.6 24.8 1.0 CD2 B:HIS117 4.8 22.2 1.0 CG2 B:VAL33 4.8 22.9 1.0 O B:HOH407 4.8 47.4 1.0 O2A B:ADP201 4.8 30.5 1.0 O2B B:ADP201 4.9 59.9 1.0 PA B:ADP201 5.0 29.7 1.0

X.Mo, X.Mo. N/A N/A.