Magnesium in PDB 3gbj: Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with Adp

The structure of Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with Adp, PDB code: 3gbj was solved by Y.Tong, L.Shen, Y.Shen, W.Tempel, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.06 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.229, 86.520, 94.948, 90.00, 106.80, 90.00
R / Rfree (%)	22.1 / 26.9

The binding sites of Magnesium atom in the Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with Adp (pdb code 3gbj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with Adp, PDB code: 3gbj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with 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 the Motor Domain of Kinesin KIF13B Bound with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2000 b:51.4 occ:1.00 O A:HOH364 2.3 36.5 1.0 O1B A:ADP2001 2.3 31.4 1.0 O A:HOH363 2.3 33.3 1.0 O A:HOH394 2.4 43.2 1.0 OG A:SER110 2.5 48.3 1.0 O A:HOH362 2.5 39.0 1.0 O2B A:ADP2001 3.3 40.2 1.0 PB A:ADP2001 3.3 33.8 1.0 CB A:SER110 3.3 42.0 1.0 O1A A:ADP2001 4.0 38.8 1.0 OD2 A:ASP253 4.1 38.1 1.0 N A:SER110 4.2 33.2 1.0 O A:HOH365 4.2 39.4 1.0 O3A A:ADP2001 4.3 34.6 1.0 O A:HOH361 4.3 32.5 1.0 CA A:SER110 4.3 35.0 1.0 O A:HOH366 4.4 38.0 1.0 O3B A:ADP2001 4.5 33.2 1.0 OD1 A:ASP253 4.5 33.5 1.0 PA A:ADP2001 4.5 37.4 1.0 NH2 A:ARG208 4.6 73.3 1.0 O2A A:ADP2001 4.7 39.8 1.0 CG A:ASP253 4.8 39.4 1.0 OG A:SER219 4.9 74.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with 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 the Motor Domain of Kinesin KIF13B Bound with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2000 b:53.2 occ:1.00 O B:HOH360 2.2 27.3 1.0 O B:HOH361 2.3 35.0 1.0 O B:HOH359 2.4 33.2 1.0 O1B B:ADP2001 2.4 30.5 1.0 O B:HOH362 2.4 53.5 1.0 OG B:SER110 2.5 35.2 1.0 CB B:SER110 3.4 26.0 1.0 PB B:ADP2001 3.5 24.3 1.0 O2B B:ADP2001 3.5 22.8 1.0 OD2 B:ASP253 4.1 27.6 1.0 O1A B:ADP2001 4.1 31.6 1.0 O B:HOH377 4.2 30.9 1.0 N B:SER110 4.3 27.7 1.0 CA B:SER110 4.4 29.1 1.0 O B:HOH378 4.5 28.1 1.0 O B:HOH379 4.5 36.9 1.0 O3A B:ADP2001 4.5 27.9 1.0 OD1 B:ASP253 4.5 32.3 1.0 NH2 B:ARG208 4.6 48.6 1.0 O3B B:ADP2001 4.6 21.8 1.0 PA B:ADP2001 4.7 27.2 1.0 CG B:ASP253 4.7 28.0 1.0 O2A B:ADP2001 5.0 33.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with 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 the Motor Domain of Kinesin KIF13B Bound with Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2000 b:52.2 occ:1.00 O C:HOH358 2.3 34.0 1.0 O1B C:ADP2001 2.3 34.6 1.0 OG C:SER110 2.4 45.6 1.0 O C:HOH359 2.4 43.7 1.0 O C:HOH1 2.5 48.0 1.0 O C:HOH2 2.5 45.9 1.0 CB C:SER110 3.1 30.2 1.0 PB C:ADP2001 3.4 35.4 1.0 O2B C:ADP2001 3.5 41.6 1.0 OD2 C:ASP253 3.8 40.3 1.0 N C:SER110 3.9 36.9 1.0 CA C:SER110 4.1 32.7 1.0 O1A C:ADP2001 4.1 39.1 1.0 OD1 C:ASP253 4.3 40.4 1.0 O C:HOH382 4.3 37.9 1.0 O3A C:ADP2001 4.4 35.0 1.0 CG C:ASP253 4.5 41.0 1.0 PA C:ADP2001 4.6 35.8 1.0 NH2 C:ARG208 4.6 79.9 1.0 O3B C:ADP2001 4.6 33.9 1.0 O2A C:ADP2001 4.6 36.8 1.0 O C:HOH362 4.7 41.3 1.0 O C:HOH381 4.8 50.7 1.0 CB C:LYS109 4.9 33.3 1.0 CE C:LYS109 5.0 31.3 1.0 C C:LYS109 5.0 39.0 1.0

Y.Tong, L.Shen, Y.Shen, W.Tempel, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park. Crystal Structure of the Motor Domain of Kinesin KIF13B Bound with Adp To Be Published.