Magnesium in PDB 5zbr: Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form

The structure of Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form, PDB code: 5zbr was solved by J.Q.Ren, S.Wang, W.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.11 / 2.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	110.303, 110.303, 95.124, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 24

The binding sites of Magnesium atom in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form (pdb code 5zbr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form, PDB code: 5zbr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form


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 Kinesin-3 KIF13B Motor Domain in Amppnp Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:37.2 occ:1.00 O B:HOH538 1.9 25.9 1.0 O1G B:ANP401 1.9 35.1 0.6 O B:HOH553 2.1 33.6 1.0 OG B:SER110 2.2 35.5 1.0 O1B B:ANP401 2.2 22.9 1.0 O B:HOH576 2.3 42.8 1.0 CB B:SER110 3.2 28.6 1.0 PG B:ANP401 3.2 35.5 0.6 PB B:ANP401 3.4 29.4 1.0 N3B B:ANP401 3.7 26.9 1.0 N B:SER110 3.8 26.0 1.0 O B:HOH674 3.9 50.2 1.0 OD1 B:ASP253 4.0 35.1 1.0 CA B:SER110 4.1 21.2 1.0 O2G B:ANP401 4.1 35.2 1.0 OD2 B:ASP253 4.2 33.4 1.0 O3G B:ANP401 4.2 33.4 0.4 O2A B:ANP401 4.3 42.9 1.0 O2B B:ANP401 4.5 25.6 1.0 CG B:ASP253 4.5 38.8 1.0 O3A B:ANP401 4.5 32.2 1.0 O B:HOH690 4.6 55.3 1.0 PA B:ANP401 4.8 31.2 1.0 CB B:LYS109 4.8 28.9 1.0 CE B:LYS109 4.8 20.7 1.0 NH1 B:ARG208 4.8 56.7 1.0 O1A B:ANP401 4.8 32.9 1.0 O B:HOH572 4.9 45.6 1.0 C B:LYS109 4.9 24.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form


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 Kinesin-3 KIF13B Motor Domain in Amppnp Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:97.9 occ:1.00 OD1 B:ASN321 2.7 49.0 1.0 O B:VAL358 2.8 46.9 1.0 N B:ASN96 3.0 35.4 1.0 CG B:ASN321 3.4 45.8 1.0 ND2 B:ASN360 3.4 44.3 1.0 O B:ASN321 3.5 45.4 1.0 N B:VAL358 3.6 48.4 1.0 CA B:TYR95 3.7 46.7 1.0 ND2 B:ASN321 3.7 51.1 1.0 ND2 B:ASN96 3.7 43.8 1.0 C B:TYR95 3.8 42.5 1.0 C B:VAL358 3.8 55.2 1.0 CB B:ASN96 3.8 33.5 1.0 C B:ASN321 3.8 46.6 1.0 CD1 B:TYR95 3.9 54.8 1.0 CA B:ASN96 3.9 36.7 1.0 CG B:ASN96 3.9 39.0 1.0 CB B:TYR95 4.0 48.4 1.0 O B:ASN96 4.0 40.0 1.0 CA B:ALA357 4.1 50.1 1.0 CB B:ALA357 4.1 48.4 1.0 N B:SER322 4.2 48.6 1.0 C B:ALA357 4.2 44.2 1.0 CG B:ASN360 4.2 45.3 1.0 OD1 B:ASN360 4.2 54.0 1.0 CA B:VAL358 4.4 56.0 1.0 CG B:TYR95 4.4 47.1 1.0 C B:ASN96 4.5 36.5 1.0 CB B:ASN321 4.5 48.7 1.0 CA B:SER322 4.5 44.8 1.0 CA B:ASN321 4.6 45.5 1.0 O B:GLY94 4.7 46.4 1.0 OD1 B:ASN96 4.7 44.6 1.0 CE1 B:TYR95 4.9 51.9 1.0 N B:TYR95 4.9 33.8 1.0 N B:VAL359 4.9 57.6 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form


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 Kinesin-3 KIF13B Motor Domain in Amppnp Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:29.4 occ:0.55 O1G A:ANP401 1.9 40.2 0.8 O1B A:ANP401 2.0 29.2 1.0 O A:HOH520 2.0 29.9 1.0 O A:HOH541 2.1 37.5 1.0 OG A:SER110 2.2 35.2 1.0 O A:HOH586 2.2 46.0 1.0 PG A:ANP401 3.1 38.0 0.3 CB A:SER110 3.2 28.5 1.0 PB A:ANP401 3.2 30.5 1.0 N3B A:ANP401 3.5 25.0 1.0 N A:SER110 3.9 29.4 1.0 O A:HOH588 4.0 42.0 1.0 O2G A:ANP401 4.0 66.4 1.0 O2A A:ANP401 4.1 44.8 1.0 CA A:SER110 4.1 27.6 1.0 OD2 A:ASP253 4.1 33.9 1.0 O3G A:ANP401 4.2 34.8 1.0 O2B A:ANP401 4.2 27.8 1.0 O3A A:ANP401 4.3 29.8 1.0 OD1 A:ASP253 4.3 37.9 1.0 PA A:ANP401 4.5 40.6 1.0 CG A:ASP253 4.6 34.3 1.0 O A:HOH605 4.7 43.5 1.0 O1A A:ANP401 4.7 35.4 1.0 CB A:LYS109 4.8 24.0 1.0 CE A:LYS109 4.9 24.4 1.0 C A:LYS109 5.0 31.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form


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 Kinesin-3 KIF13B Motor Domain in Amppnp Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:43.0 occ:1.00 O C:HOH538 2.0 36.2 1.0 O1G C:ANP401 2.0 53.2 1.0 O C:HOH516 2.0 31.8 1.0 O1B C:ANP401 2.1 33.3 1.0 OG C:SER110 2.1 41.6 1.0 O C:HOH571 2.3 56.8 1.0 CB C:SER110 3.0 32.9 1.0 PG C:ANP401 3.3 40.9 0.5 PB C:ANP401 3.4 32.5 1.0 N3B C:ANP401 3.7 31.3 0.8 O C:HOH604 3.8 49.9 1.0 N C:SER110 3.8 33.3 1.0 CA C:SER110 4.0 33.7 1.0 O2A C:ANP401 4.0 48.7 1.0 O C:HOH541 4.0 53.6 1.0 OD2 C:ASP253 4.0 39.1 1.0 O2G C:ANP401 4.2 55.1 0.7 OD1 C:ASP253 4.3 43.6 1.0 O3G C:ANP401 4.3 33.8 1.0 O3A C:ANP401 4.4 35.6 1.0 O2B C:ANP401 4.4 31.0 1.0 PA C:ANP401 4.5 42.8 1.0 CG C:ASP253 4.6 39.4 1.0 O1A C:ANP401 4.7 37.6 1.0 O C:HOH525 4.7 45.8 1.0 NH1 C:ARG208 4.9 69.6 1.0 CB C:LYS109 4.9 29.0 1.0 O C:HOH537 4.9 57.9 1.0 C C:LYS109 5.0 35.4 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Kinesin-3 KIF13B Motor Domain in Amppnp Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:63.2 occ:1.00 O C:VAL358 2.7 52.7 1.0 N C:ASN96 2.8 39.2 1.0 ND2 C:ASN321 3.0 60.4 1.0 ND2 C:ASN360 3.1 57.4 1.0 CA C:TYR95 3.3 49.6 1.0 C C:TYR95 3.5 51.1 1.0 O C:ASN321 3.6 52.6 1.0 CB C:TYR95 3.7 48.2 1.0 CG C:ASN321 3.7 63.6 1.0 N C:VAL358 3.7 58.2 1.0 CD1 C:TYR95 3.7 45.3 1.0 CA C:ASN96 3.8 39.4 1.0 CB C:ASN96 3.8 39.4 1.0 C C:VAL358 3.8 60.1 1.0 CB C:ALA357 3.9 52.5 1.0 OD1 C:ASN321 3.9 71.5 1.0 O C:ASN96 4.0 51.2 1.0 CG C:ASN360 4.0 61.5 1.0 CG C:ASN96 4.0 50.5 1.0 C C:ASN321 4.0 58.1 1.0 OD1 C:ASN360 4.1 67.1 1.0 ND2 C:ASN96 4.1 52.3 1.0 CG C:TYR95 4.2 47.8 1.0 CA C:ALA357 4.2 53.1 1.0 O C:GLY94 4.3 51.3 1.0 C C:ASN96 4.3 47.4 1.0 C C:ALA357 4.3 60.9 1.0 CA C:VAL358 4.4 59.1 1.0 N C:SER322 4.5 51.9 1.0 N C:TYR95 4.5 47.8 1.0 OD1 C:ASN96 4.6 55.5 1.0 CA C:SER322 4.6 51.2 1.0 O C:TYR95 4.7 42.4 1.0 CB C:ASN321 4.8 56.5 1.0 CA C:ASN321 4.8 52.6 1.0 CE1 C:TYR95 4.9 52.9 1.0 C C:GLY94 4.9 52.5 1.0 N C:VAL359 4.9 54.8 1.0 CG2 C:VAL358 5.0 65.5 1.0

J.Ren, Y.Zhang, S.Wang, L.Huo, J.Lou, W.Feng. Structural Delineation of the Neck Linker of Kinesin-3 For Processive Movement. J. Mol. Biol. V. 430 2030 2018.
ISSN: ESSN 1089-8638
PubMed: 29752968
DOI: 10.1016/J.JMB.2018.05.010