Magnesium in PDB 4qpm: Structure of BUB1 Kinase Domain

All present enzymatic activity of Structure of BUB1 Kinase Domain:
2.7.11.1;

The structure of Structure of BUB1 Kinase Domain, PDB code: 4qpm was solved by Z.H.Lin, L.Y.Jia, D.R.Tomchick, X.L.Luo, H.T.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.88 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.013, 47.180, 93.146, 90.00, 107.40, 90.00
R / Rfree (%)	22.9 / 26.9

The structure of Structure of BUB1 Kinase Domain also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Structure of BUB1 Kinase Domain (pdb code 4qpm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of BUB1 Kinase Domain, PDB code: 4qpm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of BUB1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of BUB1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1502 b:21.1 occ:1.00 O2A A:ADP1501 1.9 21.5 1.0 O1B A:ADP1501 2.0 25.3 1.0 O A:HOH1602 2.1 26.0 1.0 O A:HOH1601 2.1 23.6 1.0 OD1 A:ASN922 2.1 24.4 1.0 OD2 A:ASP946 2.1 24.1 1.0 HD21 A:ASN922 3.0 28.7 1.0 CG A:ASN922 3.1 24.3 1.0 CG A:ASP946 3.2 27.2 1.0 PB A:ADP1501 3.3 27.6 1.0 PA A:ADP1501 3.3 23.9 1.0 ND2 A:ASN922 3.4 23.9 1.0 HB2 A:ASP946 3.4 31.9 1.0 H5'2 A:ADP1501 3.6 29.1 1.0 O A:HOH1610 3.7 44.4 1.0 CB A:ASP946 3.8 26.6 1.0 O A:HOH1603 3.8 32.1 1.0 O3A A:ADP1501 3.8 20.9 1.0 MG A:MG1503 3.8 26.1 1.0 HB3 A:ASP946 3.9 31.9 1.0 O3B A:ADP1501 3.9 26.5 1.0 HA3 A:GLY796 4.0 35.5 1.0 H A:ALA797 4.0 44.0 1.0 OD2 A:ASP917 4.2 30.1 1.0 HA2 A:GLY796 4.3 35.5 1.0 OD1 A:ASP946 4.3 30.3 1.0 HD22 A:ASN922 4.3 28.7 1.0 HA A:ASN922 4.3 29.7 1.0 OD2 A:ASP921 4.3 45.5 1.0 O1A A:ADP1501 4.3 24.0 1.0 HE3 A:LYS919 4.3 54.6 1.0 O5' A:ADP1501 4.4 21.1 1.0 C5' A:ADP1501 4.4 24.3 1.0 CB A:ASN922 4.5 24.5 1.0 H3' A:ADP1501 4.5 32.5 1.0 O2B A:ADP1501 4.5 30.6 1.0 HD12 A:ILE945 4.6 37.4 1.0 CA A:GLY796 4.6 29.6 1.0 O3' A:ADP1501 4.6 25.8 1.0 O A:HOH1605 4.7 25.4 1.0 O A:ASP921 4.7 32.4 1.0 HD11 A:ILE945 4.8 37.4 1.0 HE2 A:LYS919 4.8 54.6 1.0 CA A:ASN922 4.8 24.7 1.0 N A:ALA797 4.8 36.7 1.0 HB3 A:ASN922 4.9 29.4 1.0 HD13 A:ILE945 4.9 37.4 1.0 CD1 A:ILE945 5.0 31.2 1.0 C3' A:ADP1501 5.0 27.1 1.0

Magnesium binding site 2 out of 4 in the Structure of BUB1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of BUB1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1503 b:26.1 occ:1.00 O3B A:ADP1501 2.0 26.5 1.0 O A:HOH1604 2.1 23.8 1.0 O A:HOH1603 2.1 32.1 1.0 O A:HOH1605 2.1 25.4 1.0 OD1 A:ASP946 2.1 30.3 1.0 OD2 A:ASP946 2.1 24.1 1.0 CG A:ASP946 2.4 27.2 1.0 PB A:ADP1501 3.1 27.6 1.0 O1B A:ADP1501 3.3 25.3 1.0 HD2 A:PHE798 3.6 45.1 1.0 HZ1 A:LYS821 3.6 34.8 1.0 MG A:MG1502 3.8 21.1 1.0 H A:GLY948 3.8 31.2 1.0 OD2 A:ASP917 3.8 30.1 1.0 CB A:ASP946 3.9 26.6 1.0 HA3 A:GLY948 3.9 29.9 1.0 O A:HOH1602 4.0 26.0 1.0 HE21 A:GLN949 4.0 67.3 1.0 O A:HOH1614 4.0 37.6 1.0 O3A A:ADP1501 4.1 20.9 1.0 HE2 A:PHE798 4.1 44.5 1.0 HB3 A:ASP946 4.2 31.9 1.0 O2B A:ADP1501 4.2 30.6 1.0 HD21 A:ASN922 4.2 28.7 1.0 HB2 A:ASP946 4.3 31.9 1.0 H A:GLN949 4.4 36.2 1.0 CD2 A:PHE798 4.4 37.6 1.0 O2A A:ADP1501 4.4 21.5 1.0 NZ A:LYS821 4.4 29.0 1.0 HB2 A:GLN949 4.4 46.4 1.0 N A:GLY948 4.5 26.0 1.0 HA A:ASP946 4.6 30.2 1.0 HZ2 A:LYS821 4.6 34.8 1.0 CA A:GLY948 4.6 24.9 1.0 O A:HOH1606 4.6 18.3 1.0 CE2 A:PHE798 4.6 37.1 1.0 HB3 A:ALA797 4.7 46.1 1.0 PA A:ADP1501 4.7 23.9 1.0 HZ3 A:LYS821 4.7 34.8 1.0 CA A:ASP946 4.7 25.2 1.0 NE2 A:GLN949 4.8 56.1 1.0 C A:ASP946 4.8 25.1 1.0 HB3 A:ASP917 4.8 36.5 1.0 O A:ASP946 4.8 23.6 1.0 N A:GLN949 4.9 30.2 0.9 CG A:ASP917 4.9 31.5 1.0 H A:ALA797 4.9 44.0 1.0 ND2 A:ASN922 4.9 23.9 1.0 O1A A:ADP1501 5.0 24.0 1.0

Magnesium binding site 3 out of 4 in the Structure of BUB1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of BUB1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1502 b:28.7 occ:1.00 O1B B:ADP1501 1.9 25.8 1.0 O2A B:ADP1501 2.0 21.8 1.0 O B:HOH1602 2.1 24.8 1.0 O B:HOH1601 2.1 26.3 1.0 OD1 B:ASN922 2.1 23.9 1.0 OD2 B:ASP946 2.1 26.9 1.0 CG B:ASP946 3.1 26.6 1.0 CG B:ASN922 3.1 24.0 1.0 HD21 B:ASN922 3.2 30.1 1.0 PB B:ADP1501 3.2 26.4 1.0 PA B:ADP1501 3.3 24.7 1.0 HB2 B:ASP946 3.3 31.2 1.0 ND2 B:ASN922 3.5 25.1 1.0 O B:HOH1604 3.5 30.0 1.0 CB B:ASP946 3.6 26.0 1.0 H5'2 B:ADP1501 3.7 28.8 1.0 MG B:MG1503 3.7 25.7 1.0 O3A B:ADP1501 3.7 22.2 1.0 HB3 B:ASP946 3.7 31.2 1.0 O3B B:ADP1501 3.8 27.6 1.0 H B:ALA797 4.0 40.5 1.0 OD1 B:ASP946 4.1 25.5 1.0 HA3 B:GLY796 4.2 30.6 1.0 OD2 B:ASP917 4.2 33.2 1.0 O1A B:ADP1501 4.3 26.4 1.0 HA B:ASN922 4.3 27.5 1.0 HD22 B:ASN922 4.4 30.1 1.0 O5' B:ADP1501 4.4 23.6 1.0 O2B B:ADP1501 4.4 26.4 1.0 CB B:ASN922 4.5 23.0 1.0 HE3 B:LYS919 4.5 59.7 1.0 HA2 B:GLY796 4.5 30.6 1.0 HD12 B:ILE945 4.5 40.8 1.0 C5' B:ADP1501 4.5 24.0 1.0 H3' B:ADP1501 4.5 33.1 1.0 O B:HOH1603 4.6 30.4 1.0 OD2 B:ASP921 4.6 46.5 1.0 HD11 B:ILE945 4.6 40.8 1.0 HE2 B:LYS919 4.6 59.7 1.0 O B:ASP921 4.7 32.6 1.0 CA B:GLY796 4.8 25.5 1.0 CA B:ASN922 4.8 22.9 1.0 HB3 B:ASN922 4.8 27.6 1.0 O3' B:ADP1501 4.8 28.6 1.0 N B:ALA797 4.9 33.8 1.0 CD1 B:ILE945 4.9 34.0 1.0 HD13 B:ILE945 4.9 40.8 1.0

Magnesium binding site 4 out of 4 in the Structure of BUB1 Kinase Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of BUB1 Kinase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1503 b:25.7 occ:1.00 O3B B:ADP1501 2.0 27.6 1.0 O B:HOH1605 2.1 28.4 1.0 O B:HOH1604 2.1 30.0 1.0 O B:HOH1603 2.1 30.4 1.0 OD1 B:ASP946 2.1 25.5 1.0 OD2 B:ASP946 2.1 26.9 1.0 CG B:ASP946 2.4 26.6 1.0 PB B:ADP1501 3.1 26.4 1.0 O1B B:ADP1501 3.2 25.8 1.0 HZ1 B:LYS821 3.6 34.4 1.0 HD2 B:PHE798 3.7 42.5 1.0 MG B:MG1502 3.7 28.7 1.0 H B:GLY948 3.8 32.1 1.0 HG2 B:GLN949 3.8 59.4 1.0 HA3 B:GLY948 3.8 32.1 1.0 CB B:ASP946 3.9 26.0 1.0 OD2 B:ASP917 4.0 33.2 1.0 O B:HOH1601 4.1 26.3 1.0 O3A B:ADP1501 4.1 22.2 1.0 O2B B:ADP1501 4.2 26.4 1.0 O B:HOH1609 4.2 39.8 1.0 O B:HOH1702 4.3 35.7 1.0 HB2 B:ASP946 4.3 31.2 1.0 HB3 B:ASP946 4.3 31.2 1.0 HE2 B:PHE798 4.4 44.6 1.0 NZ B:LYS821 4.4 28.7 1.0 HD21 B:ASN922 4.4 30.1 1.0 H B:GLN949 4.5 38.2 1.0 N B:GLY948 4.5 26.8 1.0 O2A B:ADP1501 4.5 21.8 1.0 CD2 B:PHE798 4.5 35.4 1.0 CA B:GLY948 4.5 26.7 1.0 O B:HOH1607 4.6 17.6 1.0 HB3 B:ALA797 4.6 41.5 1.0 HA B:ASP946 4.6 29.1 1.0 HZ2 B:LYS821 4.6 34.4 1.0 HZ3 B:LYS821 4.7 34.4 1.0 CG B:GLN949 4.7 49.5 1.0 CA B:ASP946 4.7 24.3 1.0 PA B:ADP1501 4.7 24.7 1.0 O B:ASP946 4.8 24.0 1.0 C B:ASP946 4.8 24.4 1.0 HG3 B:GLN949 4.8 59.4 1.0 CE2 B:PHE798 4.9 37.1 1.0 HB3 B:ASP917 4.9 37.5 1.0 N B:GLN949 4.9 31.9 1.0 H B:ALA797 4.9 40.5 1.0

Z.Lin, L.Jia, D.R.Tomchick, X.Luo, H.Yu. Substrate-Specific Activation of the Mitotic Kinase BUB1 Through Intramolecular Autophosphorylation and Kinetochore Targeting. Structure 2014.
ISSN: ISSN 0969-2126
PubMed: 25308863
DOI: 10.1016/J.STR.2014.08.020