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Magnesium in PDB 4qpm: Structure of BUB1 Kinase Domain

Enzymatic activity of Structure of BUB1 Kinase Domain

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

Protein crystallography data

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

Other elements in 4qpm:

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

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

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 4qpm

Go back to Magnesium Binding Sites List in 4qpm
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 4qpm

Go back to Magnesium Binding Sites List in 4qpm
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 4qpm

Go back to Magnesium Binding Sites List in 4qpm
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 4qpm

Go back to Magnesium Binding Sites List in 4qpm
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

Reference:

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
Page generated: Tue Aug 20 02:07:58 2024

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