Atomistry » Magnesium » PDB 4ava-4b2q » 4azc
Atomistry »
  Magnesium »
    PDB 4ava-4b2q »
      4azc »

Magnesium in PDB 4azc: Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh

Protein crystallography data

The structure of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh, PDB code: 4azc was solved by B.Pluvinage, K.A.Stubbs, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.81 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.200, 115.600, 132.000, 90.00, 99.40, 90.00
R / Rfree (%) 19 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh (pdb code 4azc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh, PDB code: 4azc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 1 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2043

b:15.3
occ:1.00
 O A:HOH3036 3.0 16.7 1.0
N A:TYR959 3.3 16.9 1.0
NZ A:LYS642 3.3 10.9 1.0
O A:HOH3592 3.3 40.7 1.0
O A:HOH3492 3.4 37.0 1.0
ND2 A:ASN710 3.5 15.4 1.0
CE A:LYS642 3.5 12.6 1.0
CA A:GLU958 3.8 17.4 1.0
C A:GLU958 4.0 17.3 1.0
O A:ALA957 4.1 16.6 1.0
CB A:TYR959 4.2 16.3 1.0
CG A:GLU958 4.2 19.0 1.0
O A:HOH3270 4.2 30.9 1.0
O A:HOH3021 4.2 19.0 1.0
CA A:TYR959 4.2 17.0 1.0
O A:TYR959 4.5 17.3 1.0
CB A:GLU958 4.5 18.1 1.0
O A:HOH3020 4.5 11.3 1.0
CG A:ASN710 4.7 17.6 1.0
O A:HOH3022 4.7 12.1 1.0
N A:GLU958 4.8 17.1 1.0
C A:TYR959 4.8 17.2 1.0
C A:ALA957 4.9 16.9 1.0

Magnesium binding site 2 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 2 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2044

b:16.1
occ:1.00
 O A:HOH3593 3.1 22.4 1.0
N A:VAL765 3.2 19.0 1.0
O A:HOH3594 3.4 28.7 1.0
CG2 A:VAL765 3.7 17.1 1.0
CB A:LYS764 3.7 21.1 1.0
CA A:LYS764 3.8 20.8 1.0
CB A:VAL765 3.9 17.8 1.0
C A:LYS764 4.0 20.0 1.0
CA A:VAL765 4.1 17.4 1.0
O A:HOH3399 4.1 32.1 1.0
O A:VAL765 4.8 15.6 1.0
O A:HOH3180 4.8 27.2 1.0
O A:HOH3398 4.9 25.0 1.0
CG A:LYS764 4.9 22.6 1.0

Magnesium binding site 3 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 3 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2045

b:22.4
occ:1.00
 O A:MET947 2.6 8.4 1.0
O A:ASN898 2.9 9.9 1.0
CE1 A:TYR902 3.3 10.4 1.0
OG A:SER949 3.3 9.5 1.0
N A:SER949 3.4 10.4 1.0
CD1 A:TYR902 3.4 10.5 1.0
CA A:LEU948 3.5 10.2 1.0
C A:MET947 3.6 9.7 1.0
C A:THR897 3.6 9.0 1.0
O A:THR897 3.6 9.2 1.0
C A:ASN898 3.7 9.3 1.0
C A:LEU948 3.8 10.3 1.0
CB A:TRP901 3.8 11.1 1.0
CB A:SER949 3.9 9.8 1.0
N A:ASN898 3.9 8.9 1.0
CG2 A:THR897 3.9 7.8 1.0
N A:LEU948 4.0 9.6 1.0
CE3 A:TRP901 4.0 9.0 1.0
CA A:THR897 4.1 9.8 1.0
CA A:SER949 4.2 9.8 1.0
CA A:ASN898 4.4 9.5 1.0
C A:TRP901 4.4 11.2 1.0
N A:TYR902 4.4 11.2 1.0
CA A:TRP901 4.5 10.9 1.0
CZ A:TYR902 4.6 11.3 1.0
N A:GLY899 4.6 9.6 1.0
N A:TRP901 4.7 10.4 1.0
CB A:THR897 4.7 9.9 1.0
CB A:LEU948 4.7 10.8 1.0
CG A:TRP901 4.7 10.5 1.0
CD2 A:TRP901 4.7 10.5 1.0
CG A:TYR902 4.7 10.9 1.0
O A:LEU948 4.8 10.6 1.0
O A:TRP901 4.9 11.0 1.0
CA A:GLY899 4.9 9.4 1.0
CA A:TYR902 5.0 11.5 1.0
CG A:LEU948 5.0 12.2 1.0
CA A:MET947 5.0 9.8 1.0

Magnesium binding site 4 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 4 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2046

b:25.7
occ:1.00
 OH A:TYR854 2.8 12.1 1.0
CG A:GLN862 3.0 17.3 0.5
NZ A:LYS890 3.4 23.0 1.0
NZ A:LYS865 3.4 26.5 1.0
CZ A:TYR854 3.6 9.0 1.0
CE1 A:TYR854 3.7 11.3 1.0
CE A:LYS865 3.7 24.0 1.0
CB A:GLN862 3.8 16.4 0.5
CG A:GLN862 3.9 17.6 0.5
CE A:LYS890 4.0 21.7 1.0
CD A:LYS890 4.0 19.4 1.0
OE1 A:GLN862 4.0 20.4 0.5
CD A:GLN862 4.2 18.7 0.3
CB A:GLN862 4.3 16.4 0.5
NE2 A:GLN862 4.3 19.0 0.3
CB A:ASP859 4.4 18.6 1.0
CD A:GLN862 4.4 20.3 0.7
CA A:GLN862 4.6 16.3 0.5
CA A:GLN862 4.6 16.4 0.5
OD2 A:ASP859 4.7 20.9 1.0
O A:HOH3302 4.8 28.4 1.0
O A:ASP859 4.8 19.9 1.0
CE2 A:TYR854 4.9 11.2 1.0
CD1 A:TYR854 4.9 10.1 1.0
CG A:ASP859 5.0 19.8 1.0

Magnesium binding site 5 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 5 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2045

b:16.6
occ:1.00
 NZ B:LYS642 3.1 18.9 1.0
O B:HOH3391 3.2 36.3 1.0
N B:TYR959 3.2 22.9 1.0
O B:HOH3027 3.3 22.6 1.0
O B:HOH3399 3.4 43.7 1.0
CE B:LYS642 3.5 19.0 1.0
ND2 B:ASN710 3.6 24.9 1.0
CA B:GLU958 3.7 23.6 1.0
O B:ALA957 3.9 24.6 1.0
C B:GLU958 3.9 23.1 1.0
CB B:TYR959 4.1 21.9 1.0
CG B:GLU958 4.2 24.4 1.0
CA B:TYR959 4.2 22.3 1.0
O B:HOH3018 4.3 17.7 1.0
O B:TYR959 4.5 21.8 1.0
CB B:GLU958 4.5 23.8 1.0
O B:HOH3017 4.5 19.9 1.0
N B:GLU958 4.6 23.7 1.0
C B:ALA957 4.7 24.1 1.0
C B:TYR959 4.8 22.2 1.0
CG B:ASN710 4.8 26.2 1.0
O B:HOH3019 4.8 20.9 1.0

Magnesium binding site 6 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 6 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2042

b:13.4
occ:1.00
 O C:HOH3036 3.1 17.8 1.0
NZ C:LYS642 3.2 12.2 1.0
N C:TYR959 3.3 18.4 1.0
O C:HOH3459 3.5 42.4 1.0
ND2 C:ASN710 3.6 18.4 1.0
CE C:LYS642 3.6 12.0 1.0
CA C:GLU958 3.8 18.3 1.0
O C:ALA957 4.0 17.6 1.0
C C:GLU958 4.0 18.1 1.0
CB C:TYR959 4.1 18.2 1.0
CG C:GLU958 4.2 20.4 1.0
CA C:TYR959 4.2 18.3 1.0
O C:HOH3257 4.2 31.7 1.0
O C:HOH3020 4.3 9.9 1.0
O C:HOH3021 4.5 12.9 1.0
O C:TYR959 4.5 18.3 1.0
CB C:GLU958 4.6 18.6 1.0
N C:GLU958 4.7 18.0 1.0
CG C:ASN710 4.8 19.4 1.0
C C:ALA957 4.8 17.9 1.0
O C:HOH3022 4.8 14.8 1.0
C C:TYR959 4.9 18.4 1.0

Magnesium binding site 7 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 7 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2043

b:16.4
occ:1.00
 O C:HOH3278 3.2 31.8 1.0
N C:TYR825 3.3 13.5 1.0
N C:GLY826 3.4 13.1 1.0
C C:GLN823 3.4 15.2 1.0
CA C:GLN823 3.5 15.3 1.0
O C:HOH3221 3.6 58.7 1.0
CB C:TYR825 3.6 12.6 1.0
N C:LEU824 3.7 14.6 1.0
CA C:TYR825 3.7 13.1 1.0
O C:HOH3226 3.8 16.5 1.0
O C:GLN823 3.9 15.0 1.0
C C:TYR825 4.0 13.4 1.0
C C:LEU824 4.2 14.0 1.0
CB C:GLN823 4.2 15.2 1.0
CA C:GLY826 4.4 13.7 1.0
CA C:LEU824 4.4 14.1 1.0
O C:LEU819 4.5 14.7 1.0
N C:GLN823 4.6 16.1 1.0
O C:LYS820 4.7 16.9 1.0
CA C:LYS820 4.7 16.2 1.0
CG C:GLN823 4.8 14.7 1.0
CG C:TYR825 4.8 12.7 1.0
CG2 C:VAL861 5.0 19.0 1.0

Magnesium binding site 8 out of 8 in 4azc

Go back to Magnesium Binding Sites List in 4azc
Magnesium binding site 8 out of 8 in the Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Differential Inhibition of the Tandem GH20 Catalytic Modules in the Pneumococcal Exo-Beta-D-N-Acetylglucosaminidase, Strh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2044

b:26.4
occ:1.00
 OH C:TYR854 2.8 14.1 1.0
NZ C:LYS865 3.1 27.8 1.0
NZ C:LYS890 3.3 20.6 1.0
CG C:GLN862 3.4 17.1 1.0
CZ C:TYR854 3.6 13.2 1.0
CE1 C:TYR854 3.6 14.3 1.0
CE C:LYS865 3.6 24.2 1.0
O C:HOH3422 3.9 44.1 1.0
CE C:LYS890 4.1 19.6 1.0
O C:HOH3276 4.1 40.7 1.0
CB C:GLN862 4.3 15.8 1.0
CD C:LYS890 4.3 18.7 1.0
CB C:ASP859 4.3 20.1 1.0
CD C:GLN862 4.5 16.6 0.5
CA C:GLN862 4.5 16.1 1.0
O C:ASP859 4.7 20.7 1.0
NE2 C:GLN862 4.8 16.8 0.2
CE2 C:TYR854 4.8 13.6 1.0
CD1 C:TYR854 4.9 12.7 1.0
OD2 C:ASP859 5.0 22.3 0.8
O C:HOH3345 5.0 40.9 1.0

Reference:

B.Pluvinage, K.A.Stubbs, D.J.Vocadlo, A.B.Boraston. Inhibition of the Family 20 Glycoside Hydrolase Catalytic Modules in the Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh. Org.Biomol.Chem. V. 11 7907 2013.
ISSN: ISSN 1477-0520
PubMed: 24132305
DOI: 10.1039/C3OB41579A
Page generated: Thu Aug 15 15:11:02 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy