Atomistry » Magnesium » PDB 1bho-1c5p » 1bzy
Atomistry »
  Magnesium »
    PDB 1bho-1c5p »
      1bzy »

Magnesium in PDB 1bzy: Human Hgprtase with Transition State Inhibitor

Enzymatic activity of Human Hgprtase with Transition State Inhibitor

All present enzymatic activity of Human Hgprtase with Transition State Inhibitor:
2.4.2.8;

Protein crystallography data

The structure of Human Hgprtase with Transition State Inhibitor, PDB code: 1bzy was solved by W.Shi, C.Li, P.C.Tyler, R.H.Furneaux, C.Grubmeyer, V.L.Schramm, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.960, 102.010, 144.270, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Hgprtase with Transition State Inhibitor (pdb code 1bzy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Hgprtase with Transition State Inhibitor, PDB code: 1bzy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 1 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg900

b:12.1
occ:1.00
 O2 A:POP400 2.1 6.5 1.0
O3' A:IMU300 2.1 8.3 1.0
O A:HOH631 2.2 3.8 1.0
O A:HOH582 2.2 2.4 1.0
O2' A:IMU300 2.3 7.7 1.0
O5 A:POP400 2.5 7.5 1.0
C3' A:IMU300 3.1 8.1 1.0
C2' A:IMU300 3.2 10.2 1.0
P1 A:POP400 3.4 5.1 1.0
O A:POP400 3.4 7.5 1.0
P2 A:POP400 3.4 9.3 1.0
OD2 A:ASP134 3.8 9.6 1.0
O4 A:POP400 4.0 10.2 1.0
C4' A:IMU300 4.0 2.4 1.0
C1' A:IMU300 4.0 9.4 1.0
OD1 A:ASP134 4.1 6.9 1.0
N A:GLY69 4.1 9.6 1.0
OE2 A:GLU133 4.2 3.7 1.0
OE1 A:GLU133 4.2 7.2 1.0
O3 A:POP400 4.2 5.0 1.0
O A:LEU67 4.2 9.5 1.0
CA A:GLY69 4.3 9.4 1.0
CG A:ASP134 4.3 8.9 1.0
N4' A:IMU300 4.3 9.5 1.0
O1 A:POP400 4.4 6.8 1.0
O A:LEU101 4.4 7.9 1.0
O A:HOH607 4.5 2.8 1.0
O A:HOH706 4.5 12.5 1.0
CD A:GLU133 4.6 2.0 1.0
N A:LYS68 4.6 7.5 1.0
C A:LEU67 4.7 6.6 1.0
O6 A:POP400 4.8 13.5 1.0
CG1 A:VAL66 4.9 3.8 1.0
MG A:MG901 4.9 12.9 1.0

Magnesium binding site 2 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 2 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:12.9
occ:1.00
 O A:HOH630 2.1 6.0 1.0
O4 A:POP400 2.1 10.2 1.0
OD1 A:ASP193 2.1 8.3 1.0
O3 A:POP400 2.2 5.0 1.0
O A:HOH706 2.2 12.5 1.0
O A:HOH657 2.3 6.3 1.0
P1 A:POP400 3.2 5.1 1.0
P2 A:POP400 3.2 9.3 1.0
CG A:ASP193 3.2 9.4 1.0
O A:POP400 3.3 7.5 1.0
OD2 A:ASP193 3.6 8.4 1.0
O2 A:POP400 4.0 6.5 1.0
NH2 A:ARG199 4.1 7.6 1.0
O A:HOH722 4.2 17.6 1.0
O A:ASP193 4.2 10.1 1.0
O2' A:IMU300 4.2 7.7 1.0
O6 A:POP400 4.2 13.5 1.0
N3 A:IMU300 4.2 6.6 1.0
O5 A:POP400 4.2 7.5 1.0
NH1 A:ARG199 4.3 2.5 1.0
O1 A:POP400 4.4 6.8 1.0
O A:HOH721 4.4 6.8 1.0
C1' A:IMU300 4.4 9.4 1.0
N A:ASP193 4.5 7.1 1.0
CB A:ASP193 4.5 4.4 1.0
CZ A:ARG199 4.6 6.6 1.0
C A:ASP193 4.6 6.4 1.0
CB A:TYR104 4.7 7.2 1.0
CA A:ASP193 4.8 6.7 1.0
MG A:MG900 4.9 12.1 1.0
C2' A:IMU300 5.0 10.2 1.0
N2 A:IMU300 5.0 5.5 1.0

Magnesium binding site 3 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 3 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg900

b:6.4
occ:1.00
 O2 B:POP400 2.1 8.5 1.0
O3' B:IMU300 2.1 12.9 1.0
O B:HOH577 2.2 6.7 1.0
O2' B:IMU300 2.3 12.9 1.0
O B:HOH635 2.3 8.1 1.0
O5 B:POP400 2.4 20.7 1.0
C3' B:IMU300 3.1 11.7 1.0
C2' B:IMU300 3.1 11.5 1.0
P2 B:POP400 3.2 19.2 1.0
O B:POP400 3.2 13.6 1.0
P1 B:POP400 3.3 9.5 1.0
O4 B:POP400 3.8 21.8 1.0
C4' B:IMU300 3.9 8.5 1.0
C1' B:IMU300 3.9 12.9 1.0
OD2 B:ASP134 4.0 5.1 1.0
N4' B:IMU300 4.1 13.4 1.0
N B:GLY69 4.2 4.5 1.0
OE2 B:GLU133 4.2 8.4 1.0
OD1 B:ASP134 4.2 10.5 1.0
O1 B:POP400 4.3 11.6 1.0
O3 B:POP400 4.3 10.8 1.0
OE1 B:GLU133 4.3 8.1 1.0
O B:HOH655 4.3 6.8 1.0
O B:LEU101 4.3 6.2 1.0
O B:HOH588 4.3 10.1 1.0
O B:LEU67 4.3 6.3 1.0
CG B:ASP134 4.5 13.3 1.0
CA B:GLY69 4.5 5.2 1.0
N B:LYS68 4.6 5.7 1.0
MG B:MG901 4.6 11.4 1.0
CD B:GLU133 4.6 10.2 1.0
O6 B:POP400 4.6 15.2 1.0
C B:LEU67 4.7 4.5 1.0

Magnesium binding site 4 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 4 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:11.4
occ:1.00
 O3 B:POP400 2.1 10.8 1.0
O4 B:POP400 2.2 21.8 1.0
OD1 B:ASP193 2.2 8.6 1.0
O B:HOH655 2.2 6.8 1.0
O B:HOH704 2.2 17.7 1.0
O B:HOH597 2.4 10.9 1.0
P1 B:POP400 3.0 9.5 1.0
O B:POP400 3.1 13.6 1.0
P2 B:POP400 3.2 19.2 1.0
CG B:ASP193 3.2 5.3 1.0
O2 B:POP400 3.6 8.5 1.0
OD2 B:ASP193 3.6 6.0 1.0
NH2 B:ARG199 4.0 6.4 1.0
NH1 B:ARG199 4.0 3.8 1.0
O B:HOH570 4.1 11.1 1.0
O2' B:IMU300 4.1 12.9 1.0
O6 B:POP400 4.2 15.2 1.0
O5 B:POP400 4.2 20.7 1.0
O B:ASP193 4.3 8.1 1.0
O1 B:POP400 4.3 11.6 1.0
N3 B:IMU300 4.3 12.5 1.0
C1' B:IMU300 4.4 12.9 1.0
CZ B:ARG199 4.5 5.2 1.0
O B:HOH646 4.5 12.3 1.0
N B:ASP193 4.5 6.7 1.0
CB B:ASP193 4.5 6.3 1.0
MG B:MG900 4.6 6.4 1.0
C B:ASP193 4.8 7.2 1.0
CB B:TYR104 4.8 11.0 1.0
CA B:ASP193 4.9 7.3 1.0
C2' B:IMU300 4.9 11.5 1.0

Magnesium binding site 5 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 5 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg900

b:25.4
occ:1.00
 O2 C:POP400 2.1 19.8 1.0
O3' C:IMU300 2.2 20.5 1.0
O C:HOH654 2.2 10.2 1.0
O C:HOH757 2.2 15.7 1.0
O5 C:POP400 2.4 21.1 1.0
O2' C:IMU300 2.5 25.6 1.0
C3' C:IMU300 3.2 23.0 1.0
C2' C:IMU300 3.3 23.5 1.0
P1 C:POP400 3.4 22.7 1.0
P2 C:POP400 3.5 22.3 1.0
O C:POP400 3.6 24.3 1.0
OE2 C:GLU133 3.9 22.3 1.0
OD2 C:ASP134 3.9 15.6 1.0
OD1 C:ASP134 4.0 11.9 1.0
N C:GLY69 4.0 10.5 1.0
C4' C:IMU300 4.1 23.2 1.0
O1 C:POP400 4.1 27.2 1.0
C1' C:IMU300 4.1 21.5 1.0
OE1 C:GLU133 4.1 22.9 1.0
O4 C:POP400 4.2 19.7 1.0
O C:LEU67 4.2 18.9 1.0
O C:LEU101 4.3 18.7 1.0
CG C:ASP134 4.3 10.3 1.0
CA C:GLY69 4.3 9.2 1.0
CD C:GLU133 4.4 19.9 1.0
N C:LYS68 4.4 13.9 1.0
N4' C:IMU300 4.5 24.0 1.0
O3 C:POP400 4.6 20.7 1.0
C C:LEU67 4.6 13.1 1.0
O C:HOH640 4.6 10.8 1.0
CG1 C:VAL66 4.7 11.8 1.0
O C:HOH596 4.7 8.1 1.0
MG C:MG901 4.8 29.6 1.0
O6 C:POP400 4.8 23.8 1.0
O C:VAL66 4.8 16.2 1.0

Magnesium binding site 6 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 6 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:29.6
occ:1.00
 OD1 C:ASP193 2.2 10.6 1.0
O C:HOH586 2.2 17.2 1.0
O4 C:POP400 2.2 19.7 1.0
O3 C:POP400 2.3 20.7 1.0
O C:HOH640 2.3 10.8 1.0
O C:HOH698 2.5 30.4 1.0
P1 C:POP400 2.9 22.7 1.0
O C:POP400 2.9 24.3 1.0
P2 C:POP400 3.1 22.3 1.0
O2 C:POP400 3.3 19.8 1.0
CG C:ASP193 3.3 14.0 1.0
OD2 C:ASP193 3.7 12.5 1.0
O5 C:POP400 4.0 21.1 1.0
NH1 C:ARG199 4.1 14.0 1.0
NH2 C:ARG199 4.1 13.6 1.0
O2' C:IMU300 4.2 25.6 1.0
N3 C:IMU300 4.2 21.0 1.0
O6 C:POP400 4.3 23.8 1.0
O1 C:POP400 4.3 27.2 1.0
C1' C:IMU300 4.5 21.5 1.0
N C:ASP193 4.5 12.1 1.0
CB C:ASP193 4.5 12.0 1.0
O C:ASP193 4.5 13.2 1.0
CZ C:ARG199 4.6 16.4 1.0
O C:HOH752 4.6 14.0 1.0
MG C:MG900 4.8 25.4 1.0
CA C:ASP193 4.8 12.7 1.0
C C:ASP193 4.8 12.0 1.0
CB C:TYR104 4.9 24.3 1.0
N2 C:IMU300 4.9 24.2 1.0
NZ C:LYS102 5.0 25.3 1.0
C2' C:IMU300 5.0 23.5 1.0

Magnesium binding site 7 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 7 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg900

b:12.7
occ:1.00
 O2 D:POP400 2.1 6.3 1.0
O3' D:IMU300 2.1 4.8 1.0
O D:HOH653 2.2 10.5 1.0
O D:HOH659 2.3 3.3 1.0
O2' D:IMU300 2.3 8.6 1.0
O5 D:POP400 2.5 8.6 1.0
C3' D:IMU300 3.1 5.5 1.0
C2' D:IMU300 3.2 9.0 1.0
P2 D:POP400 3.4 9.3 1.0
P1 D:POP400 3.4 9.4 1.0
O D:POP400 3.4 13.8 1.0
O4 D:POP400 3.9 11.7 1.0
C4' D:IMU300 3.9 10.7 1.0
C1' D:IMU300 4.0 8.5 1.0
OD2 D:ASP134 4.0 5.8 1.0
OD1 D:ASP134 4.1 6.8 1.0
OE2 D:GLU133 4.1 7.9 1.0
O D:HOH549 4.2 3.5 1.0
OE1 D:GLU133 4.2 9.4 1.0
O D:LEU67 4.2 12.6 1.0
O3 D:POP400 4.2 7.7 1.0
N D:GLY69 4.3 10.2 1.0
N4' D:IMU300 4.3 11.3 1.0
O D:LEU101 4.4 13.5 1.0
O1 D:POP400 4.4 4.8 1.0
CG D:ASP134 4.5 6.6 1.0
CA D:GLY69 4.5 9.1 1.0
O D:HOH751 4.5 9.2 1.0
CD D:GLU133 4.6 9.5 1.0
N D:LYS68 4.6 12.1 1.0
C D:LEU67 4.7 10.3 1.0
CG1 D:VAL66 4.7 9.4 1.0
O6 D:POP400 4.8 13.4 1.0
O D:VAL66 4.9 12.5 1.0

Magnesium binding site 8 out of 8 in 1bzy

Go back to Magnesium Binding Sites List in 1bzy
Magnesium binding site 8 out of 8 in the Human Hgprtase with Transition State Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Hgprtase with Transition State Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:10.8
occ:1.00
 O4 D:POP400 2.2 11.7 1.0
O D:HOH627 2.2 3.5 1.0
O D:HOH751 2.2 9.2 1.0
OD1 D:ASP193 2.3 8.6 1.0
O D:HOH770 2.3 11.8 1.0
O3 D:POP400 2.3 7.7 1.0
CG D:ASP193 3.3 13.2 1.0
P2 D:POP400 3.3 9.3 1.0
P1 D:POP400 3.4 9.4 1.0
O D:POP400 3.4 13.8 1.0
OD2 D:ASP193 3.6 11.8 1.0
O D:ASP193 4.1 6.5 1.0
N3 D:IMU300 4.1 10.9 1.0
O2 D:POP400 4.2 6.3 1.0
NH2 D:ARG199 4.2 3.9 1.0
O6 D:POP400 4.2 13.4 1.0
NH1 D:ARG199 4.3 5.4 1.0
O2' D:IMU300 4.3 8.6 1.0
O5 D:POP400 4.4 8.6 1.0
C1' D:IMU300 4.4 8.5 1.0
O D:HOH581 4.5 21.2 1.0
N D:ASP193 4.5 10.8 1.0
O1 D:POP400 4.5 4.8 1.0
CB D:ASP193 4.6 9.2 1.0
C D:ASP193 4.6 9.5 1.0
CB D:TYR104 4.6 12.8 1.0
CZ D:ARG199 4.6 6.0 1.0
CA D:ASP193 4.8 9.4 1.0
N2 D:IMU300 4.9 5.8 1.0
C4 D:IMU300 5.0 12.7 1.0
C2' D:IMU300 5.0 9.0 1.0
C2 D:IMU300 5.0 8.7 1.0

Reference:

W.Shi, C.M.Li, P.C.Tyler, R.H.Furneaux, C.Grubmeyer, V.L.Schramm, S.C.Almo. The 2.0 A Structure of Human Hypoxanthine-Guanine Phosphoribosyltransferase in Complex with A Transition-State Analog Inhibitor. Nat.Struct.Biol. V. 6 588 1999.
ISSN: ISSN 1072-8368
PubMed: 10360366
DOI: 10.1038/9376
Page generated: Tue Aug 13 02:16:39 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