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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

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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

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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

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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

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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

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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

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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

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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

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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

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