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Magnesium in PDB 1cjb: Malarial Purine Phosphoribosyltransferase

Enzymatic activity of Malarial Purine Phosphoribosyltransferase

All present enzymatic activity of Malarial Purine Phosphoribosyltransferase:
2.4.2.8;

Protein crystallography data

The structure of Malarial Purine Phosphoribosyltransferase, PDB code: 1cjb was solved by W.Shi, C.M.Li, P.C.Tyler, R.H.Furneaux, S.M.Cahill, M.E.Girvin, 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) 20.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 105.490, 110.390, 173.700, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Malarial Purine Phosphoribosyltransferase (pdb code 1cjb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Malarial Purine Phosphoribosyltransferase, PDB code: 1cjb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1cjb

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Magnesium binding site 1 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:26.4
occ:1.00
O A:HOH516 2.0 21.1 1.0
O2 A:POP400 2.1 22.9 1.0
O3' A:IRP300 2.2 22.9 1.0
O2' A:IRP300 2.3 23.9 1.0
O A:HOH603 2.3 25.3 1.0
O5 A:POP400 2.4 25.5 1.0
C3' A:IRP300 3.1 23.7 1.0
C2' A:IRP300 3.2 24.9 1.0
O A:POP400 3.3 24.2 1.0
P2 A:POP400 3.3 24.0 1.0
P1 A:POP400 3.3 23.4 1.0
O4 A:POP400 3.9 24.5 1.0
C4' A:IRP300 3.9 23.1 1.0
C1' A:IRP300 3.9 23.2 1.0
OD2 A:ASP145 4.0 25.4 1.0
O A:VAL113 4.1 32.8 1.0
OD1 A:ASP145 4.1 23.9 1.0
O A:HOH543 4.2 18.6 1.0
N4' A:IRP300 4.2 23.6 1.0
N A:GLY78 4.3 26.0 1.0
OE1 A:GLU144 4.3 35.3 1.0
O3 A:POP400 4.3 23.6 1.0
O A:LEU76 4.3 27.3 1.0
OE2 A:GLU144 4.4 34.5 1.0
O1 A:POP400 4.4 26.2 1.0
O A:HOH616 4.4 22.4 1.0
CG A:ASP145 4.5 26.1 1.0
CA A:GLY78 4.6 24.1 1.0
N A:LYS77 4.6 26.3 1.0
O A:LEU75 4.6 27.4 1.0
O6 A:POP400 4.7 22.6 1.0
CD A:GLU144 4.7 34.6 1.0
C A:LEU76 4.7 27.4 1.0

Magnesium binding site 2 out of 8 in 1cjb

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Magnesium binding site 2 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:27.8
occ:1.00
OD1 A:ASP204 2.1 19.6 1.0
O A:HOH616 2.1 22.4 1.0
O A:HOH664 2.2 29.0 1.0
O3 A:POP400 2.2 23.6 1.0
O4 A:POP400 2.2 24.5 1.0
O A:HOH542 2.3 29.7 1.0
CG A:ASP204 3.1 21.0 1.0
P1 A:POP400 3.3 23.4 1.0
P2 A:POP400 3.4 24.0 1.0
O A:POP400 3.5 24.2 1.0
OD2 A:ASP204 3.5 24.5 1.0
O2 A:POP400 4.0 22.9 1.0
N3 A:IRP300 4.1 18.5 1.0
O A:ASP204 4.1 23.0 1.0
NH2 A:ARG210 4.2 18.9 1.0
O2' A:IRP300 4.3 23.9 1.0
O6 A:POP400 4.4 22.6 1.0
C1' A:IRP300 4.4 23.2 1.0
O A:HOH550 4.4 27.9 1.0
O5 A:POP400 4.4 25.5 1.0
NH1 A:ARG210 4.4 16.0 1.0
CB A:ASP204 4.4 20.3 1.0
N A:ASP204 4.5 18.7 1.0
O1 A:POP400 4.5 26.2 1.0
C A:ASP204 4.6 25.2 1.0
CZ A:ARG210 4.7 19.7 1.0
CB A:TYR116 4.7 27.5 1.0
CA A:ASP204 4.7 21.8 1.0
C4 A:IRP300 4.9 19.5 1.0
C2 A:IRP300 4.9 19.8 1.0
O A:HOH613 4.9 21.5 1.0
C9 A:IRP300 5.0 23.6 1.0
C2' A:IRP300 5.0 24.9 1.0

Magnesium binding site 3 out of 8 in 1cjb

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Magnesium binding site 3 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:26.3
occ:1.00
O2 B:POP400 2.1 25.1 1.0
O B:HOH547 2.2 19.6 1.0
O3' B:IRP300 2.2 27.5 1.0
O B:HOH557 2.2 24.0 1.0
O6 B:POP400 2.3 24.3 1.0
O2' B:IRP300 2.3 23.2 1.0
O B:POP400 3.1 22.5 1.0
C3' B:IRP300 3.2 24.2 1.0
C2' B:IRP300 3.2 22.1 1.0
P1 B:POP400 3.2 23.8 1.0
P2 B:POP400 3.3 22.7 1.0
O5 B:POP400 3.9 23.9 1.0
C1' B:IRP300 3.9 18.7 1.0
OD2 B:ASP145 4.0 22.8 1.0
O B:HOH723 4.0 25.2 1.0
C4' B:IRP300 4.0 22.2 1.0
OD1 B:ASP145 4.2 22.0 1.0
O3 B:POP400 4.2 28.7 1.0
O B:LEU76 4.2 25.5 1.0
O1 B:POP400 4.2 23.4 1.0
N4' B:IRP300 4.2 25.6 1.0
OE1 B:GLU144 4.3 29.7 1.0
OE2 B:GLU144 4.3 25.2 1.0
O B:VAL113 4.3 25.6 1.0
N B:GLY78 4.4 24.9 1.0
O B:HOH548 4.4 20.5 1.0
CG B:ASP145 4.5 25.0 1.0
O4 B:POP400 4.5 24.3 1.0
O B:LEU75 4.6 25.5 1.0
N B:LYS77 4.6 25.6 1.0
C B:LEU76 4.7 25.1 1.0
CD B:GLU144 4.7 24.4 1.0
CA B:GLY78 4.7 27.0 1.0
MG B:MG406 4.9 27.7 1.0

Magnesium binding site 4 out of 8 in 1cjb

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Magnesium binding site 4 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:27.7
occ:1.00
O B:HOH552 2.0 23.6 1.0
OD1 B:ASP204 2.1 23.1 1.0
O B:HOH548 2.2 20.5 1.0
O3 B:POP400 2.2 28.7 1.0
O5 B:POP400 2.2 23.9 1.0
O B:HOH507 2.3 19.7 1.0
CG B:ASP204 3.2 24.8 1.0
P1 B:POP400 3.3 23.8 1.0
P2 B:POP400 3.4 22.7 1.0
O B:POP400 3.6 22.5 1.0
OD2 B:ASP204 3.6 24.2 1.0
O2 B:POP400 3.9 25.1 1.0
N3 B:IRP300 3.9 17.4 1.0
NH2 B:ARG210 4.1 15.9 1.0
O B:ASP204 4.2 23.2 1.0
NH1 B:ARG210 4.2 16.4 1.0
C1' B:IRP300 4.2 18.7 1.0
O2' B:IRP300 4.3 23.2 1.0
O B:HOH500 4.3 18.2 1.0
N B:ASP204 4.4 23.1 1.0
O6 B:POP400 4.4 24.3 1.0
O4 B:POP400 4.4 24.3 1.0
CB B:ASP204 4.5 17.9 1.0
O1 B:POP400 4.6 23.4 1.0
C B:ASP204 4.6 24.2 1.0
CZ B:ARG210 4.6 17.3 1.0
C4 B:IRP300 4.7 18.1 1.0
C2 B:IRP300 4.7 23.3 1.0
CA B:ASP204 4.7 22.1 1.0
C9 B:IRP300 4.8 19.7 1.0
MG B:MG405 4.9 26.3 1.0
CB B:TYR116 4.9 20.1 1.0
C2' B:IRP300 4.9 22.1 1.0

Magnesium binding site 5 out of 8 in 1cjb

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Magnesium binding site 5 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:26.9
occ:1.00
O2 C:POP400 2.1 22.2 1.0
O3' C:IRP300 2.2 18.2 1.0
O C:HOH641 2.2 20.5 1.0
O C:HOH651 2.2 20.3 1.0
O5 C:POP400 2.3 27.8 1.0
O2' C:IRP300 2.3 22.5 1.0
C3' C:IRP300 3.2 24.5 1.0
C2' C:IRP300 3.3 21.5 1.0
P2 C:POP400 3.3 24.0 1.0
P1 C:POP400 3.4 23.9 1.0
O C:POP400 3.4 24.7 1.0
O4 C:POP400 4.0 24.2 1.0
OD1 C:ASP145 4.0 30.8 1.0
C1' C:IRP300 4.1 22.4 1.0
C4' C:IRP300 4.1 23.8 1.0
OD2 C:ASP145 4.1 32.8 1.0
OE1 C:GLU144 4.1 32.0 1.0
O C:LEU76 4.2 25.4 1.0
N C:GLY78 4.2 21.6 1.0
O C:HOH534 4.2 24.6 1.0
OE2 C:GLU144 4.2 32.2 1.0
O1 C:POP400 4.3 23.3 1.0
O C:VAL113 4.3 30.1 1.0
O C:HOH535 4.3 34.9 1.0
O3 C:POP400 4.4 23.1 1.0
N4' C:IRP300 4.4 27.6 1.0
CA C:GLY78 4.5 20.2 1.0
CG C:ASP145 4.5 31.5 1.0
O C:LEU75 4.5 27.8 1.0
N C:LYS77 4.5 22.8 1.0
CD C:GLU144 4.6 30.8 1.0
C C:LEU76 4.6 23.6 1.0
O6 C:POP400 4.6 24.4 1.0
MG C:MG406 5.0 23.7 1.0

Magnesium binding site 6 out of 8 in 1cjb

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Magnesium binding site 6 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg406

b:23.7
occ:1.00
O C:HOH585 2.0 22.2 1.0
O4 C:POP400 2.1 24.2 1.0
OD1 C:ASP204 2.2 29.3 1.0
O3 C:POP400 2.2 23.1 1.0
O C:HOH554 2.3 24.5 1.0
O C:HOH535 2.3 34.9 1.0
P1 C:POP400 3.2 23.9 1.0
CG C:ASP204 3.2 26.7 1.0
P2 C:POP400 3.2 24.0 1.0
O C:POP400 3.2 24.7 1.0
OD2 C:ASP204 3.5 23.1 1.0
O2 C:POP400 3.8 22.2 1.0
NH2 C:ARG210 4.1 22.3 1.0
N3 C:IRP300 4.2 20.3 1.0
O5 C:POP400 4.2 27.8 1.0
O2' C:IRP300 4.3 22.5 1.0
NH1 C:ARG210 4.3 17.2 1.0
O6 C:POP400 4.3 24.4 1.0
O C:ASP204 4.3 26.7 1.0
O C:HOH576 4.3 26.1 1.0
O C:HOH531 4.4 29.3 1.0
C1' C:IRP300 4.4 22.4 1.0
O1 C:POP400 4.4 23.3 1.0
N C:ASP204 4.5 23.0 1.0
CB C:ASP204 4.5 21.3 1.0
CZ C:ARG210 4.6 23.4 1.0
C C:ASP204 4.7 22.2 1.0
CB C:TYR116 4.8 24.3 1.0
CA C:ASP204 4.8 22.9 1.0
O C:HOH867 4.8 43.5 1.0
C4 C:IRP300 4.9 22.0 1.0
C2 C:IRP300 5.0 22.4 1.0
MG C:MG405 5.0 26.9 1.0

Magnesium binding site 7 out of 8 in 1cjb

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Magnesium binding site 7 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg405

b:29.2
occ:1.00
O2 D:POP400 2.1 30.0 1.0
O D:HOH685 2.1 21.8 1.0
O3' D:IRP300 2.2 22.1 1.0
O D:HOH562 2.2 28.9 1.0
O2' D:IRP300 2.3 24.5 1.0
O5 D:POP400 2.4 26.5 1.0
C3' D:IRP300 3.2 25.0 1.0
C2' D:IRP300 3.2 24.4 1.0
O D:POP400 3.3 29.5 1.0
P2 D:POP400 3.3 28.2 1.0
P1 D:POP400 3.3 29.2 1.0
O4 D:POP400 3.9 26.9 1.0
C1' D:IRP300 4.0 26.2 1.0
OD2 D:ASP145 4.0 27.6 1.0
C4' D:IRP300 4.1 24.8 1.0
OD1 D:ASP145 4.1 27.7 1.0
OE2 D:GLU144 4.2 27.3 1.0
O3 D:POP400 4.2 24.9 1.0
O D:HOH517 4.2 24.8 1.0
O D:VAL113 4.3 35.0 1.0
OE1 D:GLU144 4.3 27.9 1.0
N D:GLY78 4.3 25.3 1.0
O1 D:POP400 4.3 29.8 1.0
O D:LEU76 4.3 27.8 1.0
N4' D:IRP300 4.3 27.4 1.0
O D:HOH638 4.4 23.4 1.0
CG D:ASP145 4.5 25.7 1.0
CD D:GLU144 4.6 28.7 1.0
CA D:GLY78 4.6 21.1 1.0
N D:LYS77 4.6 26.6 1.0
O D:LEU75 4.7 23.4 1.0
O6 D:POP400 4.7 22.9 1.0
C D:LEU76 4.8 27.9 1.0
MG D:MG406 5.0 32.9 1.0

Magnesium binding site 8 out of 8 in 1cjb

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Magnesium binding site 8 out of 8 in the Malarial Purine Phosphoribosyltransferase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Malarial Purine Phosphoribosyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg406

b:32.9
occ:1.00
O D:HOH612 2.2 34.8 1.0
OD1 D:ASP204 2.2 27.8 1.0
O4 D:POP400 2.2 26.9 1.0
O D:HOH517 2.3 24.8 1.0
O D:HOH596 2.3 36.5 1.0
O3 D:POP400 2.3 24.9 1.0
CG D:ASP204 3.2 27.0 1.0
P1 D:POP400 3.4 29.2 1.0
P2 D:POP400 3.4 28.2 1.0
O D:POP400 3.5 29.5 1.0
OD2 D:ASP204 3.6 27.5 1.0
N3 D:IRP300 4.0 25.3 1.0
O2 D:POP400 4.0 30.0 1.0
O D:ASP204 4.1 21.8 1.0
NH2 D:ARG210 4.2 25.7 1.0
O D:HOH621 4.3 22.9 1.0
O2' D:IRP300 4.3 24.5 1.0
C1' D:IRP300 4.3 26.2 1.0
NH1 D:ARG210 4.4 28.3 1.0
N D:ASP204 4.4 24.8 1.0
O5 D:POP400 4.4 26.5 1.0
O6 D:POP400 4.4 22.9 1.0
CB D:ASP204 4.5 21.0 1.0
C D:ASP204 4.6 26.4 1.0
O1 D:POP400 4.6 29.8 1.0
CZ D:ARG210 4.7 28.9 1.0
CA D:ASP204 4.7 22.8 1.0
C4 D:IRP300 4.8 25.5 1.0
C2 D:IRP300 4.8 24.3 1.0
CB D:TYR116 4.8 31.6 1.0
O D:HOH892 4.9 40.2 1.0
C9 D:IRP300 4.9 24.2 1.0
C2' D:IRP300 5.0 24.4 1.0
MG D:MG405 5.0 29.2 1.0
O D:HOH894 5.0 35.6 1.0

Reference:

W.Shi, C.M.Li, P.C.Tyler, R.H.Furneaux, S.M.Cahill, M.E.Girvin, C.Grubmeyer, V.L.Schramm, S.C.Almo. The 2.0 A Structure of Malarial Purine Phosphoribosyltransferase in Complex with A Transition-State Analogue Inhibitor. Biochemistry V. 38 9872 1999.
ISSN: ISSN 0006-2960
PubMed: 10433693
DOI: 10.1021/BI990664P
Page generated: Tue Aug 13 02:29:04 2024

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