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Magnesium in PDB 2j4e: The Itp Complex of Human Inosine Triphosphatase

Enzymatic activity of The Itp Complex of Human Inosine Triphosphatase

All present enzymatic activity of The Itp Complex of Human Inosine Triphosphatase:
3.6.1.19;

Protein crystallography data

The structure of The Itp Complex of Human Inosine Triphosphatase, PDB code: 2j4e was solved by P.Stenmark, P.Kursula, C.Arrowsmith, H.Berglund, R.Busam, R.Collins, A.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, B.M.Hallberg, L.Holmberg Schiavone, M.Hogbom, T.Kotenyova, R.Landry, P.Loppnau, A.Magnusdottir, P.Nilsson-Ehle, T.Nyman, D.Ogg, C.Persson, J.Sagemark, M.Sundstrom, J.Uppenberg, A.G.Thorsell, H.Schuler, S.Van Den Berg, K.Wallden, J.Weigelt, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 67.998, 75.292, 110.793, 85.12, 77.72, 69.19
R / Rfree (%) 20.1 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Itp Complex of Human Inosine Triphosphatase (pdb code 2j4e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Itp Complex of Human Inosine Triphosphatase, PDB code: 2j4e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2j4e

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Magnesium binding site 1 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:60.1
occ:1.00
 O1B A:ITT1001 1.8 56.8 1.0
O2A A:ITT1001 2.1 54.3 1.0
O3G A:ITT1001 2.4 56.4 1.0
OE2 A:GLU44 2.8 31.7 1.0
PB A:ITT1001 2.9 58.0 1.0
OE1 A:GLU44 3.0 31.9 1.0
O3B A:ITT1001 3.1 56.8 1.0
CD A:GLU44 3.2 30.9 1.0
PA A:ITT1001 3.2 54.9 1.0
PG A:ITT1001 3.2 56.9 1.0
O3A A:ITT1001 3.4 56.3 1.0
NZ A:LYS56 3.6 28.2 1.0
O2B A:ITT1001 4.2 57.5 1.0
O1A A:ITT1001 4.2 54.0 1.0
O2G A:ITT1001 4.3 57.2 1.0
CE A:LYS56 4.4 29.7 1.0
O5' A:ITT1001 4.4 54.3 1.0
O1G A:ITT1001 4.4 56.2 1.0
NZ A:LYS89 4.5 31.0 1.0
CG A:GLU44 4.6 30.4 1.0
CD A:LYS89 4.8 30.8 1.0
OD2 A:ASP72 5.0 34.3 1.0

Magnesium binding site 2 out of 8 in 2j4e

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Magnesium binding site 2 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:45.7
occ:1.00
 O1B B:ITT1001 2.0 51.9 1.0
OE2 B:GLU44 2.2 29.5 1.0
O3G B:ITT1001 2.3 51.7 1.0
O2A B:ITT1001 2.6 50.3 1.0
CD B:GLU44 3.0 28.7 1.0
PB B:ITT1001 3.2 51.6 1.0
PG B:ITT1001 3.2 51.4 1.0
OE1 B:GLU44 3.4 29.1 1.0
O3B B:ITT1001 3.5 52.0 1.0
PA B:ITT1001 3.6 51.6 1.0
O3A B:ITT1001 3.6 52.2 1.0
O1G B:ITT1001 3.7 51.8 1.0
NZ B:LYS56 3.9 26.8 1.0
CG B:GLU44 4.1 28.4 1.0
NZ B:LYS89 4.2 29.6 1.0
O5' B:ITT1001 4.4 48.9 1.0
CE B:LYS56 4.5 27.8 1.0
O2B B:ITT1001 4.5 50.8 1.0
O B:LEU42 4.5 28.2 1.0
CD B:LYS89 4.6 29.8 1.0
O2G B:ITT1001 4.7 51.9 1.0
OD2 B:ASP72 4.8 33.8 1.0
O1A B:ITT1001 4.9 49.7 1.0
OD2 B:ASP41 4.9 30.8 1.0
CE B:LYS89 4.9 29.5 1.0
OD1 B:ASP72 4.9 34.5 1.0

Magnesium binding site 3 out of 8 in 2j4e

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Magnesium binding site 3 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:55.4
occ:1.00
 O1B C:ITT1001 2.1 50.9 1.0
O3G C:ITT1001 2.5 47.1 1.0
OE2 C:GLU44 2.5 31.2 1.0
O2A C:ITT1001 3.3 52.8 1.0
CD C:GLU44 3.4 28.8 1.0
PB C:ITT1001 3.5 52.1 1.0
O C:LEU42 3.5 29.7 1.0
PG C:ITT1001 3.5 47.7 1.0
O3B C:ITT1001 3.9 49.7 1.0
OE1 C:GLU44 3.9 29.4 1.0
NZ C:LYS89 4.0 27.6 1.0
O1G C:ITT1001 4.1 48.8 1.0
NZ C:LYS56 4.2 27.5 1.0
OD2 C:ASP41 4.2 32.5 1.0
CG C:GLU44 4.2 28.3 1.0
O3A C:ITT1001 4.2 52.8 1.0
PA C:ITT1001 4.4 53.9 1.0
O2B C:ITT1001 4.6 51.4 1.0
CE C:LYS56 4.6 27.8 1.0
C C:LEU42 4.7 29.5 1.0
N C:LEU42 4.9 29.9 1.0
O2G C:ITT1001 5.0 47.8 1.0
CD C:LYS89 5.0 27.2 1.0
OD1 C:ASP72 5.0 34.8 1.0

Magnesium binding site 4 out of 8 in 2j4e

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Magnesium binding site 4 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:40.1
occ:1.00
 O5 D:POP1000 1.8 32.3 1.0
OE2 D:GLU44 2.2 33.2 1.0
O3 D:POP1000 2.3 30.6 1.0
P2 D:POP1000 3.2 33.0 1.0
CD D:GLU44 3.2 30.9 1.0
P1 D:POP1000 3.5 30.4 1.0
O D:POP1000 3.7 31.2 1.0
NZ D:LYS89 3.8 29.7 1.0
O4 D:POP1000 3.8 32.1 1.0
NZ D:LYS56 3.9 27.0 1.0
CG D:GLU44 3.9 30.7 1.0
O1P D:IMP1001 4.0 42.2 1.0
O2 D:POP1000 4.1 30.6 1.0
OE1 D:GLU44 4.1 32.9 1.0
O6 D:POP1000 4.3 31.5 1.0
O D:LEU42 4.3 30.6 1.0
CD D:LYS89 4.5 28.4 1.0
CE D:LYS56 4.5 27.6 1.0
CE D:LYS89 4.7 28.8 1.0
O1 D:POP1000 4.7 31.7 1.0
OD2 D:ASP41 4.8 33.8 1.0
O2P D:IMP1001 4.9 42.0 1.0

Magnesium binding site 5 out of 8 in 2j4e

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Magnesium binding site 5 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:73.5
occ:1.00
 OE2 E:GLU44 2.0 32.9 1.0
O1B E:ITT1001 2.0 49.6 1.0
O3G E:ITT1001 2.7 47.9 1.0
O2A E:ITT1001 2.8 51.5 1.0
CD E:GLU44 3.2 30.9 1.0
PB E:ITT1001 3.5 50.7 1.0
NZ E:LYS89 3.7 30.2 1.0
PG E:ITT1001 3.9 47.5 1.0
OE1 E:GLU44 3.9 33.0 1.0
PA E:ITT1001 4.0 50.5 1.0
NZ E:LYS56 4.1 22.5 1.0
O3A E:ITT1001 4.1 50.8 1.0
O3B E:ITT1001 4.2 49.1 1.0
CG E:GLU44 4.3 30.0 1.0
CD E:LYS89 4.3 28.8 1.0
CE E:LYS89 4.4 29.4 1.0
OD1 E:ASP72 4.5 32.5 1.0
O1G E:ITT1001 4.5 47.2 1.0
CE E:LYS56 4.6 24.3 1.0
O2B E:ITT1001 4.6 51.4 1.0
O5' E:ITT1001 4.7 47.5 1.0

Magnesium binding site 6 out of 8 in 2j4e

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Magnesium binding site 6 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1002

b:31.4
occ:1.00
 O3G F:ITT1001 2.2 44.7 1.0
O1B F:ITT1001 2.4 47.9 1.0
OE2 F:GLU44 2.6 31.1 1.0
O2A F:ITT1001 2.7 48.4 1.0
OE1 F:GLU44 2.8 29.4 1.0
CD F:GLU44 2.9 28.6 1.0
PB F:ITT1001 3.4 48.6 1.0
PG F:ITT1001 3.4 44.1 1.0
O3A F:ITT1001 3.6 48.8 1.0
PA F:ITT1001 3.6 49.4 1.0
O3B F:ITT1001 3.7 46.5 1.0
NZ F:LYS56 3.8 28.6 1.0
CG F:GLU44 4.1 28.1 1.0
O1G F:ITT1001 4.3 44.5 1.0
O5' F:ITT1001 4.5 45.8 1.0
O F:LEU42 4.5 29.6 1.0
NZ F:LYS89 4.6 28.2 1.0
CE F:LYS56 4.7 28.4 1.0
O2G F:ITT1001 4.7 44.5 1.0
OD2 F:ASP72 4.7 36.7 1.0
CD F:LYS89 4.7 28.5 1.0
O2B F:ITT1001 4.7 49.0 1.0
O1A F:ITT1001 4.9 47.8 1.0

Magnesium binding site 7 out of 8 in 2j4e

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Magnesium binding site 7 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:64.3
occ:1.00
 O1B G:ITT1001 1.9 52.8 1.0
OE2 G:GLU44 2.5 33.8 1.0
O2A G:ITT1001 3.4 52.9 1.0
O3G G:ITT1001 3.4 51.0 1.0
CD G:GLU44 3.5 32.4 1.0
PB G:ITT1001 3.5 53.0 1.0
NZ G:LYS89 3.6 32.6 1.0
CD G:LYS89 3.7 31.4 1.0
OE1 G:GLU44 3.9 33.0 1.0
PA G:ITT1001 4.1 54.5 1.0
O3A G:ITT1001 4.1 53.8 1.0
CE G:LYS89 4.1 32.2 1.0
O5' G:ITT1001 4.3 52.2 1.0
O3B G:ITT1001 4.3 52.1 1.0
O2B G:ITT1001 4.4 52.1 1.0
PG G:ITT1001 4.4 50.4 1.0
CG G:GLU44 4.7 32.5 1.0
NZ G:LYS56 4.7 25.1 1.0
CG G:LYS89 4.9 30.9 1.0
O G:HOH2009 5.0 25.4 1.0
OD1 G:ASP72 5.0 37.3 1.0

Magnesium binding site 8 out of 8 in 2j4e

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Magnesium binding site 8 out of 8 in the The Itp Complex of Human Inosine Triphosphatase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Itp Complex of Human Inosine Triphosphatase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1002

b:77.5
occ:1.00
 O1B H:ITT1001 1.6 50.4 1.0
OE2 H:GLU44 1.9 31.1 1.0
O3G H:ITT1001 2.6 50.5 1.0
O2A H:ITT1001 2.7 50.0 1.0
CD H:GLU44 3.0 30.7 1.0
PB H:ITT1001 3.1 50.8 1.0
OE1 H:GLU44 3.3 32.1 1.0
PG H:ITT1001 3.6 51.2 1.0
PA H:ITT1001 3.6 50.8 1.0
O3B H:ITT1001 3.7 51.8 1.0
O3A H:ITT1001 3.7 50.5 1.0
NZ H:LYS89 3.8 30.7 1.0
CD H:LYS89 4.0 30.4 1.0
O2B H:ITT1001 4.2 51.1 1.0
CE H:LYS89 4.3 30.6 1.0
CG H:GLU44 4.3 30.2 1.0
O5' H:ITT1001 4.4 48.8 1.0
NZ H:LYS56 4.5 30.0 1.0
O1G H:ITT1001 4.6 50.1 1.0
O2G H:ITT1001 4.8 49.8 1.0
OD2 H:ASP41 4.9 35.8 1.0

Reference:

P.Stenmark, P.Kursula, S.Flodin, S.Graslund, R.Landry, P.Nordlund, H.Schuler. Crystal Structure of Human Inosine Triphosphatase: Substrate Binding and Implication of the Inosine Triphosphatase Deficiency Mutation P32T. J.Biol.Chem. V. 282 3182 2007.
ISSN: ISSN 0021-9258
PubMed: 17138556
DOI: 10.1074/JBC.M609838200
Page generated: Wed Aug 14 00:23:36 2024

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