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Magnesium in PDB 3c9r: Aathil Complexed with Atp

Enzymatic activity of Aathil Complexed with Atp

All present enzymatic activity of Aathil Complexed with Atp:
2.7.4.16;

Protein crystallography data

The structure of Aathil Complexed with Atp, PDB code: 3c9r was solved by K.M.Mcculloch, C.Kinsland, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.83 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.290, 67.140, 200.700, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aathil Complexed with Atp (pdb code 3c9r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Aathil Complexed with Atp, PDB code: 3c9r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 1 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:27.8
occ:1.00
 OD2 A:ASP71 2.4 46.6 1.0
OD2 A:ASP43 2.4 66.3 1.0
O2G B:ATP307 2.4 30.4 1.0
O3G B:ATP307 2.6 30.4 1.0
PG B:ATP307 2.8 30.4 1.0
O3B B:ATP307 2.8 30.4 1.0
OD1 A:ASP71 2.9 43.7 1.0
CG A:ASP71 3.0 46.7 1.0
CG A:ASP43 3.1 64.0 1.0
OD1 A:ASP43 3.1 64.2 1.0
MG A:MG310 3.5 27.8 1.0
O A:HOH313 3.8 54.1 1.0
O2B B:ATP307 3.9 30.4 1.0
MG A:MG311 3.9 27.8 1.0
PB B:ATP307 4.0 30.4 1.0
O A:HOH317 4.1 50.3 1.0
O1G B:ATP307 4.3 30.4 1.0
O A:VAL67 4.3 41.9 1.0
OD2 A:ASP207 4.4 60.0 1.0
OG A:SER209 4.4 66.7 1.0
CG1 A:VAL67 4.4 55.1 1.0
CB A:ASP71 4.5 43.2 1.0
CB A:ASP43 4.5 63.4 1.0
OD1 A:ASP207 4.7 60.0 1.0
CB A:SER209 4.7 63.3 1.0
O1B B:ATP307 5.0 30.4 1.0
CG A:ASP207 5.0 61.9 1.0

Magnesium binding site 2 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 2 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:27.8
occ:1.00
 OD1 A:ASP207 2.3 60.0 1.0
O2G B:ATP307 2.3 30.4 1.0
OD1 A:ASP71 2.4 43.7 1.0
O2B B:ATP307 2.4 30.4 1.0
OD1 A:ASP27 2.5 46.2 1.0
PB B:ATP307 3.2 30.4 1.0
CG A:ASP207 3.3 61.9 1.0
O3B B:ATP307 3.4 30.4 1.0
PG B:ATP307 3.4 30.4 1.0
MG A:MG309 3.5 27.8 1.0
CG A:ASP27 3.5 47.9 1.0
CG A:ASP71 3.6 46.7 1.0
O1B B:ATP307 3.6 30.4 1.0
OD2 A:ASP207 3.6 60.0 1.0
CB A:ASP27 3.9 46.6 1.0
NH2 A:ARG142 3.9 64.2 1.0
O1G B:ATP307 4.2 30.4 1.0
OD2 A:ASP71 4.2 46.6 1.0
O A:ASP207 4.2 41.8 1.0
CB A:SER209 4.4 63.3 1.0
CA A:ASP27 4.4 44.6 1.0
N A:ASP207 4.5 39.9 1.0
CB A:ASP207 4.6 60.6 1.0
OD2 A:ASP27 4.6 51.0 1.0
O3G B:ATP307 4.7 30.4 1.0
CB A:ASP71 4.7 43.2 1.0
O3A B:ATP307 4.7 30.4 1.0
C A:ASP207 4.8 40.4 1.0
CA A:ASP207 4.9 40.3 1.0
CA A:ASP71 4.9 35.0 1.0

Magnesium binding site 3 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 3 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:27.8
occ:1.00
 O1A B:ATP307 2.5 30.4 1.0
O A:HOH313 2.6 54.1 1.0
O3B B:ATP307 2.7 30.4 1.0
OD1 A:ASP43 2.7 64.2 1.0
ND2 B:ASN119 2.7 45.5 1.0
O3G B:ATP307 2.8 30.4 1.0
PG B:ATP307 3.2 30.4 1.0
PA B:ATP307 3.6 30.4 1.0
O3A B:ATP307 3.7 30.4 1.0
CG A:ASP43 3.8 64.0 1.0
PB B:ATP307 3.9 30.4 1.0
MG A:MG309 3.9 27.8 1.0
CG B:ASN119 3.9 45.9 1.0
O1G B:ATP307 3.9 30.4 1.0
O B:HOH322 4.0 48.1 1.0
O A:THR42 4.3 40.1 1.0
O2A B:ATP307 4.4 30.4 1.0
OD2 A:ASP43 4.4 66.3 1.0
OD1 B:ASN119 4.5 47.4 1.0
O2G B:ATP307 4.6 30.4 1.0
O1B B:ATP307 4.6 30.4 1.0
MG A:MG312 4.7 27.8 1.0
CA A:ASP43 4.9 44.7 1.0
CB A:ASP43 4.9 63.4 1.0
O5' B:ATP307 4.9 30.4 1.0
O2B B:ATP307 4.9 30.4 1.0

Magnesium binding site 4 out of 8 in 3c9r

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Magnesium binding site 4 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:27.8
occ:1.00
 OD1 A:ASP210 2.5 57.3 1.0
O1G B:ATP307 2.5 30.4 1.0
OD2 A:ASP210 2.8 56.3 1.0
CG A:ASP210 3.0 55.8 1.0
PG B:ATP307 3.6 30.4 1.0
O3G B:ATP307 3.7 30.4 1.0
OG A:SER209 4.4 66.7 1.0
CB A:ASP210 4.5 53.7 1.0
O3B B:ATP307 4.7 30.4 1.0
OE1 A:GLU8 4.7 82.3 1.0
MG A:MG311 4.7 27.8 1.0
O1B B:ATP307 4.7 30.4 1.0
O2A B:ATP307 4.7 30.4 1.0
CB A:SER209 4.7 63.3 1.0
O2G B:ATP307 4.9 30.4 1.0

Magnesium binding site 5 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 5 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg309

b:27.8
occ:1.00
 OD1 B:ASP71 2.3 45.7 1.0
O3G A:ATP307 2.3 30.4 1.0
O A:HOH368 2.3 25.1 1.0
OD1 B:ASP207 2.4 66.8 1.0
O2B A:ATP307 2.4 30.4 1.0
OD2 B:ASP27 2.5 51.2 1.0
PB A:ATP307 3.2 30.4 1.0
MG B:MG310 3.3 27.8 1.0
CG B:ASP207 3.4 66.1 1.0
CG B:ASP71 3.5 49.5 1.0
CG B:ASP27 3.5 52.6 1.0
OD2 B:ASP207 3.6 66.5 1.0
PG A:ATP307 3.8 30.4 1.0
CB B:ASP27 3.9 51.8 1.0
O3B A:ATP307 3.9 30.4 1.0
O1B A:ATP307 3.9 30.4 1.0
NH2 B:ARG142 4.0 73.3 1.0
OD2 B:ASP71 4.1 48.1 1.0
O B:ASP207 4.3 40.5 1.0
CA B:ASP27 4.4 57.6 1.0
CB B:ASP71 4.6 46.5 1.0
OD1 B:ASP27 4.6 52.8 1.0
O2G A:ATP307 4.6 30.4 1.0
O3A A:ATP307 4.6 30.4 1.0
N B:ASP207 4.6 45.6 1.0
CB B:ASP207 4.7 65.1 1.0
CB B:SER209 4.7 88.5 1.0
CA B:ASP71 4.8 45.6 1.0
O1G A:ATP307 4.9 30.4 1.0
O A:HOH369 4.9 25.1 1.0
C B:ASP207 5.0 45.6 1.0

Magnesium binding site 6 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 6 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:27.8
occ:1.00
 OD2 B:ASP43 2.3 54.8 1.0
OD2 B:ASP71 2.4 48.1 1.0
O2G A:ATP307 2.4 30.4 1.0
O3G A:ATP307 2.6 30.4 1.0
O1B A:ATP307 2.8 30.4 1.0
OD1 B:ASP71 2.8 45.7 1.0
CG B:ASP71 3.0 49.5 1.0
OD1 B:ASP43 3.0 51.2 1.0
CG B:ASP43 3.0 55.7 1.0
PG A:ATP307 3.0 30.4 1.0
PB A:ATP307 3.3 30.4 1.0
MG B:MG309 3.3 27.8 1.0
O B:HOH314 3.5 49.1 1.0
O3B A:ATP307 3.7 30.4 1.0
MG B:MG311 3.9 27.8 1.0
O2B A:ATP307 3.9 30.4 1.0
O B:VAL67 4.4 42.6 1.0
O1G A:ATP307 4.4 30.4 1.0
CB B:ASP71 4.5 46.5 1.0
CB B:ASP43 4.5 54.1 1.0
OD2 B:ASP207 4.6 66.5 1.0
OG B:SER209 4.8 91.4 1.0
O3A A:ATP307 4.9 30.4 1.0
O B:HOH317 4.9 54.9 1.0
OD1 B:ASP207 4.9 66.8 1.0

Magnesium binding site 7 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 7 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:27.8
occ:1.00
 O1A A:ATP307 2.3 30.4 1.0
O2G A:ATP307 2.4 30.4 1.0
OD1 B:ASP43 2.5 51.2 1.0
OD1 A:ASN119 2.6 48.9 1.0
O B:HOH317 2.7 54.9 1.0
O1B A:ATP307 2.8 30.4 1.0
O3B A:ATP307 3.5 30.4 1.0
CG B:ASP43 3.5 55.7 1.0
PA A:ATP307 3.7 30.4 1.0
PB A:ATP307 3.7 30.4 1.0
PG A:ATP307 3.7 30.4 1.0
CG A:ASN119 3.8 48.5 1.0
MG B:MG310 3.9 27.8 1.0
O B:THR42 4.0 42.3 1.0
O3A A:ATP307 4.1 30.4 1.0
OD2 B:ASP43 4.2 54.8 1.0
O B:HOH328 4.2 56.6 1.0
O B:HOH314 4.3 49.1 1.0
O2A A:ATP307 4.4 30.4 1.0
CA B:ASP43 4.5 45.8 1.0
CB B:ASP43 4.5 54.1 1.0
O1G A:ATP307 4.5 30.4 1.0
CB A:ASN119 4.7 43.0 1.0
ND2 A:ASN119 4.7 43.2 1.0
O3G A:ATP307 4.7 30.4 1.0
O5' A:ATP307 4.8 30.4 1.0

Magnesium binding site 8 out of 8 in 3c9r

Go back to Magnesium Binding Sites List in 3c9r
Magnesium binding site 8 out of 8 in the Aathil Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Aathil Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg312

b:27.8
occ:1.00
 O1G A:ATP307 2.2 30.4 1.0
OD2 B:ASP210 2.6 96.2 1.0
OD1 B:ASP210 2.9 98.4 1.0
CG B:ASP210 3.1 94.5 1.0
PG A:ATP307 3.5 30.4 1.0
O3B A:ATP307 3.9 30.4 1.0
O2G A:ATP307 4.1 30.4 1.0
OG B:SER209 4.3 91.4 1.0
CB B:ASP210 4.6 90.3 1.0
OE1 B:GLU8 4.6 87.7 1.0
OE2 B:GLU8 4.7 85.1 1.0
O2A A:ATP307 4.7 30.4 1.0
O3G A:ATP307 4.9 30.4 1.0
CB B:SER209 5.0 88.5 1.0

Reference:

K.M.Mcculloch, C.Kinsland, T.P.Begley, S.E.Ealick. Structural Studies of Thiamin Monophosphate Kinase in Complex with Substrates and Products. Biochemistry V. 47 3810 2008.
ISSN: ISSN 0006-2960
PubMed: 18311927
DOI: 10.1021/BI800041H
Page generated: Sun Aug 10 18:03:47 2025

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