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Magnesium in PDB 3c9t: Aathil Complexed with Amppcp and Tmp

Enzymatic activity of Aathil Complexed with Amppcp and Tmp

All present enzymatic activity of Aathil Complexed with Amppcp and Tmp:
2.7.4.16;

Protein crystallography data

The structure of Aathil Complexed with Amppcp and Tmp, PDB code: 3c9t 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) 31.65 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.750, 66.843, 196.860, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 27

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aathil Complexed with Amppcp and Tmp (pdb code 3c9t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Aathil Complexed with Amppcp and Tmp, PDB code: 3c9t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3c9t

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Magnesium binding site 1 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:25.7
occ:1.00
 OD1 A:ASP210 2.4 54.0 1.0
OD2 A:ASP210 2.6 50.3 1.0
O1 A:TPS308 2.6 54.0 1.0
CG A:ASP210 2.9 50.4 1.0
O3G B:ACP307 3.0 64.5 1.0
O2 A:TPS308 3.2 60.6 1.0
P1 A:TPS308 3.4 54.4 1.0
PG B:ACP307 3.7 59.7 1.0
O2G B:ACP307 3.8 58.2 1.0
OE2 A:GLU8 4.0 67.8 1.0
O1G B:ACP307 4.0 61.4 1.0
O7 A:TPS308 4.1 57.0 1.0
MG A:MG312 4.2 40.4 1.0
OG A:SER209 4.3 48.3 1.0
CB A:ASP210 4.4 48.7 1.0
O1A B:ACP307 4.6 63.9 1.0
ND1 A:HIS305 4.7 53.7 1.0
O3 A:TPS308 4.7 58.1 1.0
CE1 A:HIS305 4.7 54.1 1.0
CD A:GLU8 4.9 66.2 1.0
O A:TRP303 4.9 65.5 1.0
C7 A:TPS308 4.9 56.1 1.0
CD1 A:TRP303 4.9 53.1 1.0
OE1 A:GLU8 5.0 69.6 1.0
C6 A:TPS308 5.0 52.1 1.0

Magnesium binding site 2 out of 10 in 3c9t

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Magnesium binding site 2 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:33.0
occ:1.00
 OD2 A:ASP43 2.4 57.0 1.0
OD2 A:ASP71 2.5 46.9 1.0
OD1 A:ASP43 2.5 60.7 1.0
O2G B:ACP307 2.7 58.2 1.0
CG A:ASP43 2.8 56.2 1.0
O1G B:ACP307 2.9 61.4 1.0
PG B:ACP307 3.0 59.7 1.0
C3B B:ACP307 3.1 63.2 1.0
CG A:ASP71 3.3 44.5 1.0
OD1 A:ASP71 3.5 40.3 1.0
MG A:MG313 3.9 25.3 1.0
MG B:MG311 4.1 25.0 1.0
O A:VAL67 4.2 41.7 1.0
O2 A:TPS308 4.2 60.6 1.0
CB A:ASP43 4.3 51.1 1.0
CG2 A:VAL67 4.4 45.6 1.0
O3G B:ACP307 4.5 64.5 1.0
OD1 A:ASP207 4.6 56.8 1.0
PB B:ACP307 4.6 63.0 1.0
CB A:SER209 4.6 44.9 1.0
O A:HOH320 4.6 38.5 1.0
CB A:ASP71 4.7 43.9 1.0
OG A:SER209 4.8 48.3 1.0
CE2 A:TYR262 4.9 39.3 1.0
OD2 A:ASP207 5.0 58.1 1.0

Magnesium binding site 3 out of 10 in 3c9t

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Magnesium binding site 3 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:40.4
occ:1.00
 OD2 A:ASP210 2.3 50.3 1.0
NE2 A:HIS218 2.6 62.7 1.0
OD1 A:ASP215 2.7 41.8 1.0
CG A:ASP210 3.3 50.4 1.0
CD2 A:HIS218 3.4 61.8 1.0
CE1 A:HIS218 3.6 62.2 1.0
CB A:ASP210 3.8 48.7 1.0
CG A:ASP215 3.9 41.4 1.0
O1A B:ACP307 4.0 63.9 1.0
MG A:MG309 4.2 25.7 1.0
O3G B:ACP307 4.4 64.5 1.0
OD1 A:ASP210 4.4 54.0 1.0
OD2 A:ASP215 4.5 41.9 1.0
CG A:HIS218 4.5 60.8 1.0
O2A B:ACP307 4.6 62.3 1.0
ND1 A:HIS218 4.6 62.7 1.0
OG A:SER209 4.7 48.3 1.0
PA B:ACP307 4.8 59.4 1.0
CA A:ASP215 4.9 45.1 1.0
CB A:ASP215 5.0 43.3 1.0

Magnesium binding site 4 out of 10 in 3c9t

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Magnesium binding site 4 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg313

b:25.3
occ:1.00
 OD2 A:ASP207 2.4 58.1 1.0
OD1 A:ASP71 2.4 40.3 1.0
OD1 A:ASP27 2.6 55.4 1.0
C3B B:ACP307 2.8 63.2 1.0
CG A:ASP207 3.4 55.5 1.0
O2G B:ACP307 3.5 58.2 1.0
CG A:ASP71 3.5 44.5 1.0
CG A:ASP27 3.7 54.0 1.0
OD1 A:ASP207 3.8 56.8 1.0
PG B:ACP307 3.8 59.7 1.0
O1B B:ACP307 3.8 64.1 1.0
PB B:ACP307 3.9 63.0 1.0
MG A:MG310 3.9 33.0 1.0
OD2 A:ASP71 4.0 46.9 1.0
OG A:SER209 4.0 48.3 1.0
O A:ASP207 4.1 50.0 1.0
NH2 A:ARG142 4.2 57.7 1.0
CB A:ASP27 4.2 53.4 1.0
O3A B:ACP307 4.3 61.7 1.0
O3G B:ACP307 4.4 64.5 1.0
CA A:ASP27 4.4 52.3 1.0
N A:ASP207 4.6 50.1 1.0
CB A:SER209 4.6 44.9 1.0
CB A:ASP207 4.7 52.4 1.0
OD2 A:ASP27 4.7 54.3 1.0
CB A:ASP71 4.8 43.9 1.0
C A:ASP207 4.8 50.2 1.0
CA A:ASP207 4.9 50.6 1.0
O1G B:ACP307 5.0 61.4 1.0

Magnesium binding site 5 out of 10 in 3c9t

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Magnesium binding site 5 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg314

b:25.6
occ:1.00
 O2 B:TPS308 2.3 55.1 1.0
OD1 B:ASP43 2.3 49.8 1.0
OD1 A:ASN119 2.4 49.2 1.0
O3G A:ACP307 2.4 63.0 1.0
CG A:ASN119 3.3 44.5 1.0
P1 B:TPS308 3.3 49.5 1.0
O3 B:TPS308 3.4 52.8 1.0
CG B:ASP43 3.5 50.7 1.0
ND2 A:ASN119 3.5 44.0 1.0
PG A:ACP307 3.8 60.6 1.0
MG B:MG313 4.1 27.0 1.0
O2G A:ACP307 4.1 64.5 1.0
OD2 B:ASP43 4.2 52.1 1.0
O1 B:TPS308 4.2 48.5 1.0
CA B:ASP43 4.5 48.4 1.0
O7 B:TPS308 4.5 52.4 1.0
CB B:ASP43 4.5 49.0 1.0
N B:VAL44 4.6 45.7 1.0
O1G A:ACP307 4.6 63.0 1.0
O2B A:ACP307 4.7 64.3 1.0
CB A:ASN119 4.7 41.1 1.0
C3B A:ACP307 4.7 63.1 1.0
O A:ILE120 4.8 43.2 1.0
O B:THR42 4.8 48.8 1.0
MG B:MG310 5.0 30.8 1.0

Magnesium binding site 6 out of 10 in 3c9t

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Magnesium binding site 6 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:25.0
occ:1.00
 O2 A:TPS308 2.3 60.6 1.0
O1G B:ACP307 2.4 61.4 1.0
ND2 B:ASN119 2.5 44.1 1.0
OD2 A:ASP43 3.0 57.0 1.0
O3 A:TPS308 3.1 58.1 1.0
CG A:ASP43 3.2 56.2 1.0
P1 A:TPS308 3.2 54.4 1.0
CG B:ASN119 3.3 42.5 1.0
OD1 B:ASN119 3.3 41.9 1.0
OD1 A:ASP43 3.5 60.7 1.0
PG B:ACP307 3.9 59.7 1.0
CA A:ASP43 4.0 48.9 1.0
CB A:ASP43 4.0 51.1 1.0
MG A:MG310 4.1 33.0 1.0
N A:VAL44 4.1 47.3 1.0
O7 A:TPS308 4.3 57.0 1.0
O1 A:TPS308 4.3 54.0 1.0
O2G B:ACP307 4.3 58.2 1.0
C A:ASP43 4.6 49.4 1.0
CB B:ASN119 4.7 42.8 1.0
O3G B:ACP307 4.7 64.5 1.0
O B:ILE120 4.7 41.1 1.0
O A:THR42 4.8 46.3 1.0
O A:VAL44 4.8 42.7 1.0
C3B B:ACP307 5.0 63.2 1.0

Magnesium binding site 7 out of 10 in 3c9t

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Magnesium binding site 7 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:30.8
occ:1.00
 OD2 B:ASP210 2.4 56.1 1.0
OD1 B:ASP210 2.6 52.3 1.0
O1 B:TPS308 2.7 48.5 1.0
O2G A:ACP307 2.8 64.5 1.0
CG B:ASP210 2.9 51.8 1.0
O2 B:TPS308 3.3 55.1 1.0
P1 B:TPS308 3.5 49.5 1.0
PG A:ACP307 4.0 60.6 1.0
O7 B:TPS308 4.1 52.4 1.0
MG B:MG314 4.2 35.9 1.0
CD1 B:TRP303 4.3 60.6 1.0
CB B:ASP210 4.4 49.1 1.0
O1G A:ACP307 4.4 63.0 1.0
OE2 B:GLU8 4.4 67.2 1.0
O3G A:ACP307 4.5 63.0 1.0
OG B:SER209 4.5 47.1 1.0
OE1 B:GLU8 4.7 66.7 1.0
O3 B:TPS308 4.8 52.8 1.0
C7 B:TPS308 4.9 50.8 1.0
C6 B:TPS308 4.9 46.4 1.0
O1A A:ACP307 4.9 61.4 1.0
CD B:GLU8 5.0 65.0 1.0
MG A:MG314 5.0 25.6 1.0
CE1 B:HIS305 5.0 48.6 1.0

Magnesium binding site 8 out of 10 in 3c9t

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Magnesium binding site 8 out of 10 in the Aathil Complexed with Amppcp and Tmp


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 Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg312

b:29.9
occ:1.00
 OD1 B:ASP207 2.3 57.5 1.0
OD1 B:ASP71 2.6 46.7 1.0
OD2 B:ASP27 2.7 50.0 1.0
C3B A:ACP307 2.9 63.1 1.0
O1G A:ACP307 2.9 63.0 1.0
CG B:ASP207 3.4 54.9 1.0
PG A:ACP307 3.4 60.6 1.0
OD2 B:ASP207 3.7 56.5 1.0
CG B:ASP27 3.7 51.9 1.0
OG B:SER209 3.8 47.1 1.0
CG B:ASP71 3.8 50.8 1.0
O B:ASP207 3.8 51.4 1.0
MG B:MG313 4.0 27.0 1.0
PB A:ACP307 4.0 61.1 1.0
O1B A:ACP307 4.2 65.4 1.0
CB B:ASP27 4.2 51.4 1.0
OD2 B:ASP71 4.2 54.1 1.0
O2G A:ACP307 4.3 64.5 1.0
NH2 B:ARG142 4.4 57.4 1.0
CB B:SER209 4.4 47.2 1.0
O3A A:ACP307 4.5 61.9 1.0
O3G A:ACP307 4.5 63.0 1.0
N B:ASP207 4.6 54.5 1.0
CB B:ASP207 4.7 54.5 1.0
C B:ASP207 4.7 51.0 1.0
CA B:ASP27 4.8 52.6 1.0
OD1 B:ASP27 4.8 52.5 1.0
CA B:ASP207 4.9 53.0 1.0

Magnesium binding site 9 out of 10 in 3c9t

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Magnesium binding site 9 out of 10 in the Aathil Complexed with Amppcp and Tmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Aathil Complexed with Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg313

b:27.0
occ:1.00
 OD2 B:ASP43 2.3 52.1 1.0
OD2 B:ASP71 2.4 54.1 1.0
O3G A:ACP307 2.4 63.0 1.0
O1G A:ACP307 2.8 63.0 1.0
PG A:ACP307 3.0 60.6 1.0
CG B:ASP71 3.1 50.8 1.0
C3B A:ACP307 3.2 63.1 1.0
CG B:ASP43 3.2 50.7 1.0
OD1 B:ASP71 3.3 46.7 1.0
OD1 B:ASP43 3.3 49.8 1.0
MG B:MG312 4.0 29.9 1.0
O B:VAL67 4.0 49.2 1.0
O B:HOH318 4.0 41.1 1.0
MG A:MG314 4.1 25.6 1.0
O2G A:ACP307 4.4 64.5 1.0
O2 B:TPS308 4.4 55.1 1.0
CB B:ASP71 4.5 49.1 1.0
CB B:ASP43 4.6 49.0 1.0
PB A:ACP307 4.6 61.1 1.0
OD2 B:ASP207 4.7 56.5 1.0
C B:VAL67 4.9 47.5 1.0
O B:THR42 5.0 48.8 1.0
CE2 B:TYR262 5.0 48.0 1.0

Magnesium binding site 10 out of 10 in 3c9t

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Magnesium binding site 10 out of 10 in the Aathil Complexed with Amppcp and Tmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Aathil Complexed with Amppcp and Tmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg314

b:35.9
occ:1.00
 OD1 B:ASP210 2.5 52.3 1.0
OD1 B:ASP215 2.6 55.1 1.0
CE1 B:HIS218 3.0 73.9 1.0
NE2 B:HIS218 3.2 72.3 1.0
CG B:ASP210 3.6 51.8 1.0
CG B:ASP215 3.8 55.6 1.0
ND1 B:HIS218 3.8 74.2 1.0
CD2 B:HIS218 4.1 71.4 1.0
CB B:ASP210 4.1 49.1 1.0
MG B:MG310 4.2 30.8 1.0
O1A A:ACP307 4.2 61.4 1.0
CG B:HIS218 4.4 71.0 1.0
O2G A:ACP307 4.4 64.5 1.0
OD2 B:ASP210 4.5 56.1 1.0
OD2 B:ASP215 4.6 54.6 1.0
O2A A:ACP307 4.6 61.6 1.0
OG B:SER209 4.7 47.1 1.0
CA B:ASP215 4.8 55.4 1.0
CB B:ASP215 4.8 56.1 1.0
PA A:ACP307 4.9 58.4 1.0
OE2 B:GLU8 4.9 67.2 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: Wed Aug 14 09:31:19 2024

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