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Magnesium in PDB 3arn: Human Dutpase in Complex with Novel Uracil Derivative

Enzymatic activity of Human Dutpase in Complex with Novel Uracil Derivative

All present enzymatic activity of Human Dutpase in Complex with Novel Uracil Derivative:
3.6.1.23;

Protein crystallography data

The structure of Human Dutpase in Complex with Novel Uracil Derivative, PDB code: 3arn was solved by K.T.Chong, S.Miyahara, H.Miyakoshi, M.Fukuoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.53 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.404, 83.147, 89.586, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dutpase in Complex with Novel Uracil Derivative (pdb code 3arn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Dutpase in Complex with Novel Uracil Derivative, PDB code: 3arn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3arn

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Magnesium binding site 1 out of 6 in the Human Dutpase in Complex with Novel Uracil Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dutpase in Complex with Novel Uracil Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg166

b:48.7
occ:1.00
 O C:HOH253 2.1 35.1 1.0
O A:HOH250 2.1 39.0 1.0
O A:HOH251 2.1 42.0 1.0
O B:HOH255 2.2 40.5 1.0
O B:HOH252 2.2 41.3 1.0
OD2 B:ASP95 2.7 19.8 1.0
OD2 A:ASP95 2.9 21.4 1.0
OD2 C:ASP95 2.9 16.0 1.0
O C:HOH412 3.4 31.4 1.0
CG B:ASP95 3.8 15.9 1.0
CG A:ASP95 4.0 17.3 1.0
CG C:ASP95 4.0 15.5 1.0
OD1 B:ASP95 4.1 14.3 1.0
OD1 A:ASP95 4.3 14.1 1.0
OD1 C:ASP95 4.4 21.1 1.0
O B:VAL96 4.6 11.0 1.0
O C:VAL96 4.7 10.4 1.0
O A:VAL96 4.8 11.7 1.0
O B:HOH387 5.0 24.9 1.0
O B:HOH227 5.0 18.9 1.0

Magnesium binding site 2 out of 6 in 3arn

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Magnesium binding site 2 out of 6 in the Human Dutpase in Complex with Novel Uracil Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dutpase in Complex with Novel Uracil Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg167

b:26.1
occ:1.00
 NE2 A:HIS92 2.0 25.8 1.0
CE1 A:HIS92 3.0 28.7 1.0
CD2 A:HIS92 3.0 21.8 1.0
ND1 A:HIS92 4.1 23.3 1.0
CG A:HIS92 4.2 17.2 1.0
CD A:LYS91 4.7 32.0 1.0
CB A:LYS91 4.7 17.0 1.0

Magnesium binding site 3 out of 6 in 3arn

Go back to Magnesium Binding Sites List in 3arn
Magnesium binding site 3 out of 6 in the Human Dutpase in Complex with Novel Uracil Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dutpase in Complex with Novel Uracil Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg168

b:17.7
occ:1.00
 O B:HOH413 2.1 20.7 1.0
OE1 B:GLU135 2.3 17.8 1.0
OE1 C:GLU135 2.3 15.9 1.0
OE1 A:GLU135 2.3 18.2 1.0
CD C:GLU135 3.2 12.9 1.0
CD A:GLU135 3.2 15.3 1.0
CD B:GLU135 3.2 15.7 1.0
O B:HOH416 3.5 22.6 1.0
CB C:GLU135 3.6 10.7 1.0
CB A:GLU135 3.7 10.8 1.0
CB B:GLU135 3.7 11.8 1.0
CG C:GLU135 4.0 14.3 1.0
CG A:GLU135 4.0 13.1 1.0
CG B:GLU135 4.0 13.6 1.0
OE2 C:GLU135 4.1 12.6 1.0
OE2 B:GLU135 4.1 12.1 1.0
OE2 A:GLU135 4.1 13.3 1.0
CA C:GLU135 4.4 9.1 1.0
CA A:GLU135 4.4 10.2 1.0
CA B:GLU135 4.4 12.5 1.0
O C:ARG136 4.4 11.1 1.0
O A:ARG136 4.4 12.5 1.0
O B:ARG136 4.5 12.2 1.0
C A:GLU135 4.8 10.1 1.0
N C:ARG136 4.8 10.1 1.0
C B:GLU135 4.8 10.8 1.0
C C:GLU135 4.8 10.1 1.0
N B:ARG136 4.8 11.0 1.0
N A:ARG136 4.8 10.5 1.0
OH C:TYR79 4.9 8.9 1.0
OH A:TYR79 5.0 10.7 1.0

Magnesium binding site 4 out of 6 in 3arn

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Magnesium binding site 4 out of 6 in the Human Dutpase in Complex with Novel Uracil Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dutpase in Complex with Novel Uracil Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg166

b:2.0
occ:1.00
 NE2 B:HIS34 2.1 15.1 1.0
CD2 B:HIS34 3.0 11.7 1.0
CE1 B:HIS34 3.0 14.7 1.0
ND1 B:HIS34 4.2 12.1 1.0
CG B:HIS34 4.2 12.4 1.0
CE1 B:TYR54 4.5 10.9 1.0

Magnesium binding site 5 out of 6 in 3arn

Go back to Magnesium Binding Sites List in 3arn
Magnesium binding site 5 out of 6 in the Human Dutpase in Complex with Novel Uracil Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Dutpase in Complex with Novel Uracil Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg167

b:36.8
occ:1.00
 NE2 B:HIS92 2.1 25.1 1.0
CE1 B:HIS92 3.0 24.7 1.0
CD2 B:HIS92 3.1 23.0 1.0
ND1 B:HIS92 4.1 22.9 1.0
O B:HOH397 4.2 36.4 1.0
CG B:HIS92 4.2 19.0 1.0
CB B:LYS91 4.7 17.0 1.0

Magnesium binding site 6 out of 6 in 3arn

Go back to Magnesium Binding Sites List in 3arn
Magnesium binding site 6 out of 6 in the Human Dutpase in Complex with Novel Uracil Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Dutpase in Complex with Novel Uracil Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg166

b:22.7
occ:1.00
 NE2 C:HIS92 2.1 25.1 1.0
CE1 C:HIS92 3.0 24.1 1.0
CD2 C:HIS92 3.1 21.0 1.0
ND1 C:HIS92 4.1 21.5 1.0
CG C:HIS92 4.2 18.5 1.0
CD C:LYS91 4.6 31.1 1.0
CB C:LYS91 4.7 15.2 1.0

Reference:

S.Miyahara, H.Miyakoshi, T.Yokogawa, K.T.Chong, J.Taguchi, T.Muto, K.Endoh, W.Yano, T.Wakasa, H.Ueno, Y.Takao, A.Fujioka, A.Hashimoto, K.Itou, K.Yamamura, M.Nomura, H.Nagasawa, S.Shuto, M.Fukuoka. Discovery of A Novel Class of Potent Human Deoxyuridine Triphosphatase Inhibitors Remarkably Enhancing the Antitumor Activity of Thymidylate Synthase Inhibitors J.Med.Chem. V. 55 2970 2012.
ISSN: ISSN 0022-2623
PubMed: 22339362
DOI: 10.1021/JM201628Y
Page generated: Mon Dec 14 07:54:04 2020

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