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Calcium in PDB 4m5m: The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase

Enzymatic activity of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase

All present enzymatic activity of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase:
2.7.6.3;

Protein crystallography data

The structure of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, PDB code: 4m5m was solved by M.Yun, D.Hoagland, G.Kumar, B.Waddell, C.O.Rock, R.E.Lee, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.88 / 1.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.942, 57.862, 38.686, 90.00, 115.64, 90.00
R / Rfree (%) 17 / 19.1

Calcium Binding Sites:

The binding sites of Calcium atom in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase (pdb code 4m5m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, PDB code: 4m5m:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4m5m

Go back to Calcium Binding Sites List in 4m5m
Calcium binding site 1 out of 3 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:6.7
occ:1.00
 OD1 A:ASP97 2.3 7.7 1.0
O A:HOH525 2.3 7.8 1.0
O A:HOH524 2.3 8.3 1.0
OD1 A:ASP95 2.3 8.3 1.0
O1A A:APC402 2.4 7.6 1.0
O1B A:APC402 2.4 7.1 1.0
CG A:ASP95 3.2 7.6 1.0
OD2 A:ASP95 3.3 7.9 1.0
CG A:ASP97 3.4 7.0 1.0
PA A:APC402 3.4 8.1 1.0
PB A:APC402 3.5 7.0 1.0
CA A:CA404 3.8 6.8 1.0
C3A A:APC402 3.8 7.9 1.0
O5' A:APC402 3.8 9.4 1.0
OD2 A:ASP97 3.9 7.5 1.0
O2B A:APC402 4.3 9.1 1.0
O1 A:GOL407 4.3 14.2 1.0
NH1 A:ARG82 4.4 12.0 1.0
OE2 A:GLU77 4.4 9.0 1.0
NH2 A:ARG82 4.5 11.9 1.0
O A:LEU96 4.5 7.6 1.0
O A:HOH526 4.5 8.3 1.0
NH1 A:ARG92 4.6 10.8 1.0
CB A:ASP95 4.6 7.8 1.0
CB A:ASP97 4.7 7.1 1.0
C2 A:APC402 4.8 7.2 1.0
N3 A:APC402 4.8 7.5 1.0
C A:LEU96 4.8 6.2 1.0
O3B A:APC402 4.8 7.7 1.0
N A:LEU96 4.8 6.7 1.0
CA A:ASP97 4.8 6.6 1.0
O A:HOH502 4.8 9.7 1.0
O2A A:APC402 4.9 9.1 1.0
CZ A:ARG82 4.9 11.9 1.0
N A:ASP97 4.9 6.4 1.0
CA A:ASP95 5.0 6.9 1.0
O3G A:APC402 5.0 10.6 1.0

Calcium binding site 2 out of 3 in 4m5m

Go back to Calcium Binding Sites List in 4m5m
Calcium binding site 2 out of 3 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:6.8
occ:1.00
 OD2 A:ASP97 2.3 7.5 1.0
O2G A:APC402 2.3 8.7 1.0
OD2 A:ASP95 2.4 7.9 1.0
O A:HOH501 2.4 8.7 1.0
O A:HOH502 2.4 9.7 1.0
O1B A:APC402 2.4 7.1 1.0
CG A:ASP97 3.2 7.0 1.0
CG A:ASP95 3.4 7.6 1.0
OD1 A:ASP97 3.4 7.7 1.0
PG A:APC402 3.5 7.3 1.0
PB A:APC402 3.5 7.0 1.0
O3B A:APC402 3.7 7.7 1.0
CA A:CA403 3.8 6.7 1.0
OD1 A:ASP95 3.8 8.3 1.0
O3G A:APC402 4.1 10.6 1.0
O2B A:APC402 4.1 9.1 1.0
O A:HOH503 4.1 11.9 1.0
NH1 A:ARG121 4.1 9.6 1.0
CB A:ASP97 4.5 7.1 1.0
S6 A:DX4401 4.6 8.6 1.0
NE2 A:HIS115 4.6 8.2 1.0
CB A:ASP95 4.7 7.8 1.0
CE A:MET124 4.7 13.8 1.0
O1G A:APC402 4.7 7.2 1.0
O A:HOH581 4.7 9.9 1.0
NH1 A:ARG92 4.8 10.8 1.0
N7 A:DX4401 4.8 8.6 1.0
O1 A:GOL407 5.0 14.2 1.0

Calcium binding site 3 out of 3 in 4m5m

Go back to Calcium Binding Sites List in 4m5m
Calcium binding site 3 out of 3 in the The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:11.1
occ:1.00
 O A:HOH585 2.3 12.8 1.0
O A:ILE28 2.3 9.4 1.0
O A:SER31 2.3 9.9 1.0
O A:HOH584 2.3 16.8 1.0
O A:HOH549 2.5 13.2 1.0
O A:GLY26 3.1 11.8 1.0
C A:SER31 3.4 9.1 1.0
C A:ILE28 3.5 9.4 1.0
C A:GLY26 4.0 10.3 1.0
N A:SER31 4.0 9.1 1.0
N A:ILE28 4.1 9.0 1.0
CA A:SER31 4.1 8.9 1.0
C A:ASP27 4.3 10.1 1.0
CB A:SER31 4.3 8.2 1.0
CA A:ILE28 4.4 8.8 1.0
N A:PRO29 4.4 10.0 1.0
CA A:PRO29 4.4 10.3 1.0
N A:HIS32 4.5 8.5 1.0
O A:HOH593 4.5 24.1 1.0
CA A:ASP27 4.6 10.3 1.0
ND1 A:HIS32 4.6 18.2 1.0
N A:ASP27 4.6 9.7 1.0
C A:PRO29 4.7 9.4 1.0
CA A:HIS32 4.7 9.3 1.0
O A:HOH550 4.7 32.0 1.0
O A:LEU25 4.8 9.0 1.0
O A:ASP27 4.8 11.3 1.0
N A:GLU30 4.8 9.5 1.0
CA A:GLY26 4.9 9.8 1.0
CE1 A:HIS32 5.0 18.5 1.0
CB A:ILE28 5.0 8.4 1.0

Reference:

M.K.Yun, D.Hoagland, G.Kumar, M.B.Waddell, C.O.Rock, R.E.Lee, S.W.White. The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase. Bioorg.Med.Chem. V. 22 2157 2014.
ISSN: ISSN 0968-0896
PubMed: 24613625
DOI: 10.1016/J.BMC.2014.02.022
Page generated: Sun Jul 14 10:07:23 2024

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