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Calcium in PDB 4m5g: 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: 4m5g 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) 22.20 / 1.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.875, 57.417, 38.327, 90.00, 113.96, 90.00
R / Rfree (%) 14.4 / 17.7

Other elements in 4m5g:

The structure of The Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

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 4m5g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 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: 4m5g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4m5g

Go back to Calcium Binding Sites List in 4m5g
Calcium binding site 1 out of 2 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:Ca303

b:6.9
occ:1.00
 OD1 A:ASP95 2.3 8.3 1.0
O1A A:APC301 2.3 7.9 1.0
O A:HOH428 2.3 8.8 1.0
OD1 A:ASP97 2.3 8.4 1.0
O A:HOH429 2.4 10.0 1.0
O1B A:APC301 2.4 8.3 1.0
CG A:ASP95 3.2 8.2 1.0
PA A:APC301 3.4 9.4 1.0
OD2 A:ASP95 3.5 10.2 1.0
CG A:ASP97 3.5 8.2 1.0
PB A:APC301 3.5 8.9 1.0
C3A A:APC301 3.8 8.6 1.0
CA A:CA304 3.8 8.7 1.0
O5' A:APC301 3.8 11.5 1.0
OD2 A:ASP97 4.0 10.6 1.0
OE2 A:GLU77 4.3 8.8 1.0
O2B A:APC301 4.4 11.3 1.0
O A:HOH452 4.4 16.8 1.0
NH2 A:ARG82 4.4 18.8 1.0
NH1 A:ARG82 4.4 17.6 1.0
O A:LEU96 4.5 7.5 1.0
CB A:ASP95 4.6 7.3 1.0
O A:HOH430 4.6 8.6 1.0
N3 A:APC301 4.7 6.8 1.0
C2 A:APC301 4.7 6.4 1.0
CB A:ASP97 4.7 6.7 1.0
O3B A:APC301 4.7 8.9 1.0
C A:LEU96 4.8 5.7 1.0
O2A A:APC301 4.8 11.4 1.0
CA A:ASP97 4.8 5.7 1.0
O2G A:APC301 4.9 8.8 1.0
O3G A:APC301 4.9 10.2 1.0
N A:LEU96 4.9 5.9 1.0
N A:ASP97 4.9 6.1 1.0
CZ A:ARG82 4.9 18.4 1.0
O A:HOH402 4.9 15.5 1.0

Calcium binding site 2 out of 2 in 4m5g

Go back to Calcium Binding Sites List in 4m5g
Calcium binding site 2 out of 2 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:Ca304

b:8.7
occ:1.00
 O A:HOH401 2.3 15.9 1.0
OD2 A:ASP97 2.3 10.6 1.0
O2G A:APC301 2.3 8.8 1.0
O A:HOH402 2.4 15.5 1.0
OD2 A:ASP95 2.4 10.2 1.0
O1B A:APC301 2.4 8.3 1.0
CG A:ASP97 3.2 8.2 1.0
OD1 A:ASP97 3.4 8.4 1.0
PB A:APC301 3.4 8.9 1.0
CG A:ASP95 3.5 8.2 1.0
PG A:APC301 3.5 7.2 1.0
O3B A:APC301 3.6 8.9 1.0
CA A:CA303 3.8 6.9 1.0
OD1 A:ASP95 3.9 8.3 1.0
NH1 A:ARG121 4.1 7.6 1.0
O2B A:APC301 4.1 11.3 1.0
O A:HOH403 4.2 13.2 1.0
O3G A:APC301 4.3 10.2 1.0
NH1 A:ARG92 4.3 22.5 1.0
O A:HOH525 4.4 16.0 1.0
O A:HOH547 4.5 34.7 1.0
NE2 A:HIS115 4.5 7.4 1.0
N11 A:YH1302 4.6 14.2 1.0
CB A:ASP97 4.6 6.7 1.0
O A:HOH536 4.6 23.1 1.0
CE A:MET124 4.6 13.9 1.0
O1G A:APC301 4.7 7.9 1.0
CB A:ASP95 4.7 7.3 1.0
O A:HOH428 5.0 8.8 1.0
C3A A:APC301 5.0 8.6 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: Wed Jul 9 00:13:01 2025

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