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Calcium in PDB 4m5l: 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: 4m5l 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) 19.86 / 1.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.903, 57.991, 38.643, 90.00, 115.49, 90.00
R / Rfree (%) 17.3 / 18.6

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 4m5l). 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: 4m5l:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4m5l

Go back to Calcium Binding Sites List in 4m5l
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:Ca302

b:9.1
occ:1.00
 O A:HOH418 2.3 13.0 1.0
OD2 A:ASP97 2.3 11.2 1.0
O2G A:APC301 2.3 10.1 1.0
O A:HOH431 2.4 14.6 1.0
O1B A:APC301 2.4 9.1 1.0
OD2 A:ASP95 2.4 10.5 1.0
CG A:ASP97 3.2 9.3 1.0
OD1 A:ASP97 3.4 9.7 1.0
PB A:APC301 3.4 9.0 1.0
CG A:ASP95 3.5 9.1 1.0
PG A:APC301 3.5 8.7 1.0
O3B A:APC301 3.6 9.4 1.0
CA A:CA303 3.8 8.1 1.0
OD1 A:ASP95 3.9 9.9 1.0
NH1 A:ARG121 4.1 8.5 1.0
O2B A:APC301 4.2 10.9 1.0
O3G A:APC301 4.2 11.4 1.0
O A:HOH426 4.3 13.7 1.0
O A:HOH528 4.3 26.3 1.0
O A:HOH432 4.3 15.6 1.0
O A:HOH453 4.5 17.0 1.0
N11 A:YH4306 4.5 14.1 1.0
CB A:ASP97 4.6 8.2 1.0
NE2 A:HIS115 4.6 9.4 1.0
NH1 A:ARG92 4.6 19.5 1.0
O1G A:APC301 4.7 8.3 1.0
CB A:ASP95 4.7 8.0 1.0
CE A:MET124 4.8 14.0 1.0
S12 A:YH4306 5.0 22.4 1.0
C3A A:APC301 5.0 9.0 1.0

Calcium binding site 2 out of 3 in 4m5l

Go back to Calcium Binding Sites List in 4m5l
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:Ca303

b:8.1
occ:1.00
 OD1 A:ASP97 2.3 9.7 1.0
OD1 A:ASP95 2.3 9.9 1.0
O1A A:APC301 2.3 8.5 1.0
O A:HOH412 2.4 10.5 1.0
O A:HOH410 2.4 9.8 1.0
O1B A:APC301 2.4 9.1 1.0
CG A:ASP95 3.2 9.1 1.0
CG A:ASP97 3.4 9.3 1.0
PA A:APC301 3.4 9.1 1.0
OD2 A:ASP95 3.5 10.5 1.0
PB A:APC301 3.5 9.0 1.0
CA A:CA302 3.8 9.1 1.0
C3A A:APC301 3.8 9.0 1.0
O5' A:APC301 3.9 9.8 1.0
OD2 A:ASP97 3.9 11.2 1.0
NH1 A:ARG82 4.3 16.2 1.0
O2B A:APC301 4.4 10.9 1.0
O1 A:GOL305 4.4 20.9 1.0
OE2 A:GLU77 4.4 10.1 1.0
NH2 A:ARG82 4.5 18.6 1.0
O A:LEU96 4.6 8.8 1.0
O A:HOH402 4.6 8.5 1.0
NH1 A:ARG92 4.6 19.5 1.0
CB A:ASP95 4.6 8.0 1.0
CB A:ASP97 4.7 8.2 1.0
C2 A:APC301 4.7 7.8 1.0
N3 A:APC301 4.8 7.4 1.0
O3B A:APC301 4.8 9.4 1.0
CZ A:ARG82 4.8 17.9 1.0
C A:LEU96 4.8 7.2 1.0
CA A:ASP97 4.8 7.3 1.0
O2A A:APC301 4.8 10.2 1.0
N A:LEU96 4.9 6.8 1.0
O3G A:APC301 4.9 11.4 1.0
N A:ASP97 4.9 7.3 1.0
O A:HOH431 5.0 14.6 1.0
O2G A:APC301 5.0 10.1 1.0

Calcium binding site 3 out of 3 in 4m5l

Go back to Calcium Binding Sites List in 4m5l
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:Ca304

b:10.5
occ:1.00
 O A:SER31 2.3 12.4 1.0
O A:ILE28 2.3 9.7 1.0
O A:HOH448 2.3 18.8 1.0
O A:HOH436 2.4 20.2 1.0
O A:GLY26 2.4 11.6 1.0
O A:HOH472 2.6 18.7 1.0
C A:ILE28 3.5 9.2 1.0
C A:SER31 3.5 11.2 1.0
C A:GLY26 3.6 10.7 1.0
N A:ILE28 4.0 8.9 1.0
C A:ASP27 4.0 10.3 1.0
N A:SER31 4.0 10.0 1.0
CA A:SER31 4.2 10.0 1.0
CA A:ASP27 4.3 10.4 1.0
CA A:ILE28 4.3 8.8 1.0
N A:ASP27 4.3 9.5 1.0
N A:PRO29 4.4 9.9 1.0
CA A:PRO29 4.4 10.4 1.0
O A:ASP27 4.5 11.6 1.0
CB A:SER31 4.5 10.0 1.0
O A:HOH507 4.5 38.8 1.0
N A:HIS32 4.5 10.9 1.0
O A:HOH530 4.6 27.0 1.0
CA A:GLY26 4.6 10.9 1.0
C A:PRO29 4.6 9.8 1.0
O A:HOH429 4.7 15.1 1.0
CA A:HIS32 4.8 12.0 1.0
O A:LEU25 4.8 11.1 1.0
N A:GLU30 4.8 9.8 1.0
ND1 A:HIS32 4.9 26.0 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 10:07:07 2024

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