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Calcium in PDB 4m5h: 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: 4m5h 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) 32.31 / 1.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.775, 57.588, 38.464, 90.00, 115.41, 90.00
R / Rfree (%) 13.4 / 14.9

Other elements in 4m5h:

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) 3 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 4m5h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 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: 4m5h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4m5h

Go back to Calcium Binding Sites List in 4m5h
Calcium binding site 1 out of 4 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:5.1
occ:1.00
 OD1 A:ASP97 2.3 6.7 1.0
OD1 A:ASP95 2.3 6.2 1.0
O A:HOH412 2.3 7.2 1.0
O A:HOH406 2.3 6.8 1.0
O1A A:APC301 2.3 6.5 1.0
O1B A:APC301 2.4 6.1 1.0
CG A:ASP95 3.3 5.5 1.0
PA A:APC301 3.4 7.3 1.0
CG A:ASP97 3.4 5.7 1.0
PB A:APC301 3.5 6.9 1.0
OD2 A:ASP95 3.6 6.3 1.0
C3A A:APC301 3.7 7.9 1.0
O5' A:APC301 3.8 8.6 1.0
CA A:CA304 3.8 6.2 1.0
OD2 A:ASP97 4.0 7.5 1.0
NH1 A:ARG82 4.2 11.5 1.0
O2B A:APC301 4.3 8.7 1.0
OE2 A:GLU77 4.4 4.9 0.5
O A:HOH457 4.4 12.5 1.0
O A:LEU96 4.5 5.9 1.0
O A:HOH402 4.5 5.5 1.0
OE2 A:GLU77 4.6 6.9 0.5
CB A:ASP95 4.6 5.1 1.0
CB A:ASP97 4.7 5.1 1.0
NH2 A:ARG82 4.7 15.8 1.0
C2 A:APC301 4.7 5.1 1.0
N3 A:APC301 4.7 5.2 1.0
O3B A:APC301 4.7 7.2 1.0
CA A:ASP97 4.7 5.2 1.0
C A:LEU96 4.7 4.6 1.0
O3G A:APC301 4.8 7.8 1.0
O2A A:APC301 4.8 8.8 1.0
N A:ASP97 4.8 4.9 1.0
N A:LEU96 4.9 4.3 1.0
CZ A:ARG82 4.9 13.3 1.0
O2G A:APC301 4.9 7.2 1.0

Calcium binding site 2 out of 4 in 4m5h

Go back to Calcium Binding Sites List in 4m5h
Calcium binding site 2 out of 4 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:6.2
occ:1.00
 OD2 A:ASP97 2.3 7.5 1.0
O A:HOH580 2.3 11.2 1.0
O2G A:APC301 2.3 7.2 1.0
O1B A:APC301 2.4 6.1 1.0
OD2 A:ASP95 2.4 6.3 1.0
O A:HOH428 2.5 10.3 1.0
CG A:ASP97 3.1 5.7 1.0
OD1 A:ASP97 3.3 6.7 1.0
PB A:APC301 3.4 6.9 1.0
CG A:ASP95 3.5 5.5 1.0
PG A:APC301 3.5 6.0 1.0
O3B A:APC301 3.6 7.2 1.0
CA A:CA303 3.8 5.1 1.0
OD1 A:ASP95 3.8 6.2 1.0
NH1 A:ARG121 4.1 6.6 1.0
O2B A:APC301 4.1 8.7 1.0
NH1 A:ARG92 4.2 16.8 1.0
O A:HOH409 4.2 7.8 1.0
O3G A:APC301 4.2 7.8 1.0
O A:HOH413 4.3 9.2 1.0
N11 A:YH2302 4.5 8.5 1.0
NE2 A:HIS115 4.5 6.9 1.0
CE A:MET124 4.5 12.0 1.0
CB A:ASP97 4.5 5.1 1.0
O1G A:APC301 4.7 6.2 1.0
CB A:ASP95 4.7 5.1 1.0
O A:HOH429 4.8 11.1 1.0
C3A A:APC301 5.0 7.9 1.0

Calcium binding site 3 out of 4 in 4m5h

Go back to Calcium Binding Sites List in 4m5h
Calcium binding site 3 out of 4 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:Ca305

b:9.1
occ:1.00
 O A:HOH585 2.4 11.6 1.0
O A:HOH584 2.4 19.6 1.0
OE2 A:GLU87 2.4 11.1 1.0
OD2 A:ASP49 2.4 8.4 1.0
O A:HOH484 2.5 16.3 1.0
OD1 A:ASP49 2.5 7.1 1.0
OE1 A:GLU87 2.6 14.3 1.0
CG A:ASP49 2.8 6.7 1.0
CD A:GLU87 2.9 13.3 1.0
CB A:ASP49 4.4 6.4 1.0
CG A:GLU87 4.4 13.6 1.0
O A:HOH542 4.4 19.3 1.0
CB A:PRO47 4.5 9.8 1.0
O A:ASP49 4.6 5.7 1.0
O A:HOH497 4.6 22.9 1.0
O A:HOH414 4.9 9.8 1.0

Calcium binding site 4 out of 4 in 4m5h

Go back to Calcium Binding Sites List in 4m5h
Calcium binding site 4 out of 4 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 4 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:Ca306

b:10.2
occ:1.00
 O A:ILE28 2.3 7.8 1.0
O A:HOH472 2.4 18.8 1.0
O A:SER31 2.4 10.2 1.0
O A:HOH478 2.4 19.0 1.0
O A:GLY26 2.5 10.8 1.0
O A:HOH450 2.6 12.0 1.0
C A:SER31 3.4 8.9 1.0
C A:ILE28 3.5 7.7 1.0
C A:GLY26 3.6 9.4 1.0
N A:ILE28 4.0 7.6 1.0
N A:SER31 4.0 7.8 1.0
C A:ASP27 4.1 8.3 1.0
CA A:SER31 4.1 8.1 1.0
CA A:ILE28 4.3 7.2 1.0
CA A:ASP27 4.3 8.5 1.0
CB A:SER31 4.3 8.3 1.0
O A:HOH545 4.3 23.8 1.0
N A:PRO29 4.4 8.3 1.0
CA A:PRO29 4.4 8.8 1.0
N A:ASP27 4.4 8.0 1.0
N A:HIS32 4.5 8.5 1.0
O A:ASP27 4.6 9.6 1.0
C A:PRO29 4.6 7.9 1.0
CA A:GLY26 4.7 9.7 1.0
O A:LEU25 4.7 8.7 1.0
O A:HOH458 4.8 15.0 1.0
CA A:HIS32 4.8 9.3 1.0
ND1 A:HIS32 4.8 20.2 1.0
N A:GLU30 4.8 7.9 1.0
CB A:ILE28 5.0 6.9 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 10:05:48 2024

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