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Chlorine in PDB 5hna: Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251

Protein crystallography data

The structure of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251, PDB code: 5hna was solved by Y.-L.Liu, Y.Zhang, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.96 / 2.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.447, 108.616, 140.668, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 26.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251 (pdb code 5hna). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251, PDB code: 5hna:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5hna

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Chlorine binding site 1 out of 4 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:91.0
occ:1.00
CL1 A:63D401 0.0 91.0 1.0
CBD A:63D401 1.7 42.2 1.0
CBG A:63D401 2.6 47.7 1.0
CAL A:63D401 2.7 50.8 1.0
NZ A:LYS81 2.7 37.1 1.0
CZ A:PHE283 3.4 37.4 1.0
OAE A:63D401 3.4 52.0 1.0
SBH A:63D401 3.6 42.0 1.0
CE A:LYS81 3.6 43.0 1.0
CE1 A:PHE283 3.7 39.5 1.0
CAM A:63D401 3.8 62.5 1.0
CBE A:63D401 4.0 57.5 1.0
NH1 A:ARG84 4.1 37.8 1.0
NH2 A:ARG84 4.4 26.7 1.0
CBF A:63D401 4.4 65.9 1.0
NAB A:63D401 4.6 43.9 1.0
CE2 A:PHE283 4.6 37.1 1.0
OAD A:63D401 4.7 39.4 1.0
CZ A:ARG84 4.7 34.0 1.0
ND2 A:ASN83 4.8 43.3 1.0
CD A:LYS81 5.0 49.0 1.0

Chlorine binding site 2 out of 4 in 5hna

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Chlorine binding site 2 out of 4 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:75.0
occ:1.00
CL1 B:63D401 0.0 75.0 1.0
CBD B:63D401 1.7 50.0 1.0
CBG B:63D401 2.7 51.4 1.0
CAL B:63D401 2.7 52.9 1.0
OAE B:63D401 3.1 48.3 1.0
CZ B:PHE283 3.3 28.3 1.0
NH1 B:ARG84 3.4 25.8 1.0
SBH B:63D401 3.4 43.7 1.0
NH2 B:ARG84 3.7 30.9 1.0
NZ B:LYS81 3.7 38.3 1.0
CAM B:63D401 3.9 68.2 1.0
CZ B:ARG84 3.9 27.5 1.0
CE1 B:PHE283 4.0 34.3 1.0
CE B:LYS81 4.0 46.1 1.0
CBE B:63D401 4.0 64.9 1.0
CE2 B:PHE283 4.2 35.4 1.0
OE1 B:GLN119 4.2 48.0 1.0
NAB B:63D401 4.3 42.5 1.0
CBF B:63D401 4.5 75.2 1.0
OAD B:63D401 4.7 51.1 1.0
O B:HOH512 4.8 26.3 1.0

Chlorine binding site 3 out of 4 in 5hna

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Chlorine binding site 3 out of 4 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:95.6
occ:1.00
CL1 C:63D401 0.0 95.6 1.0
CBD C:63D401 1.7 63.7 1.0
CBG C:63D401 2.7 64.8 1.0
CAL C:63D401 2.8 67.6 1.0
NH1 C:ARG84 2.9 39.9 1.0
OAE C:63D401 3.2 62.2 1.0
CZ C:PHE283 3.4 47.6 1.0
NZ C:LYS81 3.5 59.3 1.0
SBH C:63D401 3.5 53.1 1.0
CZ C:ARG84 3.8 34.2 1.0
NH2 C:ARG84 3.8 42.3 1.0
CAM C:63D401 4.0 73.1 1.0
CBE C:63D401 4.1 73.1 1.0
CE1 C:PHE283 4.1 44.5 1.0
CE2 C:PHE283 4.2 51.3 1.0
NE2 C:GLN119 4.2 50.0 1.0
CE C:LYS81 4.2 67.1 1.0
NAB C:63D401 4.5 45.9 1.0
CBF C:63D401 4.6 76.3 1.0
OAD C:63D401 4.7 55.6 1.0
NE C:ARG84 5.0 35.1 1.0

Chlorine binding site 4 out of 4 in 5hna

Go back to Chlorine Binding Sites List in 5hna
Chlorine binding site 4 out of 4 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase Complexed with Bph-1251 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:68.8
occ:1.00
CL1 D:63D401 0.0 68.8 1.0
CBD D:63D401 1.7 59.8 1.0
CAL D:63D401 2.7 67.5 1.0
CBG D:63D401 2.7 58.4 1.0
OAE D:63D401 3.0 54.8 1.0
NZ D:LYS81 3.2 47.4 1.0
NH1 D:ARG84 3.3 48.2 1.0
SBH D:63D401 3.4 48.7 1.0
CZ D:PHE283 3.6 46.0 1.0
NH2 D:ARG84 3.9 47.4 1.0
CAM D:63D401 4.0 68.2 1.0
CBE D:63D401 4.0 71.5 1.0
CE D:LYS81 4.0 45.5 1.0
CZ D:ARG84 4.1 47.7 1.0
CE1 D:PHE283 4.2 54.2 1.0
NE2 D:GLN119 4.2 51.7 1.0
NAB D:63D401 4.3 48.0 1.0
CBF D:63D401 4.5 76.4 1.0
OAD D:63D401 4.6 55.9 1.0
CE2 D:PHE283 4.6 45.7 1.0

Reference:

C.G Ricci, Y.L.Liu, Y.Zhang, Y.Wang, W.Zhu, E.Oldfield, J.A.Mccammon. Dynamic Structure and Inhibition of A Malaria Drug Target: Geranylgeranyl Diphosphate Synthase. Biochemistry V. 55 5180 2016.
ISSN: ISSN 0006-2960
PubMed: 27564465
DOI: 10.1021/ACS.BIOCHEM.6B00398
Page generated: Sat Dec 12 11:49:01 2020

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