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Chlorine in PDB 4da6: Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir

Enzymatic activity of Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir

All present enzymatic activity of Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir:
2.4.2.1;

Protein crystallography data

The structure of Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir, PDB code: 4da6 was solved by N.H.Martins, P.O.Giuseppe, A.N.Meza, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.17 / 1.70
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 135.551, 135.551, 57.772, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 20.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir (pdb code 4da6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir, PDB code: 4da6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4da6

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Chlorine binding site 1 out of 5 in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir


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 the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:36.9
occ:1.00
 O A:HOH535 2.9 36.3 1.0
NH1 A:ARG87 3.1 25.3 1.0
NH2 A:ARG87 3.2 24.0 1.0
O4' A:GA2301 3.4 31.2 1.0
N A:SER90 3.5 25.2 1.0
O1' A:GA2301 3.5 28.6 1.0
C1' A:GA2301 3.6 27.5 1.0
CZ A:ARG87 3.6 21.9 1.0
CA A:GLY89 3.9 22.9 1.0
O A:SER90 3.9 23.3 1.0
C4' A:GA2301 4.1 32.9 1.0
OG A:SER90 4.2 27.4 1.0
C A:GLY89 4.2 23.5 1.0
OE1 A:GLU180 4.3 23.5 1.0
C2' A:GA2301 4.4 29.4 1.0
CA A:SER90 4.5 24.3 1.0
O A:HOH423 4.5 25.3 1.0
C A:SER90 4.6 24.4 1.0
N A:GLY20 4.7 22.7 1.0
O A:HOH519 4.7 47.0 1.0
CA A:GLY20 4.8 23.0 1.0
CD A:GLU180 4.9 22.1 1.0
CB A:SER90 4.9 24.2 1.0
N9 A:GA2301 4.9 25.7 1.0
NE A:ARG87 5.0 23.0 1.0
OE2 A:GLU180 5.0 23.8 1.0

Chlorine binding site 2 out of 5 in 4da6

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Chlorine binding site 2 out of 5 in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir


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 the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:25.1
occ:1.00
 O A:HOH475 3.2 37.8 1.0
O A:HOH444 3.2 22.5 1.0
ND2 A:ASN161 3.3 22.4 1.0
O A:HOH450 3.3 23.7 1.0
OG A:SER164 3.4 28.9 1.0
O A:HOH406 3.4 19.5 1.0
CE2 A:PHE154 3.7 23.2 1.0
CB A:ASN161 3.9 21.0 1.0
CB A:SER164 3.9 25.3 1.0
CG A:ASN161 4.1 20.3 1.0
CB A:ALA156 4.1 19.1 1.0
O A:GLN158 4.1 20.5 1.0
CA A:SER164 4.2 23.8 1.0
CG2 A:ILE166 4.3 27.1 1.0
CD2 A:PHE154 4.4 20.3 1.0
O A:HOH442 4.6 22.0 1.0
CZ A:PHE154 4.6 19.5 1.0
CG2 A:VAL177 4.7 21.8 1.0
O A:HOH455 4.8 29.8 1.0
OD2 A:ASP112 4.9 19.9 1.0
N A:GLN165 5.0 22.6 1.0

Chlorine binding site 3 out of 5 in 4da6

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Chlorine binding site 3 out of 5 in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir


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 the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:30.0
occ:0.50
 N A:LYS56 3.2 29.2 1.0
CG A:LYS55 3.7 36.4 1.0
CA A:LYS55 3.8 31.7 1.0
CB A:LYS56 3.8 28.4 1.0
CG A:LYS56 4.0 29.9 1.0
C A:LYS55 4.0 30.4 1.0
CA A:LYS56 4.1 28.1 1.0
CB A:LYS55 4.2 32.0 1.0
O A:GLY54 4.5 34.0 1.0
O A:LYS56 4.7 27.1 1.0
O A:HOH430 4.8 30.2 1.0
C A:LYS56 4.9 27.0 1.0
CD A:LYS55 5.0 42.2 1.0
N A:LYS55 5.0 32.2 1.0

Chlorine binding site 4 out of 5 in 4da6

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Chlorine binding site 4 out of 5 in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir


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 the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:40.9
occ:1.00
 O A:HOH478 3.1 40.0 1.0
N A:GLU41 3.1 28.6 1.0
CA A:ASN40 3.8 27.4 1.0
OD1 A:ASN40 3.9 27.3 1.0
CA A:GLY6 3.9 35.0 1.0
N A:VAL42 3.9 28.6 1.0
CG2 A:VAL42 3.9 28.8 1.0
C A:ASN40 3.9 27.1 1.0
CA A:GLU41 4.0 29.2 1.0
CB A:GLU41 4.2 30.2 1.0
O A:TYR39 4.2 30.1 1.0
O A:GLY6 4.3 37.2 1.0
C A:GLU41 4.3 28.4 1.0
N A:GLY6 4.4 33.3 1.0
C A:GLY6 4.4 36.2 1.0
CG A:ASN40 4.6 27.1 1.0
N A:ASN40 4.7 28.1 1.0
C A:TYR39 4.8 29.0 1.0
CG A:GLU41 4.8 35.1 1.0
CB A:ASN40 4.8 25.9 1.0
CA A:VAL42 4.8 27.6 1.0
CB A:VAL42 4.9 27.7 1.0

Chlorine binding site 5 out of 5 in 4da6

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Chlorine binding site 5 out of 5 in the Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Hexameric Purine Nucleoside Phosphorylase From Bacillus Subtilis in Complex with Ganciclovir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:36.5
occ:1.00
 O A:HOH550 2.9 40.0 1.0
O A:HOH487 2.9 39.2 1.0
N A:LYS168 3.2 22.9 1.0
CB A:LYS168 3.5 22.5 0.5
CA A:GLN165 3.5 22.3 1.0
CB A:LYS168 3.6 22.8 0.5
O A:HOH463 3.6 34.2 1.0
CB A:GLU167 3.7 26.3 0.5
C A:GLN165 3.7 22.4 1.0
O A:GLN165 3.7 22.3 1.0
CB A:GLU167 3.8 26.3 0.5
CA A:LYS168 3.9 22.4 0.5
N A:GLU167 4.0 25.4 1.0
CA A:LYS168 4.0 22.5 0.5
CA A:GLU167 4.1 25.5 0.5
C A:GLU167 4.1 25.0 1.0
CA A:GLU167 4.1 25.6 0.5
CB A:GLN165 4.1 22.3 1.0
O A:SER164 4.3 23.9 1.0
CG A:GLU167 4.4 28.5 0.5
N A:ILE166 4.5 23.7 1.0
CG A:GLN165 4.7 22.0 1.0
N A:GLN165 4.7 22.6 1.0
CG A:LYS168 4.7 23.1 0.5
C A:ILE166 4.9 24.8 1.0
OE1 A:GLU167 4.9 33.5 0.5
C A:SER164 4.9 23.4 1.0
CD A:LYS168 4.9 24.0 0.5
CG A:GLU167 4.9 29.2 0.5
CG A:LYS168 5.0 23.2 0.5

Reference:

P.O.De Giuseppe, N.H.Martins, A.N.Meza, C.R.Dos Santos, H.D.Pereira, M.T.Murakami. Insights Into Phosphate Cooperativity and Influence of Substrate Modifications on Binding and Catalysis of Hexameric Purine Nucleoside Phosphorylases. Plos One V. 7 44282 2012.
ISSN: ESSN 1932-6203
PubMed: 22957058
DOI: 10.1371/JOURNAL.PONE.0044282
Page generated: Fri Jul 11 14:17:37 2025

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