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Sodium in PDB 4phi: Crystal Structure of Hewl with Hexatungstotellurate(VI)

Enzymatic activity of Crystal Structure of Hewl with Hexatungstotellurate(VI)

All present enzymatic activity of Crystal Structure of Hewl with Hexatungstotellurate(VI):
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hewl with Hexatungstotellurate(VI), PDB code: 4phi was solved by A.Bijelic, C.Molitor, S.G.Mauracher, R.Al-Oweini, U.Kortz, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.25 / 1.81
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.010, 60.010, 261.840, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 20

Other elements in 4phi:

The structure of Crystal Structure of Hewl with Hexatungstotellurate(VI) also contains other interesting chemical elements:

Tungsten (W) 48 atoms
Tellurium (Te) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hewl with Hexatungstotellurate(VI) (pdb code 4phi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Hewl with Hexatungstotellurate(VI), PDB code: 4phi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4phi

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Sodium binding site 1 out of 6 in the Crystal Structure of Hewl with Hexatungstotellurate(VI)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Hewl with Hexatungstotellurate(VI) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:39.4
occ:1.00
O A:HOH464 1.8 30.8 1.0
HG12 A:ILE88 2.7 36.5 1.0
H A:ILE88 2.7 31.7 1.0
HA A:ASP87 3.0 36.0 1.0
O A:HOH447 3.2 30.8 1.0
HZ A:PHE3 3.2 36.2 1.0
HE1 A:HIS15 3.5 35.7 1.0
N A:ILE88 3.5 27.1 1.0
HG23 A:ILE88 3.5 37.7 1.0
CG1 A:ILE88 3.6 29.7 1.0
O A:HOH450 3.7 30.8 1.0
HB1 A:ALA11 3.7 35.9 1.0
O A:SER86 3.8 28.9 1.0
CA A:ASP87 3.9 33.1 1.0
O A:HOH326 3.9 36.9 1.0
HG13 A:ILE88 4.0 36.5 1.0
OD1 A:ASP87 4.0 35.4 1.0
CZ A:PHE3 4.1 29.1 1.0
CE1 A:HIS15 4.1 32.0 1.0
C A:ASP87 4.2 29.3 1.0
CG2 A:ILE88 4.3 29.9 1.0
CB A:ILE88 4.3 29.2 1.0
HD11 A:ILE88 4.4 36.7 1.0
HE2 A:PHE3 4.4 33.9 1.0
CD1 A:ILE88 4.4 30.0 1.0
HD13 A:ILE88 4.4 36.7 1.0
HB2 A:ALA11 4.5 35.9 1.0
CA A:ILE88 4.5 26.6 1.0
CB A:ALA11 4.5 29.9 1.0
CG A:ASP87 4.6 36.1 1.0
NE2 A:HIS15 4.6 33.7 1.0
HG21 A:ILE88 4.6 37.7 1.0
C A:SER86 4.7 29.2 1.0
CE2 A:PHE3 4.7 28.4 1.0
N A:ASP87 4.8 30.1 1.0
CB A:ASP87 4.8 32.5 1.0
H A:THR89 4.9 30.6 1.0
HG1 A:THR89 5.0 38.5 1.0
O A:HOH341 5.0 30.8 1.0

Sodium binding site 2 out of 6 in 4phi

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Sodium binding site 2 out of 6 in the Crystal Structure of Hewl with Hexatungstotellurate(VI)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Hewl with Hexatungstotellurate(VI) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na206

b:32.8
occ:1.00
HB3 C:ARG45 2.8 26.8 1.0
HB3 B:ARG45 2.8 29.2 1.0
O B:HOH453 2.9 30.8 1.0
O D:HOH441 3.2 30.8 1.0
O B:HOH401 3.2 19.2 1.0
O C:HOH371 3.3 24.3 1.0
O B:HOH420 3.5 37.1 1.0
CB C:ARG45 3.7 24.1 1.0
O D:HOH439 3.7 30.8 1.0
CB B:ARG45 3.8 23.9 1.0
O B:HOH454 3.8 30.8 1.0
O C:HOH395 3.8 44.6 1.0
HG2 C:ARG45 3.9 35.6 1.0
HB2 C:ARG45 3.9 26.8 1.0
HG2 B:ARG45 4.0 38.1 1.0
HB2 B:ARG45 4.0 29.2 1.0
H C:ARG45 4.2 26.0 1.0
H B:ARG45 4.2 24.3 1.0
CG C:ARG45 4.2 28.0 1.0
HG3 C:ARG45 4.3 35.6 1.0
CG B:ARG45 4.3 28.3 1.0
HG3 B:ARG45 4.4 38.1 1.0
O B:ARG45 4.6 24.9 1.0
O C:ARG45 4.7 24.4 1.0
O B:HOH442 4.7 30.9 1.0
CA C:ARG45 4.7 25.1 1.0
CA B:ARG45 4.8 23.4 1.0
N C:ARG45 4.8 24.0 1.0
N B:ARG45 4.8 21.4 1.0
O D:HOH431 4.9 30.8 1.0
O B:HOH456 4.9 30.8 1.0
O B:HOH458 4.9 30.8 1.0
O31 B:TEW202 5.0 35.5 0.4

Sodium binding site 3 out of 6 in 4phi

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Sodium binding site 3 out of 6 in the Crystal Structure of Hewl with Hexatungstotellurate(VI)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Hewl with Hexatungstotellurate(VI) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na207

b:33.5
occ:1.00
H B:ASN59 2.1 25.9 1.0
O B:HOH468 2.2 30.8 1.0
O B:HOH358 2.6 30.9 1.0
HB2 B:ASN59 2.8 24.1 1.0
N B:ASN59 2.9 22.4 1.0
O B:HOH439 2.9 30.9 1.0
HA B:ILE58 2.9 16.1 1.0
HB3 B:ASN59 3.0 24.1 1.0
HD1 B:TRP63 3.2 20.2 1.0
CB B:ASN59 3.2 21.7 1.0
HE1 B:TRP63 3.3 24.6 1.0
CA B:ASN59 3.7 19.9 1.0
CD1 B:TRP63 3.7 17.7 1.0
NE1 B:TRP63 3.7 19.9 1.0
CA B:ILE58 3.7 14.5 1.0
C B:ILE58 3.8 17.4 1.0
HG23 B:ILE58 3.8 22.9 1.0
O B:GLN57 3.8 18.1 1.0
O B:HOH371 3.9 30.8 1.0
HD13 B:ILE98 4.2 18.9 1.0
HA B:ASN59 4.3 20.4 1.0
O B:HOH430 4.4 44.6 1.0
CG2 B:ILE58 4.5 18.0 1.0
HG12 B:ILE58 4.6 20.8 1.0
HG22 B:ILE58 4.6 22.9 1.0
CG B:ASN59 4.6 23.6 1.0
CB B:ILE58 4.7 14.6 1.0
C B:GLN57 4.7 16.9 1.0
N B:ILE58 4.7 16.0 1.0
C B:ASN59 4.7 24.6 1.0
O B:ASN59 4.8 22.3 1.0
OD1 B:ASP52 4.8 25.0 1.0
HD11 B:ILE98 4.8 18.9 1.0
CG B:TRP63 4.9 17.7 1.0
O B:ILE58 4.9 17.2 1.0
HD22 B:ASN59 4.9 32.6 1.0
CE2 B:TRP63 5.0 17.4 1.0
CD1 B:ILE98 5.0 16.6 1.0

Sodium binding site 4 out of 6 in 4phi

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Sodium binding site 4 out of 6 in the Crystal Structure of Hewl with Hexatungstotellurate(VI)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Hewl with Hexatungstotellurate(VI) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:46.0
occ:1.00
O C:HOH424 2.2 30.9 1.0
O A:HOH363 2.4 39.3 1.0
HO1 A:GOL204 3.6 42.4 1.0
O1 A:GOL204 3.7 37.8 1.0
H C:GLY71 4.1 39.4 1.0
HO2 A:GOL204 4.3 38.9 1.0
H11 A:GOL204 4.4 39.3 1.0
C1 A:GOL204 4.7 36.4 1.0
HA2 C:GLY71 4.8 31.2 1.0
H31 A:GOL204 4.9 63.2 1.0
N C:GLY71 4.9 35.0 1.0

Sodium binding site 5 out of 6 in 4phi

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Sodium binding site 5 out of 6 in the Crystal Structure of Hewl with Hexatungstotellurate(VI)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Hewl with Hexatungstotellurate(VI) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:37.2
occ:1.00
H C:ILE88 2.6 32.6 1.0
HG12 C:ILE88 2.8 32.3 1.0
O C:HOH417 2.8 30.9 1.0
HA C:ASP87 2.9 36.0 1.0
O C:HOH418 3.0 30.9 1.0
HZ C:PHE3 3.3 41.7 1.0
N C:ILE88 3.5 28.0 1.0
O C:HOH339 3.6 30.9 1.0
OD1 C:ASP87 3.6 32.8 1.0
HE1 C:HIS15 3.7 40.4 1.0
O C:HOH447 3.7 30.8 1.0
HG23 C:ILE88 3.7 32.9 1.0
CG1 C:ILE88 3.7 28.2 1.0
CA C:ASP87 3.8 29.4 1.0
HB1 C:ALA11 3.8 38.0 1.0
O C:SER86 3.8 30.6 1.0
HG13 C:ILE88 4.0 32.3 1.0
O C:HOH448 4.0 30.8 1.0
C C:ASP87 4.1 28.5 1.0
CZ C:PHE3 4.2 32.2 1.0
CG C:ASP87 4.3 31.4 1.0
HE2 C:PHE3 4.3 36.7 1.0
CE1 C:HIS15 4.4 36.2 1.0
CB C:ILE88 4.4 27.1 1.0
HB2 C:ALA11 4.4 38.0 1.0
CG2 C:ILE88 4.5 28.1 1.0
CA C:ILE88 4.5 28.6 1.0
HD11 C:ILE88 4.5 43.8 1.0
CB C:ASP87 4.6 28.0 1.0
CB C:ALA11 4.6 32.5 1.0
CD1 C:ILE88 4.6 33.8 1.0
H C:THR89 4.6 28.7 1.0
O C:HOH355 4.6 30.9 1.0
HD13 C:ILE88 4.7 43.8 1.0
C C:SER86 4.7 28.9 1.0
CE2 C:PHE3 4.7 30.1 1.0
N C:ASP87 4.7 26.8 1.0
HG21 C:ILE88 4.8 32.9 1.0
HG1 C:THR89 4.8 34.0 1.0
HB2 C:ASP87 4.8 32.9 1.0
NE2 C:HIS15 4.9 33.9 1.0
HB3 C:ALA11 5.0 38.0 1.0

Sodium binding site 6 out of 6 in 4phi

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Sodium binding site 6 out of 6 in the Crystal Structure of Hewl with Hexatungstotellurate(VI)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Hewl with Hexatungstotellurate(VI) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:41.8
occ:1.00
HH22 D:ARG14 2.1 39.2 1.0
O D:HOH328 2.5 34.0 1.0
O D:GLU7 2.8 26.6 1.0
HG2 D:GLU7 2.9 25.1 1.0
NH2 D:ARG14 3.0 31.5 1.0
HG3 D:GLU7 3.0 25.1 1.0
HB2 D:ALA11 3.1 30.4 1.0
HH21 D:ARG14 3.4 39.2 1.0
CG D:GLU7 3.4 22.7 1.0
HB3 D:ALA10 3.4 33.1 1.0
HH12 D:ARG14 3.4 35.0 1.0
HA D:GLU7 3.5 30.1 1.0
C D:GLU7 3.7 25.0 1.0
H D:ALA11 3.8 24.2 1.0
HE2 D:PHE3 3.9 25.4 1.0
CZ D:ARG14 3.9 31.1 1.0
CA D:GLU7 4.0 25.4 1.0
NH1 D:ARG14 4.0 30.1 1.0
CB D:ALA11 4.1 23.0 1.0
N D:ALA11 4.1 20.7 1.0
HA D:ALA11 4.3 29.5 1.0
CB D:GLU7 4.3 24.7 1.0
CB D:ALA10 4.3 27.9 1.0
CA D:ALA11 4.4 23.0 1.0
HB1 D:ALA10 4.4 33.1 1.0
HB3 D:ALA11 4.5 30.4 1.0
CD D:GLU7 4.5 20.7 1.0
OE2 D:GLU7 4.6 25.7 1.0
HD2 D:PHE3 4.6 30.4 1.0
HB1 D:ALA11 4.6 30.4 1.0
CE2 D:PHE3 4.7 21.8 1.0
O D:HOH363 4.8 30.9 1.0
C D:ALA10 4.8 26.8 1.0
HH11 D:ARG14 4.8 35.0 1.0
HB2 D:GLU7 4.9 29.1 1.0
N D:LEU8 4.9 24.1 1.0
HB2 D:ALA10 4.9 33.1 1.0
HB3 D:GLU7 4.9 29.1 1.0
HA D:LEU8 4.9 30.2 1.0

Reference:

A.Bijelic, C.Molitor, S.G.Mauracher, R.Al-Oweini, U.Kortz, A.Rompel. Hen Egg-White Lysozyme Crystallisation: Protein Stacking and Structure Stability Enhanced By A Tellurium(VI)-Centred Polyoxotungstate. Chembiochem V. 16 233 2015.
ISSN: ESSN 1439-7633
PubMed: 25521080
DOI: 10.1002/CBIC.201402597
Page generated: Tue Dec 15 06:58:17 2020

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