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Sodium in PDB 4epi: The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds

Enzymatic activity of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds

All present enzymatic activity of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds:
3.2.1.17;

Protein crystallography data

The structure of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds, PDB code: 4epi was solved by N.Seddiki, J.W.Fairman, N.Noinaj, P.Lukacik, T.Barnard, S.K.Buchanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.10 / 1.74
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.397, 122.882, 52.299, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 20

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds (pdb code 4epi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds, PDB code: 4epi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4epi

Go back to Sodium Binding Sites List in 4epi
Sodium binding site 1 out of 4 in the The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.0
occ:1.00
 O A:HOH823 2.2 34.1 1.0
OE1 A:GLU119 2.7 14.7 1.0
O A:HOH595 2.8 15.8 1.0
NA A:NA404 3.4 0.7 1.0
OE2 A:GLU119 3.4 12.6 1.0
CD A:GLU119 3.4 13.2 1.0
CA A:GLY115 3.6 11.4 1.0
O A:GLU114 3.7 12.0 1.0
O A:HOH640 4.0 29.5 1.0
CB A:SER25 4.1 13.6 1.0
N A:THR116 4.2 11.8 1.0
C A:GLY115 4.4 11.6 1.0
C A:GLU114 4.5 11.5 1.0
N A:GLY115 4.5 11.5 1.0
CE A:LYS93 4.6 24.4 1.0
N A:SER25 4.8 12.7 1.0
CD A:LYS93 4.9 21.5 1.0
CG2 A:THR116 4.9 13.7 1.0
CG A:GLU119 4.9 13.0 1.0
OG A:SER25 4.9 15.4 1.0

Sodium binding site 2 out of 4 in 4epi

Go back to Sodium Binding Sites List in 4epi
Sodium binding site 2 out of 4 in the The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:65.3
occ:1.00
 O A:HOH628 3.5 30.4 1.0
O A:HOH823 3.7 34.1 1.0
OE2 A:GLU119 3.7 12.6 1.0
O A:HOH1027 4.0 40.1 1.0
O A:HOH994 4.4 48.5 1.0
CD A:GLU119 5.0 13.2 1.0

Sodium binding site 3 out of 4 in 4epi

Go back to Sodium Binding Sites List in 4epi
Sodium binding site 3 out of 4 in the The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:0.7
occ:1.00
 O A:HOH823 2.4 34.1 1.0
NA A:NA402 3.4 25.0 1.0
O A:HOH640 3.6 29.5 1.0
OG A:SER25 3.8 15.4 1.0
CB A:SER25 4.0 13.6 1.0
CE A:LYS93 4.1 24.4 1.0
O A:HOH1027 4.3 40.1 1.0
O A:HOH1008 4.9 46.7 1.0
NZ A:LYS93 4.9 25.0 1.0

Sodium binding site 4 out of 4 in 4epi

Go back to Sodium Binding Sites List in 4epi
Sodium binding site 4 out of 4 in the The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Pesticin-T4 Lysozyme Hybrid Stabilized By Engineered Disulfide Bonds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:19.5
occ:1.00
 O A:HOH924 3.2 32.8 1.0
N A:SER282 3.3 16.7 1.0
OG A:SER282 3.3 15.9 1.0
C A:PHE279 3.4 17.0 1.0
CA A:PHE279 3.5 16.5 1.0
O A:HOH743 3.5 34.5 1.0
N A:ASN281 3.6 17.9 1.0
O A:PHE279 3.6 17.2 1.0
OD1 A:ASN297 3.7 18.9 1.0
CB A:SER282 3.7 16.0 1.0
O A:HOH747 3.7 34.8 1.0
N A:THR280 3.8 17.9 1.0
CB A:PHE279 3.8 15.8 1.0
CB A:ASN281 3.9 19.3 1.0
CA A:ASN281 4.0 18.3 1.0
CA A:SER282 4.1 16.5 1.0
CD1 A:PHE279 4.1 15.4 1.0
C A:ASN281 4.1 17.6 1.0
CG A:PHE279 4.4 14.9 1.0
C A:THR280 4.4 18.5 1.0
CA A:THR280 4.7 18.8 1.0
O A:GLY278 4.7 17.6 1.0
CG A:ASN281 4.8 23.6 1.0
N A:PHE279 4.8 16.2 1.0
O A:HOH970 4.8 0.4 1.0
ND2 A:ASN281 4.9 27.3 1.0
CG A:ASN297 4.9 15.2 1.0

Reference:

P.Lukacik, T.J.Barnard, P.W.Keller, K.S.Chaturvedi, N.Seddiki, J.W.Fairman, N.Noinaj, T.L.Kirby, J.P.Henderson, A.C.Steven, B.J.Hinnebusch, S.K.Buchanan. Structural Engineering of A Phage Lysin That Targets Gram-Negative Pathogens. Proc.Natl.Acad.Sci.Usa V. 109 9857 2012.
ISSN: ISSN 0027-8424
PubMed: 22679291
DOI: 10.1073/PNAS.1203472109
Page generated: Mon Oct 7 15:11:20 2024

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