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Zinc in PDB 3hmb: Mutant Endolysin From Bacillus Subtilis

Enzymatic activity of Mutant Endolysin From Bacillus Subtilis

All present enzymatic activity of Mutant Endolysin From Bacillus Subtilis:
3.5.1.28;

Protein crystallography data

The structure of Mutant Endolysin From Bacillus Subtilis, PDB code: 3hmb was solved by L.Y.Low, R.Liddington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.670, 152.760, 188.880, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Mutant Endolysin From Bacillus Subtilis (pdb code 3hmb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mutant Endolysin From Bacillus Subtilis, PDB code: 3hmb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3hmb

Go back to Zinc Binding Sites List in 3hmb
Zinc binding site 1 out of 3 in the Mutant Endolysin From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant Endolysin From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:25.5
occ:1.00
ND1 A:HIS29 2.1 18.7 1.0
ND1 A:HIS130 2.3 26.1 1.0
SG A:CYS138 2.4 28.6 1.0
CE1 A:HIS29 3.0 20.2 1.0
CG A:HIS130 3.2 26.7 1.0
CG A:HIS29 3.2 20.1 1.0
CE1 A:HIS130 3.3 26.7 1.0
O A:HOH188 3.3 24.4 1.0
CB A:HIS130 3.4 24.6 1.0
CB A:CYS138 3.4 29.5 1.0
O A:HOH209 3.5 39.0 1.0
CB A:HIS29 3.6 19.3 1.0
NE2 A:HIS29 4.1 21.8 1.0
CA A:HIS29 4.2 20.9 1.0
CD2 A:HIS29 4.3 21.2 1.0
CD2 A:HIS130 4.3 26.6 1.0
NE2 A:HIS130 4.4 27.1 1.0
O A:HIS77 4.4 26.1 1.0
O A:HOH183 4.4 22.9 1.0
N A:ASN30 4.7 25.8 1.0
CA A:CYS138 4.9 31.3 1.0
OE1 A:GLU93 4.9 30.7 1.0
CA A:HIS130 4.9 25.5 1.0

Zinc binding site 2 out of 3 in 3hmb

Go back to Zinc Binding Sites List in 3hmb
Zinc binding site 2 out of 3 in the Mutant Endolysin From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant Endolysin From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:28.4
occ:1.00
ND1 B:HIS29 2.1 20.0 1.0
ND1 B:HIS130 2.2 25.3 1.0
SG B:CYS138 2.4 29.2 1.0
CE1 B:HIS29 3.0 17.8 1.0
CG B:HIS130 3.0 25.5 1.0
CE1 B:HIS130 3.2 24.7 1.0
CG B:HIS29 3.2 20.5 1.0
CB B:HIS130 3.3 25.5 1.0
CB B:CYS138 3.4 30.0 1.0
CB B:HIS29 3.6 20.9 1.0
O B:HOH206 3.7 26.1 1.0
CA B:HIS29 4.1 22.4 1.0
CD2 B:HIS130 4.1 25.0 1.0
NE2 B:HIS130 4.2 26.6 1.0
NE2 B:HIS29 4.2 19.4 1.0
CD2 B:HIS29 4.3 19.5 1.0
O B:HOH159 4.4 18.5 1.0
N B:ASN30 4.7 27.0 1.0
O B:HIS77 4.7 21.9 1.0
CA B:HIS130 4.7 24.2 1.0
CA B:CYS138 4.8 31.4 1.0
NZ B:LYS136 4.9 32.1 1.0
CE B:LYS136 4.9 29.4 1.0
O B:VAL28 4.9 20.7 1.0
CD B:LYS136 4.9 27.5 1.0

Zinc binding site 3 out of 3 in 3hmb

Go back to Zinc Binding Sites List in 3hmb
Zinc binding site 3 out of 3 in the Mutant Endolysin From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant Endolysin From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:46.2
occ:1.00
ND1 C:HIS29 2.2 37.1 1.0
ND1 C:HIS130 2.5 44.8 1.0
SG C:CYS138 2.5 50.1 1.0
CE1 C:HIS29 2.9 35.8 1.0
O C:HOH164 3.1 39.9 1.0
CG C:HIS29 3.2 35.5 1.0
CG C:HIS130 3.3 46.7 1.0
CE1 C:HIS130 3.4 45.2 1.0
CB C:CYS138 3.4 56.7 1.0
O C:HOH176 3.5 43.9 1.0
CB C:HIS130 3.5 48.8 1.0
CB C:HIS29 3.6 36.6 1.0
NE2 C:HIS29 3.9 36.2 1.0
CD2 C:HIS29 4.1 36.2 1.0
CA C:HIS29 4.1 36.7 1.0
CD2 C:HIS130 4.4 46.9 1.0
NE2 C:HIS130 4.4 45.9 1.0
O C:HIS77 4.5 43.1 1.0
N C:ASN30 4.6 39.2 1.0
OE2 C:GLU93 4.8 45.0 1.0
CA C:CYS138 4.8 59.3 1.0
O C:VAL28 4.9 36.4 1.0
CD C:LYS136 4.9 66.0 1.0
C C:HIS29 5.0 37.8 1.0

Reference:

L.Y.Low, C.Yang, M.Perego, A.Osterman, R.Liddington. Role of Net Charge on Catalytic Domain and Influence of Cell Wall Binding Domain on Bactericidal Activity, Specificity, and Host Range of Phage Lysins. J.Biol.Chem. V. 286 34391 2011.
ISSN: ISSN 0021-9258
PubMed: 21816821
DOI: 10.1074/JBC.M111.244160
Page generated: Wed Dec 16 04:24:12 2020

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