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Zinc in PDB 4qp5: Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate

Enzymatic activity of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate

All present enzymatic activity of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate:
3.4.24.75;

Protein crystallography data

The structure of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate, PDB code: 4qp5 was solved by I.Sabala, E.Jagielska, P.T.Bardelang, H.Czapinska, S.O.Dahms, J.A.Sharpe, R.James, M.E.Than, N.R.Thomas, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.04 / 1.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.279, 106.780, 34.331, 90.00, 97.42, 90.00
R / Rfree (%) 13 / 17.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate (pdb code 4qp5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate, PDB code: 4qp5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4qp5

Go back to Zinc Binding Sites List in 4qp5
Zinc binding site 1 out of 2 in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:12.4
occ:1.00
 O3 A:PO4402 1.9 15.8 1.0
OD1 A:ASP283 2.0 10.4 1.0
NE2 A:HIS279 2.1 8.3 1.0
ND1 A:HIS362 2.1 9.3 1.0
CG A:ASP283 2.7 9.0 1.0
O2 A:PO4402 2.8 13.1 1.0
P A:PO4402 2.8 17.0 1.0
OD2 A:ASP283 2.9 10.8 1.0
HB2 A:HIS362 3.0 10.2 1.0
CE1 A:HIS362 3.0 8.5 1.0
CE1 A:HIS279 3.0 8.1 1.0
CD2 A:HIS279 3.1 10.0 1.0
HE1 A:HIS362 3.1 10.2 1.0
CG A:HIS362 3.2 9.2 1.0
HE1 A:HIS279 3.2 9.7 1.0
HD2 A:HIS279 3.3 11.9 1.0
HE2 A:HIS360 3.3 13.3 1.0
CB A:HIS362 3.6 8.5 1.0
O4 A:PO4402 3.7 17.5 1.0
O A:HOH518 3.8 14.4 1.0
HA A:HIS362 3.9 9.1 1.0
O1 A:PO4402 4.0 20.1 1.0
NE2 A:HIS360 4.1 11.1 1.0
ND1 A:HIS279 4.1 8.9 1.0
NE2 A:HIS362 4.2 9.1 1.0
CB A:ASP283 4.2 9.8 1.0
CG A:HIS279 4.2 9.0 1.0
HD2 A:HIS360 4.2 14.3 1.0
CD2 A:HIS362 4.3 8.6 1.0
HB3 A:HIS362 4.3 10.2 1.0
CA A:HIS362 4.3 7.6 1.0
HE2 A:HIS329 4.4 10.7 1.0
HA A:ASP283 4.4 9.8 1.0
CD2 A:HIS360 4.5 11.9 1.0
HE2 A:TYR270 4.6 15.6 1.0
N A:ASP283 4.6 9.2 1.0
CA A:ASP283 4.7 8.2 1.0
HB2 A:ASP283 4.7 11.7 1.0
HB3 A:ASP283 4.7 11.7 1.0
C A:VAL282 4.7 9.5 0.6
C A:VAL282 4.7 9.7 0.5
HH A:TYR270 4.8 21.0 1.0
O A:HOH599 4.8 21.2 1.0
O A:VAL282 4.9 9.2 0.6
O A:VAL282 4.9 9.4 0.5
O A:HOH503 4.9 10.9 1.0
H A:ASP283 4.9 11.0 0.5
H A:ASP283 4.9 11.0 0.5
HD1 A:HIS279 4.9 10.7 1.0
HE2 A:HIS362 4.9 10.9 1.0
HB2 A:TYR265 4.9 15.1 1.0

Zinc binding site 2 out of 2 in 4qp5

Go back to Zinc Binding Sites List in 4qp5
Zinc binding site 2 out of 2 in the Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans Crystallized in the Presence of Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:13.9
occ:1.00
 ND1 B:HIS362 1.9 7.2 1.0
OD1 B:ASP283 2.0 11.1 1.0
O4 B:PO4402 2.0 17.0 1.0
NE2 B:HIS279 2.1 8.6 1.0
O2 B:PO4402 2.7 17.2 1.0
CE1 B:HIS362 2.8 8.3 1.0
CG B:ASP283 2.8 10.2 1.0
P B:PO4402 2.9 18.6 1.0
HE1 B:HIS362 2.9 10.0 1.0
CE1 B:HIS279 2.9 9.7 1.0
HB2 B:HIS362 3.0 9.2 1.0
OD2 B:ASP283 3.0 12.6 1.0
CG B:HIS362 3.0 8.7 1.0
HE1 B:HIS279 3.1 11.7 1.0
CD2 B:HIS279 3.1 9.2 1.0
HD2 B:HIS279 3.4 11.0 1.0
CB B:HIS362 3.5 7.7 1.0
HE2 B:HIS360 3.5 12.4 1.0
O1 B:PO4402 3.7 18.9 1.0
NE2 B:HIS362 3.9 8.3 1.0
HA B:HIS362 4.0 8.3 1.0
O B:HOH530 4.0 25.3 1.0
CD2 B:HIS362 4.1 8.0 1.0
O3 B:PO4402 4.1 19.1 1.0
ND1 B:HIS279 4.1 10.3 1.0
NE2 B:HIS360 4.2 10.3 1.0
CG B:HIS279 4.2 8.8 1.0
HB3 B:HIS362 4.2 9.2 1.0
CB B:ASP283 4.3 9.9 1.0
HD2 B:HIS360 4.3 11.5 1.0
CA B:HIS362 4.3 6.9 1.0
HA B:ASP283 4.5 12.1 1.0
HE2 B:HIS329 4.5 13.3 1.0
N B:ASP283 4.6 10.8 1.0
CD2 B:HIS360 4.6 9.6 1.0
HE2 B:TYR270 4.7 14.8 1.0
CA B:ASP283 4.7 10.1 1.0
C B:VAL282 4.7 8.5 1.0
HE2 B:HIS362 4.7 9.9 1.0
HB3 B:ASP283 4.7 11.8 1.0
HB2 B:ASP283 4.8 11.8 1.0
O B:HOH502 4.8 10.1 1.0
H B:ASP283 4.8 12.9 1.0
HH B:TYR270 4.8 19.3 1.0
O B:VAL282 4.8 8.8 1.0
HD1 B:HIS279 4.9 12.3 1.0
HB2 B:TYR265 4.9 15.4 1.0
H B:GLY281 4.9 11.8 1.0
HD2 B:HIS362 5.0 9.6 1.0

Reference:

I.Sabala, E.Jagielska, P.T.Bardelang, H.Czapinska, S.O.Dahms, J.A.Sharpe, R.James, M.E.Than, N.R.Thomas, M.Bochtler. Crystal Structure of the Antimicrobial Peptidase Lysostaphin From Staphylococcus Simulans. Febs J. V. 281 4112 2014.
ISSN: ISSN 1742-464X
PubMed: 25039253
DOI: 10.1111/FEBS.12929
Page generated: Sun Oct 27 06:42:35 2024

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