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Zinc in PDB 3lat: Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie

Enzymatic activity of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie

All present enzymatic activity of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie:
3.5.1.28;

Protein crystallography data

The structure of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie, PDB code: 3lat was solved by S.Zoll, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.77 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.453, 99.453, 148.783, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.5

Other elements in 3lat:

The structure of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie (pdb code 3lat). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie, PDB code: 3lat:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 3lat

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Zinc binding site 1 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn215

b:19.4
occ:1.00
 OD2 A:ASP179 2.0 19.5 1.0
O A:HOH372 2.0 18.3 1.0
ND1 A:HIS60 2.1 17.7 1.0
ND1 A:HIS165 2.1 17.2 1.0
CG A:ASP179 2.7 19.6 1.0
OD1 A:ASP179 2.7 18.2 1.0
CE1 A:HIS60 3.0 18.3 1.0
CG A:HIS165 3.0 18.3 1.0
CE1 A:HIS165 3.1 16.3 1.0
CG A:HIS60 3.2 17.4 1.0
CB A:HIS165 3.3 18.7 1.0
ZN A:ZN216 3.5 19.1 0.9
CB A:HIS60 3.6 18.4 1.0
O A:HOH338 3.8 22.5 1.0
O A:HOH373 3.9 30.0 1.0
CA A:HIS60 4.0 18.6 1.0
NE2 A:HIS60 4.1 18.2 1.0
CB A:ASP179 4.2 18.9 1.0
NE2 A:HIS165 4.2 17.5 1.0
CD2 A:HIS165 4.2 18.2 1.0
CD2 A:HIS60 4.2 18.9 1.0
CB A:HIS177 4.5 18.6 1.0
ND1 A:HIS177 4.5 18.4 1.0
O A:GLY106 4.6 19.4 1.0
CA A:HIS165 4.8 18.5 1.0
N A:ASP61 4.8 18.5 1.0
O A:ASP61 4.8 19.3 1.0
OE1 A:GLU119 4.9 20.7 1.0
CG A:HIS177 4.9 18.0 1.0
O A:VAL59 4.9 19.9 1.0
C A:HIS60 5.0 18.7 1.0

Zinc binding site 2 out of 14 in 3lat

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Zinc binding site 2 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn216

b:19.1
occ:0.90
 O A:HOH372 1.9 18.3 1.0
ND1 A:HIS177 2.1 18.4 1.0
CE1 A:HIS177 3.0 18.6 1.0
CG A:HIS177 3.2 18.0 1.0
ZN A:ZN215 3.5 19.4 1.0
OD1 A:ASP179 3.6 18.2 1.0
CB A:HIS177 3.6 18.6 1.0
O A:HOH338 3.7 22.5 1.0
O A:HOH373 3.8 30.0 1.0
CG A:ASP179 4.0 19.6 1.0
OD2 A:ASP179 4.1 19.5 1.0
NE2 A:HIS177 4.2 18.4 1.0
ND1 A:HIS165 4.3 17.2 1.0
CD2 A:HIS177 4.3 18.5 1.0
CE1 A:HIS165 4.3 16.3 1.0
O A:ASP61 4.9 19.3 1.0
CB A:ASP179 5.0 18.9 1.0

Zinc binding site 3 out of 14 in 3lat

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Zinc binding site 3 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn217

b:31.1
occ:0.75
 O A:HOH377 2.1 32.6 1.0
O A:HOH379 2.1 45.0 1.0
O A:HOH378 2.1 45.0 1.0
OD2 A:ASP152 2.1 29.5 1.0
O A:HOH375 2.1 28.2 1.0
O A:HOH376 2.2 36.9 1.0
CG A:ASP152 3.0 27.4 1.0
OD1 A:ASP152 3.2 30.8 1.0
O A:SER153 3.9 24.5 1.0
O A:HOH380 4.0 80.8 1.0
O A:HOH476 4.1 29.8 1.0
OD2 A:ASP157 4.2 37.1 1.0
O A:ARG159 4.4 26.7 1.0
CB A:ASP152 4.4 25.6 1.0
OD1 A:ASP157 4.5 33.5 1.0
N A:SER153 4.7 24.4 1.0
O A:HOH310 4.8 33.3 1.0
CG A:ASP157 4.8 32.4 1.0
CA A:ASP152 4.8 25.4 1.0
C A:ASP152 4.9 25.1 1.0
C A:SER153 4.9 24.2 1.0

Zinc binding site 4 out of 14 in 3lat

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Zinc binding site 4 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn218

b:25.3
occ:0.60
 OE1 A:GLU36 2.1 32.2 1.0
OE2 A:GLU36 2.7 35.7 1.0
CD A:GLU36 2.7 31.5 1.0
O A:HOH331 3.4 40.0 1.0
CE2 A:TYR38 4.0 20.7 1.0
CG A:GLU36 4.2 28.5 1.0
CD2 A:TYR38 4.5 19.7 1.0
CZ A:TYR38 4.7 20.5 1.0
CB A:GLU36 4.8 23.8 1.0
OH A:TYR38 4.8 21.9 1.0

Zinc binding site 5 out of 14 in 3lat

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Zinc binding site 5 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn219

b:24.3
occ:0.60
 O A:HOH454 2.0 46.0 1.0
O A:HOH457 2.1 52.1 1.0
OE2 A:GLU96 2.2 28.7 1.0
OE1 A:GLU96 2.3 24.4 1.0
CD A:GLU96 2.6 23.2 1.0
OG1 A:THR100 3.9 19.9 1.0
OH A:TYR38 4.0 21.9 1.0
CG A:GLU96 4.1 20.7 1.0
O A:HOH455 4.4 49.6 1.0
CG2 A:THR100 4.5 20.1 1.0
NE2 A:GLN143 4.5 27.5 1.0
OE1 A:GLN143 4.6 32.0 1.0
O A:HOH456 4.7 48.2 1.0
OH A:TYR139 4.7 20.9 1.0
CB A:GLU96 4.8 18.8 1.0
CB A:THR100 4.8 18.6 1.0
N A:THR100 4.8 17.9 1.0
OE2 A:GLU36 4.9 35.7 1.0
CD A:GLN143 4.9 27.1 1.0

Zinc binding site 6 out of 14 in 3lat

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Zinc binding site 6 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn220

b:30.5
occ:0.40
 OD2 A:ASP65 2.0 30.6 1.0
ZN A:ZN221 2.4 40.6 0.4
O A:HOH367 2.9 60.6 1.0
CG A:ASP65 2.9 29.3 1.0
CE1 A:HIS124 3.1 33.0 1.0
OD1 A:ASP65 3.1 28.8 1.0
ND1 A:HIS124 3.2 33.8 1.0
O A:HOH224 3.7 29.4 1.0
O A:HOH400 3.9 44.1 1.0
CB A:ASP65 4.3 28.6 1.0
NE2 A:HIS124 4.4 34.2 1.0
O A:ASP65 4.5 30.7 1.0
CG A:HIS124 4.5 31.7 1.0
O A:HOH254 4.8 53.8 1.0
OD1 A:ASN66 4.8 39.8 1.0

Zinc binding site 7 out of 14 in 3lat

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Zinc binding site 7 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn221

b:40.6
occ:0.40
 ND1 A:HIS124 2.0 33.8 1.0
ZN A:ZN220 2.4 30.5 0.4
CE1 A:HIS124 2.9 33.0 1.0
CG A:HIS124 3.0 31.7 1.0
CB A:HIS124 3.4 29.8 1.0
O A:HOH254 3.5 53.8 1.0
O A:HOH367 3.8 60.6 1.0
NE2 A:HIS124 4.0 34.2 1.0
CD2 A:HIS124 4.1 32.7 1.0
OD2 A:ASP65 4.1 30.6 1.0
CA A:HIS124 4.1 29.7 1.0
O A:HOH224 4.4 29.4 1.0
O A:THR123 4.6 26.4 1.0
CG A:ASP65 4.9 29.3 1.0
OD1 A:ASP65 4.9 28.8 1.0
O A:HIS124 5.0 30.9 1.0

Zinc binding site 8 out of 14 in 3lat

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Zinc binding site 8 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn215

b:19.3
occ:1.00
 O B:HOH312 2.0 20.2 1.0
OD2 B:ASP179 2.0 18.4 1.0
ND1 B:HIS60 2.1 17.6 1.0
ND1 B:HIS165 2.1 17.2 1.0
CG B:ASP179 2.7 19.1 1.0
OD1 B:ASP179 2.7 19.0 1.0
CE1 B:HIS60 3.0 17.3 1.0
CG B:HIS165 3.0 17.8 1.0
CE1 B:HIS165 3.1 18.5 1.0
CG B:HIS60 3.2 17.3 1.0
CB B:HIS165 3.3 19.1 1.0
ZN B:ZN216 3.5 19.6 0.9
CB B:HIS60 3.6 17.5 1.0
O B:HOH355 3.8 22.4 1.0
O B:HOH313 3.9 27.6 1.0
CA B:HIS60 4.0 18.1 1.0
NE2 B:HIS60 4.1 17.8 1.0
CB B:ASP179 4.2 18.2 1.0
NE2 B:HIS165 4.2 18.3 1.0
CD2 B:HIS165 4.2 18.6 1.0
CD2 B:HIS60 4.2 19.1 1.0
CB B:HIS177 4.5 19.5 1.0
ND1 B:HIS177 4.5 20.5 1.0
O B:GLY106 4.6 23.7 1.0
CA B:HIS165 4.8 18.9 1.0
N B:ASP61 4.8 18.1 1.0
O B:ASP61 4.9 18.1 1.0
OE1 B:GLU119 4.9 20.5 1.0
CG B:HIS177 4.9 19.1 1.0
O B:VAL59 5.0 19.2 1.0
C B:HIS60 5.0 17.9 1.0

Zinc binding site 9 out of 14 in 3lat

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Zinc binding site 9 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn216

b:19.6
occ:0.90
 O B:HOH312 1.9 20.2 1.0
ND1 B:HIS177 2.1 20.5 1.0
O5 B:BU1222 2.1 18.6 1.0
CE1 B:HIS177 3.0 20.1 1.0
CG B:HIS177 3.2 19.1 1.0
ZN B:ZN215 3.5 19.3 1.0
C1 B:BU1222 3.5 29.5 1.0
CB B:HIS177 3.6 19.5 1.0
OD1 B:ASP179 3.6 19.0 1.0
O B:HOH355 3.7 22.4 1.0
O B:HOH313 3.9 27.6 1.0
CG B:ASP179 4.0 19.1 1.0
OD2 B:ASP179 4.1 18.4 1.0
NE2 B:HIS177 4.1 19.9 1.0
C2 B:BU1222 4.2 30.3 1.0
CD2 B:HIS177 4.3 20.1 1.0
ND1 B:HIS165 4.3 17.2 1.0
CE1 B:HIS165 4.3 18.5 1.0
C4 B:BU1222 4.7 26.9 1.0
O B:ASP61 4.9 18.1 1.0
C3 B:BU1222 4.9 28.6 1.0
CB B:ASP179 5.0 18.2 1.0

Zinc binding site 10 out of 14 in 3lat

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Zinc binding site 10 out of 14 in the Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Staphylococcus Peptidoglycan Hydrolase Amie within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn217

b:19.7
occ:0.90
 OD1 B:ASP176 1.9 22.1 1.0
N1 B:IMD214 2.0 18.6 1.0
CG B:ASP176 2.7 21.6 1.0
OD2 B:ASP176 2.9 21.8 1.0
C5 B:IMD214 2.9 19.4 1.0
C2 B:IMD214 3.0 19.6 1.0
CD2 B:HIS177 4.0 20.1 1.0
O B:HOH291 4.1 19.1 1.0
C4 B:IMD214 4.1 19.0 1.0
N3 B:IMD214 4.1 18.9 1.0
CB B:ASP176 4.2 20.9 1.0
NE2 B:HIS177 4.2 19.9 1.0
C B:ASP176 4.7 20.0 1.0
CA B:ASP176 4.9 20.4 1.0
N B:HIS177 4.9 19.5 1.0
O B:HOH382 4.9 20.8 1.0
O B:ASP176 5.0 19.5 1.0

Reference:

S.Zoll, B.Patzold, M.Schlag, F.Gotz, H.Kalbacher, T.Stehle. Structural Basis of Cell Wall Cleavage By A Staphylococcal Autolysin Plos Pathog. V. 6 E1000 2010.
ISSN: ISSN 1553-7366
PubMed: 20300605
DOI: 10.1371/JOURNAL.PPAT.1000807
Page generated: Wed Dec 16 04:32:04 2020

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