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Zinc in PDB 2b13: Truncated S. Aureus Lytm, P41 Crystal Form

Enzymatic activity of Truncated S. Aureus Lytm, P41 Crystal Form

All present enzymatic activity of Truncated S. Aureus Lytm, P41 Crystal Form:
3.4.24.75;

Protein crystallography data

The structure of Truncated S. Aureus Lytm, P41 Crystal Form, PDB code: 2b13 was solved by M.Firczuk, A.Mucha, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.80 / 1.55
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 65.962, 65.962, 62.960, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Truncated S. Aureus Lytm, P41 Crystal Form (pdb code 2b13). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Truncated S. Aureus Lytm, P41 Crystal Form, PDB code: 2b13:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2b13

Go back to Zinc Binding Sites List in 2b13
Zinc binding site 1 out of 2 in the Truncated S. Aureus Lytm, P41 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Truncated S. Aureus Lytm, P41 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:15.2
occ:1.00
ND1 A:HIS293 2.1 6.4 1.0
NE2 A:HIS210 2.1 10.9 1.0
OD1 A:ASP214 2.1 9.1 1.0
O4 A:TLA501 2.2 22.1 1.0
O41 A:TLA501 2.3 12.3 1.0
C4 A:TLA501 2.4 23.3 1.0
OD2 A:ASP214 2.7 13.7 1.0
CG A:ASP214 2.7 13.2 1.0
CE1 A:HIS293 2.9 12.3 1.0
CE1 A:HIS210 2.9 15.3 1.0
CD2 A:HIS210 3.2 14.2 1.0
CG A:HIS293 3.2 10.8 1.0
CB A:HIS293 3.6 8.4 1.0
C3 A:TLA501 3.9 31.1 1.0
NE2 A:HIS293 4.1 9.8 1.0
ND1 A:HIS210 4.1 15.3 1.0
O2 A:TLA501 4.1 38.9 1.0
O A:HOH544 4.1 30.3 1.0
CB A:ASP214 4.2 11.3 1.0
CD2 A:HIS293 4.2 10.9 1.0
CG A:HIS210 4.2 12.7 1.0
NE2 A:HIS291 4.3 12.7 1.0
O A:HOH581 4.3 33.7 1.0
C2 A:TLA501 4.4 35.3 1.0
CA A:HIS293 4.5 9.4 1.0
OE1 A:GLN199 4.5 25.9 1.0
CE A:MET259 4.6 23.5 1.0
O3 A:TLA501 4.6 36.1 1.0
N A:ASP214 4.7 12.7 1.0
CD2 A:HIS291 4.8 13.8 1.0
CA A:ASP214 4.8 12.7 1.0
O A:HOH516 4.8 17.3 1.0
NE2 A:HIS260 4.9 13.7 1.0
C A:VAL213 4.9 11.6 1.0

Zinc binding site 2 out of 2 in 2b13

Go back to Zinc Binding Sites List in 2b13
Zinc binding site 2 out of 2 in the Truncated S. Aureus Lytm, P41 Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Truncated S. Aureus Lytm, P41 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:13.5
occ:1.00
OD1 B:ASP214 2.0 8.7 1.0
ND1 B:HIS293 2.1 8.6 1.0
NE2 B:HIS210 2.1 10.1 1.0
O4 B:TLA500 2.1 13.5 1.0
O41 B:TLA500 2.4 13.6 1.0
C4 B:TLA500 2.5 12.0 1.0
CG B:ASP214 2.8 9.9 1.0
OD2 B:ASP214 2.9 9.5 1.0
CE1 B:HIS293 3.0 8.1 1.0
CE1 B:HIS210 3.0 9.8 1.0
CD2 B:HIS210 3.1 8.8 1.0
CG B:HIS293 3.1 8.5 1.0
CB B:HIS293 3.6 8.0 1.0
O B:HOH506 4.0 14.8 1.0
C3 B:TLA500 4.0 14.3 1.0
NE2 B:HIS293 4.1 8.1 1.0
ND1 B:HIS210 4.1 8.9 1.0
CB B:ASP214 4.2 9.9 1.0
CD2 B:HIS293 4.2 8.5 1.0
CG B:HIS210 4.2 9.4 1.0
CA B:HIS293 4.3 8.7 1.0
OH B:TYR204 4.4 11.3 1.0
O2 B:TLA500 4.5 15.7 1.0
CE1 B:TYR204 4.5 10.5 1.0
NE2 B:HIS291 4.5 9.4 1.0
C2 B:TLA500 4.6 14.8 1.0
C B:VAL213 4.6 9.0 1.0
N B:ASP214 4.6 8.8 1.0
O A:GLY206 4.6 8.1 1.0
O B:VAL213 4.7 9.1 1.0
CA B:ASP214 4.7 9.2 1.0
O3 B:TLA500 4.8 12.5 1.0
C B:GLY212 4.8 8.9 1.0
CD2 B:HIS291 4.8 7.4 1.0
CZ B:TYR204 4.9 10.5 1.0
N B:VAL213 4.9 9.6 1.0
O B:GLY212 5.0 10.3 1.0

Reference:

M.Firczuk, A.Mucha, M.Bochtler. Crystal Structures of Active Lytm. J.Mol.Biol. V. 354 578 2005.
ISSN: ISSN 0022-2836
PubMed: 16269153
DOI: 10.1016/J.JMB.2005.09.082
Page generated: Wed Dec 16 03:18:01 2020

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