Zinc in PDB 6yj1: The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin

Protein crystallography data

The structure of The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin, PDB code: 6yj1 was solved by M.Dunne, P.Ernst, A.Sobieraj, A.Pluckthun, M.J.Loessner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.43 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 33.890, 56.380, 110.490, 90.00, 92.84, 90.00
R / Rfree (%) 25.1 / 31

Zinc Binding Sites:

The binding sites of Zinc atom in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin (pdb code 6yj1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin, PDB code: 6yj1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6yj1

Go back to Zinc Binding Sites List in 6yj1
Zinc binding site 1 out of 2 in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:26.5
occ:1.00
O A:HOH323 1.9 23.5 1.0
OD1 A:ASP53 2.0 23.8 1.0
ND1 A:HIS135 2.0 23.5 1.0
NE2 A:HIS49 2.1 19.8 1.0
CG A:ASP53 2.7 23.9 1.0
OD2 A:ASP53 2.8 23.4 1.0
CE1 A:HIS135 2.9 22.8 1.0
CD2 A:HIS49 3.0 17.6 1.0
CG A:HIS135 3.0 26.1 1.0
CE1 A:HIS49 3.1 20.8 1.0
CB A:HIS135 3.4 26.4 1.0
NE2 A:HIS135 4.0 25.4 1.0
CG A:HIS49 4.1 16.1 1.0
ND1 A:HIS49 4.1 16.0 1.0
CD2 A:HIS135 4.1 24.0 1.0
CB A:ASP53 4.1 21.6 1.0
CA A:HIS135 4.2 25.4 1.0
NH1 A:ARG32 4.4 24.8 1.0
NE2 A:HIS133 4.5 32.3 1.0
CA A:ASP53 4.6 22.1 1.0
N A:ASP53 4.6 24.0 1.0
NE2 A:HIS97 4.7 31.8 1.0
O A:HOH339 4.7 38.8 1.0
NH2 A:ARG32 4.8 25.4 1.0
O A:PHE52 4.9 23.6 1.0
C A:PHE52 4.9 22.8 1.0
CD2 A:HIS133 4.9 34.7 1.0
CB A:ALA51 5.0 23.1 1.0

Zinc binding site 2 out of 2 in 6yj1

Go back to Zinc Binding Sites List in 6yj1
Zinc binding site 2 out of 2 in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:28.2
occ:1.00
ND1 B:HIS135 1.8 18.6 1.0
OD1 B:ASP53 1.9 25.1 1.0
NE2 B:HIS49 2.0 22.1 1.0
O B:HOH337 2.3 26.4 1.0
CE1 B:HIS135 2.7 18.4 1.0
CG B:ASP53 2.7 22.4 1.0
CD2 B:HIS49 2.9 20.4 1.0
OD2 B:ASP53 2.9 25.9 1.0
CG B:HIS135 2.9 22.6 1.0
CE1 B:HIS49 3.0 20.8 1.0
CB B:HIS135 3.4 25.9 1.0
NE2 B:HIS135 3.9 20.7 1.0
CD2 B:HIS135 4.0 21.4 1.0
ND1 B:HIS49 4.0 19.1 1.0
CG B:HIS49 4.0 21.7 1.0
CA B:HIS135 4.1 25.4 1.0
CB B:ASP53 4.1 21.7 1.0
NH1 B:ARG32 4.3 20.8 1.0
NE2 B:HIS133 4.4 35.9 1.0
CA B:ASP53 4.5 25.9 1.0
N B:ASP53 4.6 26.1 1.0
O B:PHE52 4.7 24.0 1.0
NH2 B:ARG32 4.7 23.0 1.0
CD2 B:HIS133 4.8 31.5 1.0
NE2 B:HIS97 4.8 36.5 1.0
C B:PHE52 4.8 25.0 1.0
CZ B:ARG32 4.9 23.3 1.0

Reference:

A.Sobieraj, M.Dunne, P.Ernst, A.Pluckthun, M.J.Loessner. (Casp Target) Crystal Structure of the M23 Peptidase Domain of Staphylococcal Phage 2638A Endolysin To Be Published.
Page generated: Wed Dec 16 13:16:46 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy