Atomistry » Zinc » PDB 4owp-4p9c » 4ox5
Atomistry »
  Zinc »
    PDB 4owp-4p9c »
      4ox5 »

Zinc in PDB 4ox5: Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition

Protein crystallography data

The structure of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition, PDB code: 4ox5 was solved by C.N.Hoyland, C.Aldridge, R.M.Cleverley, K.Sidiq, M.C.Duchene, R.A.Daniel, W.Vollmer, R.J.Lewis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 1.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 48.855, 60.414, 138.269, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.1

Other elements in 4ox5:

The structure of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition (pdb code 4ox5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition, PDB code: 4ox5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4ox5

Go back to Zinc Binding Sites List in 4ox5
Zinc binding site 1 out of 3 in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:39.9
occ:1.00
OD2 A:ASP184 2.1 31.3 1.0
ND1 A:HIS181 2.1 31.4 1.0
CG A:ASP184 3.0 30.7 1.0
CE1 A:HIS181 3.0 31.4 1.0
CG A:HIS181 3.2 29.5 1.0
OD1 A:ASP184 3.2 36.9 1.0
CB A:HIS181 3.6 26.4 1.0
O A:ASP180 3.9 29.8 1.0
CA A:HIS181 3.9 27.4 1.0
O A:HOH417 3.9 42.5 1.0
NE2 A:HIS181 4.2 34.6 1.0
CD2 A:HIS181 4.3 29.3 1.0
CB A:ASP184 4.4 30.2 1.0
C A:ASP180 4.5 29.4 1.0
N A:HIS181 4.6 27.2 1.0
C A:HIS181 4.9 28.6 1.0
O A:HOH460 5.0 60.5 1.0
O A:HIS181 5.0 28.2 1.0

Zinc binding site 2 out of 3 in 4ox5

Go back to Zinc Binding Sites List in 4ox5
Zinc binding site 2 out of 3 in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:32.4
occ:1.00
OD1 A:ASP160 1.9 30.5 1.0
NE2 A:HIS153 2.1 32.1 1.0
ND1 A:HIS207 2.1 30.6 1.0
CG A:ASP160 2.4 33.3 1.0
OD2 A:ASP160 2.6 35.3 1.0
CE1 A:HIS153 3.0 34.1 1.0
CE1 A:HIS207 3.0 30.1 1.0
CG A:HIS207 3.2 30.5 1.0
CD2 A:HIS153 3.2 33.5 1.0
CB A:HIS207 3.5 30.9 1.0
OE1 A:GLU204 3.9 37.9 1.0
CB A:ASP160 4.0 33.1 1.0
ND1 A:HIS153 4.1 30.3 1.0
NE2 A:HIS207 4.2 28.3 1.0
CG A:HIS153 4.3 31.4 1.0
CD2 A:HIS207 4.3 25.9 1.0
CA A:HIS207 4.3 28.8 1.0
NE1 A:TRP206 4.4 36.3 1.0
CA A:DAL307 4.6 20.0 1.0
N A:DAL307 4.6 20.0 1.0
CD1 A:TRP206 4.6 35.1 1.0
N A:ASP160 4.7 28.4 1.0
CA A:ASP160 4.7 29.7 1.0
NH1 A:ARG120 4.7 62.7 1.0
NH2 A:ARG120 4.8 65.3 1.0
O A:DAL307 4.8 20.0 1.0
C A:DAL307 4.9 20.0 1.0
C A:PHE159 4.9 29.7 1.0

Zinc binding site 3 out of 3 in 4ox5

Go back to Zinc Binding Sites List in 4ox5
Zinc binding site 3 out of 3 in the Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:35.2
occ:1.00
O A:HOH408 1.9 31.0 1.0
NE2 A:HIS79 2.1 38.5 1.0
CD2 A:HIS79 3.1 35.7 1.0
CE1 A:HIS79 3.1 35.9 1.0
OE1 A:GLU232 4.0 54.1 1.0
ND1 A:HIS79 4.2 35.6 1.0
CG A:HIS79 4.2 35.6 1.0
O A:HOH404 4.3 41.2 1.0
OH A:TYR80 4.5 34.4 1.0
OE2 A:GLU232 4.5 49.7 1.0
CD A:GLU232 4.5 45.9 1.0
O A:HOH428 4.7 56.0 1.0
CZ A:TYR80 4.8 35.6 1.0

Reference:

C.N.Hoyland, C.Aldridge, R.M.Cleverley, M.C.Duchene, G.Minasov, O.Onopriyenko, K.Sidiq, P.J.Stogios, W.F.Anderson, R.A.Daniel, A.Savchenko, W.Vollmer, R.J.Lewis. Structure of the Ldcb Ld-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition. Structure V. 22 949 2014.
ISSN: ISSN 0969-2126
PubMed: 24909784
DOI: 10.1016/J.STR.2014.04.015
Page generated: Sun Oct 27 04:06:24 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy