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Zinc in PDB 4mph: Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound

Protein crystallography data

The structure of Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound, PDB code: 4mph was solved by P.J.Stogios, Z.Wawrzak, O.Onopriyenko, T.Skarina, S.Shatsman, S.N.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomicsof Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.31 / 2.03
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 76.831, 112.337, 125.666, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 18.9

Other elements in 4mph:

The structure of Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound (pdb code 4mph). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound, PDB code: 4mph:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4mph

Go back to Zinc Binding Sites List in 4mph
Zinc binding site 1 out of 2 in the Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound


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 Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:18.2
occ:0.56
OD1 A:ASP167 1.9 13.3 1.0
NE2 A:HIS160 2.0 22.3 1.0
ND1 A:HIS219 2.1 29.4 1.0
CL A:CL401 2.1 48.0 1.0
OD2 A:ASP167 2.4 20.8 1.0
CG A:ASP167 2.5 18.9 1.0
CE1 A:HIS219 2.8 22.6 1.0
CE1 A:HIS160 3.0 27.9 1.0
CD2 A:HIS160 3.1 24.2 1.0
CG A:HIS219 3.2 26.9 1.0
CB A:HIS219 3.7 18.1 1.0
CB A:ASP167 4.0 13.9 1.0
O A:HOH599 4.0 48.6 1.0
NE2 A:HIS219 4.0 24.8 1.0
ND1 A:HIS160 4.1 24.1 1.0
CD2 A:HIS219 4.2 26.0 1.0
CG A:HIS160 4.2 22.4 1.0
OE1 A:GLU216 4.2 23.6 1.0
NE1 A:TRP218 4.3 15.9 1.0
CG2 A:THR165 4.3 22.2 0.6
O A:HOH718 4.4 50.0 1.0
CA A:HIS219 4.4 16.8 1.0
CD1 A:TRP218 4.4 17.5 1.0
CA A:ASP167 4.6 15.9 1.0
NH2 A:ARG127 4.6 55.6 1.0
N A:ASP167 4.7 13.7 1.0

Zinc binding site 2 out of 2 in 4mph

Go back to Zinc Binding Sites List in 4mph
Zinc binding site 2 out of 2 in the Crystal Structure of Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound


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 Baldcb / Vany-Like L,D-Carboxypeptidase Zinc(II)- Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:17.6
occ:0.50
OD1 B:ASP167 1.9 18.8 1.0
NE2 B:HIS160 2.0 23.0 1.0
ND1 B:HIS219 2.1 25.7 1.0
CL B:CL302 2.1 54.0 1.0
OD2 B:ASP167 2.3 20.7 1.0
CG B:ASP167 2.5 22.4 1.0
CE1 B:HIS219 2.8 29.5 1.0
CE1 B:HIS160 2.8 24.2 1.0
CD2 B:HIS160 3.1 19.4 1.0
CG B:HIS219 3.2 28.9 1.0
O B:HOH642 3.6 44.5 1.0
CB B:HIS219 3.7 23.6 1.0
CB B:ASP167 4.0 21.5 1.0
ND1 B:HIS160 4.0 26.4 1.0
NE2 B:HIS219 4.0 25.4 1.0
CG B:HIS160 4.2 23.5 1.0
CD2 B:HIS219 4.2 31.0 1.0
NE1 B:TRP218 4.3 25.2 1.0
CG2 B:THR165 4.4 29.7 1.0
O B:HOH435 4.4 45.3 1.0
OE1 B:GLU216 4.4 31.4 1.0
CA B:HIS219 4.5 20.4 1.0
CD1 B:TRP218 4.5 25.9 1.0
CA B:ASP167 4.6 16.6 1.0
N B:ASP167 4.8 15.4 1.0
O B:HOH604 4.8 56.3 1.0
O B:HOH513 5.0 56.0 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: Wed Dec 16 05:35:39 2020

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