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Zinc in PDB 3zwf: Crystal Structure of Human Trnase Z, Short Form (ELAC1).

Enzymatic activity of Crystal Structure of Human Trnase Z, Short Form (ELAC1).

All present enzymatic activity of Crystal Structure of Human Trnase Z, Short Form (ELAC1).:
3.1.26.11;

Protein crystallography data

The structure of Crystal Structure of Human Trnase Z, Short Form (ELAC1)., PDB code: 3zwf was solved by C.K.Allerston, T.Krojer, G.Berridge, N.Burgess-Brown, A.Chaikuad, R.Chalk, J.M.Elkins, C.Gileadi, S.V.A.Latwiel, P.Savitsky, M.Vollmar, C.H.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, F.Von Delft, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.81 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.520, 73.790, 73.660, 90.00, 98.69, 90.00
R / Rfree (%) 18.7 / 21

Other elements in 3zwf:

The structure of Crystal Structure of Human Trnase Z, Short Form (ELAC1). also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Trnase Z, Short Form (ELAC1). (pdb code 3zwf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Trnase Z, Short Form (ELAC1)., PDB code: 3zwf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3zwf

Go back to Zinc Binding Sites List in 3zwf
Zinc binding site 1 out of 4 in the Crystal Structure of Human Trnase Z, Short Form (ELAC1).


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 Human Trnase Z, Short Form (ELAC1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1363

b:27.0
occ:0.90
O3 A:PO41365 2.1 35.7 1.0
O A:HOH2056 2.2 28.4 1.0
OD2 A:ASP253 2.2 23.3 1.0
OD2 A:ASP66 2.2 22.2 1.0
NE2 A:HIS67 2.2 22.4 1.0
NE2 A:HIS313 2.2 23.3 1.0
CE1 A:HIS313 3.0 23.5 1.0
CD2 A:HIS67 3.1 22.0 1.0
CG A:ASP253 3.1 23.4 1.0
CG A:ASP66 3.1 22.0 1.0
CE1 A:HIS67 3.2 22.4 1.0
OD1 A:ASP253 3.3 23.4 1.0
CD2 A:HIS313 3.3 23.3 1.0
P A:PO41365 3.3 29.5 1.0
OD1 A:ASP66 3.4 22.1 1.0
ZN A:ZN1364 3.4 30.1 1.0
O1 A:PO41365 3.6 26.4 1.0
O2 A:PO41365 3.9 24.4 1.0
N A:ALA13 4.1 22.9 1.0
NE2 A:HIS62 4.2 22.8 1.0
O A:HOH2012 4.2 25.9 1.0
ND1 A:HIS313 4.2 23.7 1.0
CE1 A:HIS62 4.2 22.7 1.0
CG A:HIS67 4.3 22.0 1.0
ND1 A:HIS67 4.3 22.2 1.0
CG A:HIS313 4.3 23.6 1.0
CB A:ASP66 4.4 21.9 1.0
CB A:ASP253 4.5 23.9 1.0
CA A:ALA13 4.5 23.1 1.0
O4 A:PO41365 4.6 39.2 1.0
CE1 A:HIS291 4.6 25.2 1.0
OG A:SER22 4.9 23.5 0.5

Zinc binding site 2 out of 4 in 3zwf

Go back to Zinc Binding Sites List in 3zwf
Zinc binding site 2 out of 4 in the Crystal Structure of Human Trnase Z, Short Form (ELAC1).


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 Human Trnase Z, Short Form (ELAC1). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1364

b:30.1
occ:1.00
O A:HOH2056 2.1 28.4 1.0
ND1 A:HIS64 2.2 23.3 1.0
O1 A:PO41365 2.2 26.4 1.0
NE2 A:HIS182 2.3 24.3 1.0
NE2 A:HIS62 2.3 22.8 1.0
OD2 A:ASP253 2.4 23.3 1.0
CE1 A:HIS64 3.1 24.1 1.0
CD2 A:HIS62 3.2 23.0 1.0
CG A:HIS64 3.2 23.4 1.0
CE1 A:HIS182 3.2 24.6 1.0
CD2 A:HIS182 3.3 24.5 1.0
CE1 A:HIS62 3.3 22.7 1.0
P A:PO41365 3.4 29.5 1.0
CG A:ASP253 3.4 23.4 1.0
ZN A:ZN1363 3.4 27.0 0.9
CB A:HIS64 3.6 23.2 1.0
O3 A:PO41365 3.6 35.7 1.0
CB A:ASP253 3.7 23.9 1.0
O2 A:PO41365 3.8 24.4 1.0
NH1 A:ARG183 4.1 31.4 1.0
NE2 A:HIS64 4.2 24.3 1.0
NE2 A:HIS67 4.3 22.4 1.0
CD2 A:HIS64 4.3 23.5 1.0
ND1 A:HIS182 4.3 25.1 1.0
CG A:HIS62 4.3 23.0 1.0
CG A:HIS182 4.4 25.0 1.0
ND1 A:HIS62 4.4 22.9 1.0
NH2 A:ARG183 4.4 49.6 1.0
CE1 A:HIS291 4.4 25.2 1.0
OD1 A:ASP253 4.5 23.4 1.0
CD2 A:HIS67 4.5 22.0 1.0
O4 A:PO41365 4.6 39.2 1.0
OD1 A:ASP66 4.6 22.1 1.0
CZ A:ARG183 4.7 49.1 1.0
NE2 A:HIS291 5.0 25.2 1.0

Zinc binding site 3 out of 4 in 3zwf

Go back to Zinc Binding Sites List in 3zwf
Zinc binding site 3 out of 4 in the Crystal Structure of Human Trnase Z, Short Form (ELAC1).


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 Human Trnase Z, Short Form (ELAC1). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1362

b:30.7
occ:0.79
O B:HOH2043 2.2 47.9 1.0
ND1 B:HIS64 2.2 27.1 1.0
NE2 B:HIS182 2.3 24.8 1.0
O2 B:PO41364 2.3 30.9 0.9
NE2 B:HIS62 2.3 25.9 1.0
OD2 B:ASP253 2.4 24.2 1.0
CE1 B:HIS64 3.1 28.2 1.0
CD2 B:HIS62 3.2 25.8 1.0
CE1 B:HIS182 3.2 25.6 1.0
CD2 B:HIS182 3.2 24.7 1.0
CG B:HIS64 3.3 26.5 1.0
P B:PO41364 3.3 40.6 0.9
CE1 B:HIS62 3.4 25.4 1.0
ZN B:ZN1363 3.4 54.2 0.9
CG B:ASP253 3.4 24.3 1.0
CB B:HIS64 3.6 25.6 1.0
CB B:ASP253 3.7 24.8 1.0
O4 B:PO41364 3.7 34.1 0.9
O1 B:PO41364 3.8 37.4 0.9
NH1 B:ARG183 4.2 34.2 1.0
NE2 B:HIS67 4.2 25.1 1.0
NE2 B:HIS64 4.3 28.0 1.0
ND1 B:HIS182 4.3 26.0 1.0
CG B:HIS182 4.4 25.4 1.0
CG B:HIS62 4.4 25.4 1.0
CD2 B:HIS64 4.4 27.0 1.0
ND1 B:HIS62 4.4 25.1 1.0
CD2 B:HIS67 4.5 24.5 1.0
CE1 B:HIS291 4.5 27.5 1.0
NH2 B:ARG183 4.5 48.1 1.0
OD1 B:ASP253 4.5 25.0 1.0
O3 B:PO41364 4.5 26.8 0.9
OD1 B:ASP66 4.6 25.4 1.0
CZ B:ARG183 4.7 46.1 1.0
NE2 B:HIS291 5.0 28.4 1.0

Zinc binding site 4 out of 4 in 3zwf

Go back to Zinc Binding Sites List in 3zwf
Zinc binding site 4 out of 4 in the Crystal Structure of Human Trnase Z, Short Form (ELAC1).


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 Human Trnase Z, Short Form (ELAC1). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1363

b:54.2
occ:0.91
O4 B:PO41364 2.1 34.1 0.9
OD2 B:ASP253 2.2 24.2 1.0
NE2 B:HIS67 2.2 25.1 1.0
NE2 B:HIS313 2.2 24.6 1.0
OD2 B:ASP66 2.2 25.6 1.0
O B:HOH2043 2.3 47.9 1.0
CE1 B:HIS313 3.0 25.3 1.0
CD2 B:HIS67 3.1 24.5 1.0
CG B:ASP253 3.1 24.3 1.0
CG B:ASP66 3.1 25.2 1.0
P B:PO41364 3.2 40.6 0.9
CD2 B:HIS313 3.3 24.5 1.0
CE1 B:HIS67 3.3 24.9 1.0
OD1 B:ASP253 3.3 25.0 1.0
ZN B:ZN1362 3.4 30.7 0.8
OD1 B:ASP66 3.4 25.4 1.0
O2 B:PO41364 3.6 30.9 0.9
O1 B:PO41364 3.9 37.4 0.9
O B:HOH2007 4.1 36.5 1.0
N B:ALA13 4.1 27.4 1.0
NE2 B:HIS62 4.2 25.9 1.0
ND1 B:HIS313 4.2 25.7 1.0
CE1 B:HIS62 4.3 25.4 1.0
CG B:HIS67 4.3 24.0 1.0
CG B:HIS313 4.3 25.1 1.0
ND1 B:HIS67 4.3 24.2 1.0
O3 B:PO41364 4.4 26.8 0.9
CB B:ASP253 4.5 24.8 1.0
CB B:ASP66 4.5 24.8 1.0
CE1 B:HIS291 4.6 27.5 1.0
CA B:ALA13 4.6 27.6 1.0
OG B:SER22 4.9 25.0 0.5

Reference:

C.K.Allerston, T.Krojer, G.Berridge, N.Burgess-Brown, A.Chaikuad, R.Chalk, J.M.Elkins, C.Gileadi, S.V.A.Latwiel, P.Savitsky, M.Vollmar, C.H.Arrowsmith, J.Weigelt, A.Edwards, C.Bountra, F.Von Delft, O.Gileadi. Crystal Structure of Human Trnase Z, Short Form (ELAC1). To Be Published.
Page generated: Wed Dec 16 05:00:08 2020

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