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Zinc in PDB 2vac: Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2

Protein crystallography data

The structure of Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2, PDB code: 2vac was solved by J.M.Elkins, A.C.W.Pike, O.King, E.Salah, P.Savitsky, F.Von Delft, J.Weigelt, A.Edwards, C.H.Arrowsmith, M.Sundstrom, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.817, 48.560, 70.127, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2 (pdb code 2vac). 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 N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2, PDB code: 2vac:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2vac

Go back to Zinc Binding Sites List in 2vac
Zinc binding site 1 out of 3 in the Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1138

b:16.6
occ:0.60
O A:HOH2157 1.8 21.4 1.0
N A:SER-1 2.1 24.1 1.0
NE2 A:HIS8 2.1 23.8 1.0
O A:SER-1 2.1 22.4 1.0
C A:SER-1 2.8 20.9 1.0
CA A:SER-1 2.9 22.4 1.0
CD2 A:HIS8 3.1 23.2 1.0
CE1 A:HIS8 3.1 22.7 1.0
CB A:SER-1 4.1 20.4 1.0
N A:MET0 4.1 22.3 1.0
OG A:SER-1 4.2 24.9 1.0
ND1 A:HIS8 4.2 22.1 1.0
CG A:HIS8 4.2 16.6 1.0
O A:GLY6 4.4 16.4 1.0
CA A:MET0 4.9 21.2 1.0

Zinc binding site 2 out of 3 in 2vac

Go back to Zinc Binding Sites List in 2vac
Zinc binding site 2 out of 3 in the Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1139

b:15.4
occ:1.00
NE2 A:HIS137 2.0 17.1 1.0
O A:HOH2158 2.0 13.0 1.0
OD1 A:ASP119 2.0 16.7 1.0
CG A:ASP119 2.7 14.8 1.0
OD2 A:ASP119 2.7 17.4 1.0
CD2 A:HIS137 2.9 19.9 1.0
CE1 A:HIS137 3.0 22.2 1.0
O A:GLU120 3.8 18.8 1.0
CG A:HIS137 4.1 19.0 1.0
ND1 A:HIS137 4.1 24.4 1.0
O A:HOH2137 4.2 19.9 1.0
CB A:ASP119 4.2 17.4 1.0
N A:GLU120 4.4 18.7 1.0
CA A:ASP119 4.8 14.6 1.0
C A:GLU120 4.8 18.8 1.0

Zinc binding site 3 out of 3 in 2vac

Go back to Zinc Binding Sites List in 2vac
Zinc binding site 3 out of 3 in the Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1140

b:22.8
occ:0.50
OE2 A:GLU82 2.0 24.0 1.0
O A:HOH2160 2.3 29.6 1.0
O A:HOH2161 2.4 34.2 1.0
CD A:GLU82 2.7 28.7 1.0
OE1 A:GLU82 2.9 23.1 1.0
O A:HOH2159 3.2 34.6 1.0
O A:HOH2105 3.9 33.7 1.0
CG A:GLU82 4.2 17.9 1.0
CD A:LYS118 4.3 34.3 1.0
CB A:ASN77 4.4 21.8 1.0
CE A:LYS118 4.7 38.5 1.0
CA A:ASN77 4.9 16.9 1.0
NZ A:LYS118 4.9 36.1 1.0
CG A:LYS118 5.0 22.1 1.0

Reference:

J.M.Elkins, A.C.W.Pike, O.King, E.Salah, P.Savitsky, F.Von Delft, J.Weigelt, A.Edwards, C.H.Arrowsmith, M.Sundstrom, S.Knapp. Crystal Structure of N-Terminal Actin Depolymerizing Factor Homology (Adf-H) Domain of Human Twinfilin-2 To Be Published.
Page generated: Wed Dec 16 03:54:55 2020

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