Zinc in PDB 6ze9: Non-Native Fold of the Putative VPS39 Zinc Finger Domain

Protein crystallography data

The structure of Non-Native Fold of the Putative VPS39 Zinc Finger Domain, PDB code: 6ze9 was solved by B.G.Butt, S.C.Graham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.59 / 2.90
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 104.178, 104.178, 39.423, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain (pdb code 6ze9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain, PDB code: 6ze9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6ze9

Go back to Zinc Binding Sites List in 6ze9
Zinc binding site 1 out of 3 in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Non-Native Fold of the Putative VPS39 Zinc Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:0.2
occ:1.00
NE2 A:HIS-3 2.0 0.0 1.0
O B:THR875 2.1 0.3 1.0
NE2 A:HIS-1 2.1 0.2 1.0
SG C:CYS844 2.3 0.2 1.0
CE1 A:HIS-3 2.9 0.6 1.0
C B:THR875 2.9 0.9 1.0
CD2 A:HIS-1 3.0 0.9 1.0
CD2 A:HIS-3 3.1 0.1 1.0
OXT B:THR875 3.1 0.1 1.0
CE1 A:HIS-1 3.2 0.3 1.0
CB C:CYS844 3.5 0.2 1.0
ND1 A:HIS-3 4.1 0.4 1.0
CG A:HIS-1 4.1 0.7 1.0
CG A:HIS-3 4.2 0.5 1.0
NZ C:LYS846 4.2 0.4 1.0
ND1 A:HIS-1 4.2 0.8 1.0
CA B:THR875 4.2 0.7 1.0
CA C:CYS844 4.3 0.9 1.0
N B:THR875 4.5 0.6 1.0
CG A:PRO872 4.7 0.3 1.0
OG1 B:THR875 4.7 0.7 1.0
O A:HIS-2 4.8 0.4 1.0
CE C:LYS846 4.8 0.7 1.0
O B:PRO872 4.8 0.2 1.0
C C:CYS844 4.9 0.0 1.0

Zinc binding site 2 out of 3 in 6ze9

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Zinc binding site 2 out of 3 in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Non-Native Fold of the Putative VPS39 Zinc Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:0.3
occ:1.00
O A:THR875 1.9 1.0 1.0
NE2 B:HIS-1 2.0 1.0 1.0
NE2 B:HIS-3 2.1 0.4 1.0
C A:THR875 2.8 0.8 1.0
CE1 B:HIS-1 2.8 0.3 1.0
CE1 B:HIS-3 3.0 0.9 1.0
CD2 B:HIS-1 3.1 0.0 1.0
OXT A:THR875 3.1 0.7 1.0
CD2 B:HIS-3 3.1 0.9 1.0
ND1 B:HIS-1 4.0 0.0 1.0
CG B:HIS-1 4.1 0.2 1.0
CA A:THR875 4.2 0.5 1.0
ND1 B:HIS-3 4.2 0.4 1.0
CG B:HIS-3 4.2 0.8 1.0
N A:THR875 4.5 0.9 1.0
CG B:PRO872 4.5 0.2 1.0
OG1 A:THR875 4.6 0.2 1.0
O A:PRO872 4.8 0.3 1.0
O B:HIS-2 4.8 0.9 1.0
CB A:THR875 5.0 0.2 1.0

Zinc binding site 3 out of 3 in 6ze9

Go back to Zinc Binding Sites List in 6ze9
Zinc binding site 3 out of 3 in the Non-Native Fold of the Putative VPS39 Zinc Finger Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Non-Native Fold of the Putative VPS39 Zinc Finger Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:0.2
occ:1.00
NE2 C:HIS-1 2.0 0.1 1.0
NE2 C:HIS-3 2.1 0.3 1.0
SG A:CYS844 2.3 0.0 1.0
O C:HOH1101 2.3 0.0 1.0
CE1 C:HIS-3 2.7 0.3 1.0
CD2 C:HIS-1 2.9 0.1 1.0
CE1 C:HIS-1 3.1 0.2 1.0
CD2 C:HIS-3 3.3 0.1 1.0
CB A:CYS844 3.6 0.1 1.0
ND1 C:HIS-3 4.0 0.6 1.0
CG C:HIS-1 4.0 0.1 1.0
ND1 C:HIS-1 4.2 0.8 1.0
CG C:HIS-3 4.2 0.5 1.0
CA A:CYS844 4.5 0.9 1.0
O C:HIS-2 4.8 0.7 1.0
CD A:LYS846 5.0 0.6 1.0

Reference:

B.G.Butt, E.J.Scourfield, S.C.Graham. Non-Native Fold of the Putative VPS39 Zinc Finger Domain To Be Published.
Page generated: Wed Dec 16 13:25:00 2020

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