Atomistry » Zinc » PDB 3hk5-3hqy » 3hn8
Atomistry »
  Zinc »
    PDB 3hk5-3hqy »
      3hn8 »

Zinc in PDB 3hn8: Crystal Structure of Synaptotagmin

Protein crystallography data

The structure of Crystal Structure of Synaptotagmin, PDB code: 3hn8 was solved by P.Strop, M.Vrljic, J.Ernst, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 3.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 205.675, 205.675, 143.125, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 25.9

Other elements in 3hn8:

The structure of Crystal Structure of Synaptotagmin also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Synaptotagmin (pdb code 3hn8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Synaptotagmin, PDB code: 3hn8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3hn8

Go back to Zinc Binding Sites List in 3hn8
Zinc binding site 1 out of 3 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:65.1
occ:1.00
ND1 A:HIS543 2.2 74.1 1.0
OD2 A:ASP419 2.4 99.2 1.0
SG A:CYS298 2.5 75.7 1.0
OE1 A:GLU546 2.6 95.7 1.0
CD A:GLU546 2.8 93.6 1.0
OE2 A:GLU546 2.8 90.3 1.0
CG A:HIS543 3.0 82.6 1.0
CE1 A:HIS543 3.2 86.0 1.0
CG A:ASP419 3.2 0.5 1.0
CB A:HIS543 3.2 78.5 1.0
CB A:ASP419 3.4 82.9 1.0
CA A:HIS543 3.5 72.2 1.0
CB A:CYS298 3.6 81.5 1.0
CG A:GLU546 3.8 89.8 1.0
CD2 A:HIS543 4.1 89.9 1.0
NE2 A:HIS543 4.2 88.7 1.0
OD1 A:ASP419 4.2 0.1 1.0
N A:HIS543 4.4 85.0 1.0
C A:HIS543 4.6 68.4 1.0
O A:HIS543 4.6 75.8 1.0
CB A:GLU546 4.9 80.1 1.0
CA A:ASP419 4.9 73.0 1.0

Zinc binding site 2 out of 3 in 3hn8

Go back to Zinc Binding Sites List in 3hn8
Zinc binding site 2 out of 3 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn700

b:74.5
occ:1.00
ND1 B:HIS543 2.2 79.2 1.0
SG B:CYS298 2.5 73.3 1.0
OD2 B:ASP419 2.5 74.8 1.0
OE1 B:GLU546 2.7 86.3 1.0
CD B:GLU546 2.7 88.1 1.0
OE2 B:GLU546 2.8 86.6 1.0
CG B:HIS543 3.0 88.7 1.0
CB B:HIS543 3.2 86.3 1.0
CG B:ASP419 3.3 91.4 1.0
CE1 B:HIS543 3.3 91.1 1.0
CA B:HIS543 3.4 85.6 1.0
CB B:ASP419 3.5 79.0 1.0
CB B:CYS298 3.5 90.7 1.0
CG B:GLU546 3.8 87.2 1.0
CD2 B:HIS543 4.2 93.2 1.0
N B:HIS543 4.3 0.5 1.0
NE2 B:HIS543 4.3 91.7 1.0
OD1 B:ASP419 4.3 0.2 1.0
C B:HIS543 4.5 81.8 1.0
O B:HIS543 4.6 90.9 1.0
CB B:GLU546 4.8 83.8 1.0
CA B:CYS298 4.9 99.5 1.0

Zinc binding site 3 out of 3 in 3hn8

Go back to Zinc Binding Sites List in 3hn8
Zinc binding site 3 out of 3 in the Crystal Structure of Synaptotagmin


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 Synaptotagmin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn700

b:58.3
occ:1.00
ND1 C:HIS543 2.2 73.8 1.0
OD2 C:ASP419 2.4 85.9 1.0
SG C:CYS298 2.5 76.1 1.0
OE1 C:GLU546 2.6 0.6 1.0
CD C:GLU546 2.7 0.6 1.0
OE2 C:GLU546 2.8 99.6 1.0
CG C:HIS543 3.0 74.3 1.0
CE1 C:HIS543 3.2 72.9 1.0
CG C:ASP419 3.2 81.5 1.0
CB C:HIS543 3.2 74.1 1.0
CB C:ASP419 3.4 76.8 1.0
CA C:HIS543 3.5 73.9 1.0
CB C:CYS298 3.6 80.5 1.0
CG C:GLU546 3.8 0.2 1.0
CD2 C:HIS543 4.2 74.9 1.0
NE2 C:HIS543 4.2 70.6 1.0
OD1 C:ASP419 4.3 92.6 1.0
N C:HIS543 4.4 75.5 1.0
C C:HIS543 4.6 73.3 1.0
O C:HIS543 4.6 73.0 1.0
CB C:GLU546 4.8 93.0 1.0
CA C:ASP419 5.0 73.8 1.0

Reference:

M.Vrljic, P.Strop, J.A.Ernst, R.B.Sutton, S.Chu, A.T.Brunger. Molecular Mechanism of the Synaptotagmin-Snare Interaction in CA2+-Triggered Vesicle Fusion. Nat.Struct.Mol.Biol. V. 17 325 2010.
ISSN: ISSN 1545-9993
PubMed: 20173762
DOI: 10.1038/NSMB.1764
Page generated: Sat Oct 26 06:26:28 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy