Atomistry » Zinc » PDB 3t5w-3te7 » 3tdp
Atomistry »
  Zinc »
    PDB 3t5w-3te7 »
      3tdp »

Zinc in PDB 3tdp: Crystal Structure of Hsc at pH 4.5

Protein crystallography data

The structure of Crystal Structure of Hsc at pH 4.5, PDB code: 3tdp was solved by B.K.Czyzewski, D.-N.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.44 / 2.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 120.515, 162.903, 194.104, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 24

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hsc at pH 4.5 (pdb code 3tdp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Hsc at pH 4.5, PDB code: 3tdp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3tdp

Go back to Zinc Binding Sites List in 3tdp
Zinc binding site 1 out of 5 in the Crystal Structure of Hsc at pH 4.5


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 Hsc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn258

b:48.8
occ:1.00
NZ A:LYS3 2.0 43.7 1.0
OD2 A:ASP7 2.5 58.8 1.0
CE A:LYS3 2.5 53.2 1.0
OD1 A:ASP7 2.6 55.0 1.0
CG A:ASP7 2.9 54.5 1.0
CD A:LYS3 4.0 82.0 1.0
CB A:ASP7 4.3 46.5 1.0
OE2 A:GLU255 4.5 61.8 1.0
CG A:LYS3 4.7 89.9 1.0

Zinc binding site 2 out of 5 in 3tdp

Go back to Zinc Binding Sites List in 3tdp
Zinc binding site 2 out of 5 in the Crystal Structure of Hsc at pH 4.5


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 Hsc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn259

b:52.5
occ:1.00
NZ B:LYS3 2.3 29.1 1.0
OD2 B:ASP7 2.4 66.1 1.0
OD1 B:ASP7 2.7 70.9 1.0
CE B:LYS3 2.8 54.7 1.0
CG B:ASP7 2.8 67.5 1.0
CD B:LYS3 4.0 88.3 1.0
CB B:ASP7 4.4 61.8 1.0

Zinc binding site 3 out of 5 in 3tdp

Go back to Zinc Binding Sites List in 3tdp
Zinc binding site 3 out of 5 in the Crystal Structure of Hsc at pH 4.5


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 Hsc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn258

b:0.9
occ:1.00
NZ C:LYS3 2.3 19.6 1.0
CE C:LYS3 2.6 41.6 1.0
OD1 C:ASP7 3.4 76.2 1.0
CD C:LYS3 3.5 67.3 1.0
OD2 C:ASP7 3.9 92.7 1.0
CG C:ASP7 4.0 82.3 1.0
OE1 C:GLU255 4.5 0.0 1.0
CD C:GLU255 4.9 98.1 1.0
CG C:LYS3 4.9 91.2 1.0

Zinc binding site 4 out of 5 in 3tdp

Go back to Zinc Binding Sites List in 3tdp
Zinc binding site 4 out of 5 in the Crystal Structure of Hsc at pH 4.5


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 Hsc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn258

b:63.1
occ:1.00
OD2 D:ASP7 1.9 83.8 1.0
NZ D:LYS3 2.1 73.9 1.0
CE D:LYS3 2.4 70.1 1.0
CG D:ASP7 2.6 80.6 1.0
OD1 D:ASP7 2.8 84.1 1.0
CD D:LYS3 3.7 91.1 1.0
CB D:ASP7 4.0 70.6 1.0
OE2 D:GLU255 4.6 70.2 1.0
CG D:LYS3 4.7 99.0 1.0
CD D:GLU255 4.8 70.7 1.0
OE1 D:GLU255 4.9 77.4 1.0
CA D:ASP7 4.9 65.2 1.0

Zinc binding site 5 out of 5 in 3tdp

Go back to Zinc Binding Sites List in 3tdp
Zinc binding site 5 out of 5 in the Crystal Structure of Hsc at pH 4.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Hsc at pH 4.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn258

b:61.9
occ:1.00
NZ E:LYS3 2.1 25.5 1.0
OD2 E:ASP7 2.3 67.3 1.0
OD1 E:ASP7 2.5 62.0 1.0
CG E:ASP7 2.8 63.5 1.0
CE E:LYS3 2.9 82.7 1.0
OE1 E:GLU255 3.9 0.9 1.0
CB E:ASP7 4.3 53.8 1.0
CD E:LYS3 4.3 87.1 1.0

Reference:

B.K.Czyzewski, D.N.Wang. Identification and Characterization of A Bacterial Hydrosulphide Ion Channel. Nature V. 483 494 2012.
ISSN: ISSN 0028-0836
PubMed: 22407320
DOI: 10.1038/NATURE10881
Page generated: Wed Dec 16 04:52:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy