Atomistry » Zinc » PDB 5hou-5i3a » 5hwa
Atomistry »
  Zinc »
    PDB 5hou-5i3a »
      5hwa »

Zinc in PDB 5hwa: Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form

Enzymatic activity of Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form

All present enzymatic activity of Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form:
3.2.1.132;

Protein crystallography data

The structure of Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form, PDB code: 5hwa was solved by M.Suzuki, A.Saito, A.Ando, K.Miki, J.Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.69 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.750, 79.030, 94.760, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 17

Other elements in 5hwa:

The structure of Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form also contains other interesting chemical elements:

Arsenic (As) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form (pdb code 5hwa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form, PDB code: 5hwa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 1 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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 Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:21.3
occ:0.90
O A:ACY307 1.9 26.1 1.0
O1 A:CAC305 1.9 21.4 0.8
OXT A:ACY306 2.0 17.9 1.0
OE1 A:GLU257 2.1 21.9 1.0
CD A:GLU257 2.8 19.1 1.0
OE2 A:GLU257 2.8 23.2 1.0
C A:ACY307 2.8 31.1 1.0
C A:ACY306 2.9 18.3 1.0
O A:ACY306 3.1 16.2 1.0
AS A:CAC305 3.3 19.1 0.8
OXT A:ACY307 3.4 35.5 1.0
C2 A:CAC305 3.6 21.3 0.8
O A:HOH443 3.8 29.2 1.0
CH3 A:ACY307 3.9 37.6 1.0
O A:HOH575 3.9 20.2 1.0
O A:HOH617 3.9 41.4 1.0
O A:HOH544 4.0 36.4 1.0
CG A:GLU257 4.2 17.7 1.0
O2 A:CAC305 4.2 19.7 1.0
CH3 A:ACY306 4.3 19.1 1.0
C1 A:CAC305 4.8 26.6 0.8
CB A:GLU257 4.8 16.7 1.0
CA A:GLU257 4.9 14.2 1.0

Zinc binding site 2 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 2 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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 Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:12.7
occ:0.60
OXT A:ACY308 1.3 20.0 1.0
O2 A:CAC305 1.9 19.7 1.0
OD1 A:ASP255 2.0 19.3 1.0
C A:ACY308 2.0 20.0 1.0
O A:ACY308 2.2 20.0 1.0
CG A:ASP255 2.8 20.9 1.0
OD2 A:ASP255 2.8 21.7 1.0
AS A:CAC305 3.2 19.1 0.8
CH3 A:ACY308 3.5 20.0 1.0
C1 A:CAC305 3.8 26.6 0.8
O A:HOH656 4.0 44.9 1.0
O A:HOH725 4.1 45.6 1.0
O A:HOH575 4.1 20.2 1.0
C2 A:CAC305 4.1 21.3 0.8
CB A:ASP255 4.2 16.6 1.0
O A:ASP255 4.6 19.4 1.0
O1 A:CAC305 4.6 21.4 0.8
CA A:ASP255 4.8 14.6 1.0
C A:ASP255 4.8 15.9 1.0

Zinc binding site 3 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 3 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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 Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:38.5
occ:0.80
OD2 A:ASP52 2.0 28.0 1.0
OE1 A:GLU54 2.3 40.9 1.0
CG A:ASP52 2.9 22.2 1.0
CD A:GLU54 3.0 40.8 1.0
O A:HOH751 3.0 56.5 1.0
O A:HOH691 3.0 36.1 1.0
OE2 A:GLU54 3.1 58.2 1.0
OD1 A:ASP52 3.2 19.9 1.0
O A:HOH884 3.2 61.9 1.0
O A:HOH826 3.5 58.7 1.0
O A:HOH571 3.8 37.4 1.0
O A:HOH732 4.1 28.1 1.0
CB A:ASP52 4.2 15.9 1.0
CG A:GLU54 4.4 27.6 1.0
O A:HOH627 4.5 23.7 1.0
O A:HOH586 4.5 46.4 1.0
CA A:GLU54 4.6 16.1 1.0
O A:HOH806 4.6 48.1 1.0
O A:HOH413 4.8 59.2 1.0
CB A:GLU54 4.9 19.9 1.0
N A:GLU54 4.9 15.0 1.0

Zinc binding site 4 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 4 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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 Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn312

b:26.8
occ:0.50
O A:HOH455 2.0 28.2 1.0
O A:HOH695 2.1 43.6 1.0
O A:HOH440 2.1 34.0 1.0
O A:HOH774 2.1 43.2 1.0
O A:HOH628 2.2 37.8 1.0
O A:HOH638 3.6 26.5 1.0
OG A:SER248 3.9 25.2 1.0
O A:HOH432 3.9 38.5 1.0
O A:ASN245 4.3 17.6 1.0
OE1 A:GLU249 4.3 19.1 1.0
OE2 A:GLU249 4.3 24.3 1.0
OD1 A:ASN245 4.4 23.7 1.0
CD A:GLU249 4.7 19.4 1.0
CG A:ASN245 4.8 24.8 1.0
ND2 A:ASN245 4.8 31.7 1.0
O A:HOH633 5.0 20.4 1.0

Zinc binding site 5 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 5 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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 Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn313

b:79.7
occ:1.00
O A:HOH630 2.3 39.8 1.0
O A:HOH484 2.4 34.9 1.0
O A:HOH572 2.7 41.0 1.0
O A:HOH413 3.7 59.2 1.0
O A:HOH894 3.9 70.3 1.0
O A:ASP52 4.0 16.3 1.0
OE1 A:GLU120 4.0 25.1 1.0
OE2 A:GLU120 4.2 21.3 1.0
OE2 A:GLU51 4.5 25.0 1.0
CD A:GLU120 4.5 22.3 1.0
OE2 A:GLU54 4.8 58.2 1.0

Zinc binding site 6 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 6 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn314

b:36.3
occ:0.50
N2 A:GCS304 2.2 23.0 1.0
O3 A:GCS304 2.2 33.6 1.0
O A:HOH654 2.3 42.2 1.0
C2 A:GCS304 2.9 21.5 1.0
C3 A:GCS304 3.0 23.7 1.0
O A:HOH756 3.2 37.6 1.0
O A:HOH481 3.9 47.9 1.0
O A:HOH536 4.2 29.4 1.0
O A:HOH783 4.2 44.9 1.0
O A:HOH850 4.2 50.0 1.0
C1 A:GCS304 4.3 19.7 1.0
C4 A:GCS304 4.4 26.3 1.0
O A:HOH499 4.4 19.2 1.0
O A:HOH415 4.8 36.6 1.0
O4 A:GCS303 4.8 18.9 1.0
O A:HOH620 4.9 30.3 1.0
O A:HOH461 5.0 22.1 1.0

Zinc binding site 7 out of 7 in 5hwa

Go back to Zinc Binding Sites List in 5hwa
Zinc binding site 7 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn315

b:35.5
occ:0.50
NZ A:LYS204 1.7 13.2 1.0
OD2 A:ASP237 2.3 29.0 1.0
OD2 A:ASP233 2.5 22.1 1.0
O A:HOH721 2.6 54.3 1.0
NZ A:LYS230 2.9 26.3 0.5
O A:HOH606 3.0 47.4 1.0
CG A:ASP237 3.0 25.7 1.0
OD1 A:ASP237 3.1 26.4 1.0
CE A:LYS204 3.2 20.6 1.0
O A:HOH412 3.4 51.6 1.0
O A:HOH403 3.4 21.2 0.5
CG A:ASP233 3.6 15.4 1.0
CD A:LYS204 4.2 19.6 1.0
O A:ASP233 4.3 12.1 1.0
CE A:LYS230 4.3 20.9 0.5
OD1 A:ASP233 4.4 16.4 1.0
O A:HOH462 4.4 35.5 1.0
CB A:ASP237 4.5 20.4 1.0
O A:HOH403 4.5 24.2 0.5
CB A:ASP233 4.5 11.8 1.0
C A:ASP233 4.7 11.1 1.0

Reference:

M.Suzuki, A.Saito, M.Kobayashi, T.Yokoyama, S.Omiya, J.Li, K.Sugita, A.Ando, K.Miki, J.Saito. Understanding For the Catalytic Mechanism Based on the Substrate-Bound Structure of Gh-46 Chitosanase From Bacillus Circulans Mh-K1 To Be Published.
Page generated: Wed Dec 16 06:20:56 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy