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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

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Zinc binding site 1 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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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

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Zinc binding site 2 out of 7 in the Crystal Structure of Mh-K1 Chitosanase in Substrate-Bound Form


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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

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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

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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

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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

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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

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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: Sun Oct 27 17:41:56 2024

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