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Zinc in PDB 1mwo: Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase

Enzymatic activity of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase

All present enzymatic activity of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase, PDB code: 1mwo was solved by A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.880, 78.200, 106.289, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.4

Other elements in 1mwo:

The structure of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase (pdb code 1mwo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase, PDB code: 1mwo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1mwo

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Zinc binding site 1 out of 6 in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn436

b:26.8
occ:1.00
 NE2 A:HIS152 1.9 31.9 1.0
O A:HOH816 2.0 27.7 1.0
NE2 A:HIS147 2.0 25.1 1.0
SG A:CYS166 2.3 25.8 1.0
CE1 A:HIS152 2.8 30.1 1.0
CD2 A:HIS147 2.9 24.3 1.0
CB A:CYS166 3.0 23.8 1.0
CD2 A:HIS152 3.0 31.0 1.0
CE1 A:HIS147 3.1 24.8 1.0
CA A:CYS166 3.3 24.3 1.0
ND1 A:HIS168 3.9 30.2 1.0
ND1 A:HIS152 4.0 29.8 1.0
C A:CYS166 4.1 24.0 1.0
CG A:HIS147 4.1 23.8 1.0
CG A:HIS152 4.1 30.0 1.0
ND1 A:HIS147 4.2 24.0 1.0
O A:HOH500 4.4 18.4 1.0
N A:HIS167 4.4 25.9 1.0
CB A:HIS168 4.5 30.1 1.0
ND2 A:ASN149 4.5 25.0 1.0
N A:CYS166 4.6 23.1 1.0
CG A:HIS168 4.6 30.6 1.0
N A:HIS168 4.6 28.5 1.0
O A:CYS166 4.8 23.4 1.0
CB A:ASP155 4.8 24.4 1.0
CE1 A:HIS168 4.9 29.2 1.0
O A:ILE165 4.9 22.8 1.0
CD2 A:LEU151 5.0 37.0 1.0

Zinc binding site 2 out of 6 in 1mwo

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Zinc binding site 2 out of 6 in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn437

b:19.9
occ:1.00
 OD1 A:ASP252 1.9 23.1 1.0
OD2 A:ASP256 2.0 16.4 1.0
O A:ILE292 2.2 18.5 1.0
CG A:ASP252 2.8 21.2 1.0
CG A:ASP256 2.9 17.7 1.0
OD2 A:ASP252 3.1 20.7 1.0
C A:ILE292 3.2 18.1 1.0
CB A:ASP256 3.3 18.4 1.0
CA A:ILE293 3.6 18.0 1.0
N A:ILE293 3.8 17.4 1.0
N A:TRP294 4.0 20.3 1.0
OD1 A:ASP256 4.0 17.5 1.0
CB A:ASP252 4.2 20.8 1.0
CB A:ILE292 4.3 19.6 1.0
CA A:ILE292 4.3 16.9 1.0
C A:ILE293 4.3 18.6 1.0
CG1 A:ILE292 4.5 18.7 1.0
O A:ASP252 4.7 18.9 1.0
CA A:ASP252 4.7 18.9 1.0
CB A:ILE293 4.8 15.4 1.0
CA A:ASP256 4.8 19.0 1.0
CG1 A:ILE293 4.8 14.5 1.0

Zinc binding site 3 out of 6 in 1mwo

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Zinc binding site 3 out of 6 in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn438

b:24.8
occ:1.00
 OE1 A:GLU36 1.9 23.1 1.0
NZ A:LYS33 2.1 27.6 1.0
OE2 A:GLU318 2.2 22.8 1.0
OE1 A:GLU318 2.4 21.6 1.0
CD A:GLU318 2.6 22.4 1.0
NZ A:LYS323 2.6 19.7 1.0
CD A:GLU36 2.7 25.7 1.0
OE2 A:GLU36 2.8 24.0 1.0
CE A:LYS33 3.1 28.2 1.0
CE A:LYS323 3.2 20.9 1.0
CD A:LYS33 3.6 25.6 1.0
CD A:LYS323 3.8 18.6 1.0
O A:HOH549 4.0 34.5 1.0
CG A:GLU318 4.1 20.3 1.0
CG A:GLU36 4.2 20.5 1.0
NE1 A:TRP37 4.2 15.8 1.0
O A:HOH837 4.2 33.6 1.0
CE2 A:PHE317 4.4 15.9 1.0
O A:HOH579 4.5 46.5 1.0
CD2 A:PHE317 4.6 16.8 1.0
CD1 A:TRP37 4.7 18.0 1.0
CG A:LYS323 4.8 22.4 1.0
CB A:GLU36 4.8 20.6 1.0
CG A:LYS33 5.0 24.5 1.0
CB A:GLU318 5.0 20.7 1.0

Zinc binding site 4 out of 6 in 1mwo

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Zinc binding site 4 out of 6 in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn439

b:27.9
occ:1.00
 OD2 A:ASP347 1.8 23.3 1.0
OD1 A:ASP349 2.0 23.1 1.0
OE1 A:GLU350 2.1 23.3 1.0
CG A:ASP347 2.7 27.7 1.0
OD1 A:ASP347 3.0 29.7 1.0
CG A:ASP349 3.1 22.2 1.0
CD A:GLU350 3.2 22.5 1.0
CG A:GLU350 3.5 20.8 1.0
OD2 A:ASP349 3.6 23.8 1.0
NH2 A:ARG377 3.6 33.3 1.0
OD1 A:ASN348 4.0 31.3 1.0
CB A:GLU350 4.0 21.4 1.0
CB A:ASP347 4.1 24.4 1.0
O A:HOH567 4.1 49.4 1.0
N A:GLU350 4.2 20.5 1.0
N A:ASP349 4.3 21.1 1.0
OE2 A:GLU350 4.3 22.5 1.0
C A:ASP349 4.4 21.1 1.0
CB A:ASP349 4.4 21.8 1.0
CA A:ASP349 4.5 21.5 1.0
CA A:GLU350 4.8 20.4 1.0
CZ A:ARG377 4.8 33.9 1.0
OH A:TYR345 4.9 24.5 1.0
O A:ASP349 4.9 21.4 1.0

Zinc binding site 5 out of 6 in 1mwo

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Zinc binding site 5 out of 6 in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn440

b:24.9
occ:1.00
 OE2 A:GLU80 1.9 21.1 1.0
OE2 A:GLU88 1.9 22.2 1.0
CD A:GLU88 2.8 22.8 1.0
CD A:GLU80 2.9 20.8 1.0
OE1 A:GLU88 2.9 24.4 1.0
OE1 A:GLU80 3.1 23.1 1.0
O A:HOH527 3.7 34.9 1.0
O A:GLY24 4.1 25.9 1.0
CG A:GLU88 4.2 21.3 1.0
CG A:GLU80 4.3 22.1 1.0
OG A:SER85 4.4 23.9 1.0
CB A:SER85 4.5 22.2 1.0
N A:SER85 4.5 19.9 1.0
OD2 A:ASP28 4.7 24.5 1.0
O A:HOH487 4.9 16.3 1.0

Zinc binding site 6 out of 6 in 1mwo

Go back to Zinc Binding Sites List in 1mwo
Zinc binding site 6 out of 6 in the Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of the Hyperthermostable Pyrocoocus Woesei Alpha-Amylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn441

b:37.5
occ:1.00
 OE2 A:GLU222 2.1 21.0 1.0
O A:HOH822 2.1 33.2 1.0
O A:HOH553 2.2 31.7 1.0
O A:HOH655 2.4 38.5 1.0
OE1 A:GLU222 2.4 15.4 1.0
CD A:GLU222 2.6 18.3 1.0
O A:HOH564 3.1 39.1 1.0
OD1 A:ASP289 3.7 24.3 1.0
OD1 A:ASP198 3.7 18.7 1.0
CG A:GLU222 4.1 17.7 1.0
O A:HOH465 4.2 22.3 1.0
CG A:ASP289 4.4 22.6 1.0
O A:HOH576 4.4 31.2 1.0
N A:TYR199 4.4 19.9 1.0
NH2 A:ARG196 4.5 15.8 1.0
CE3 A:TRP224 4.5 27.6 1.0
CB A:TYR199 4.6 21.8 1.0
OD2 A:ASP289 4.6 28.1 1.0
CG A:ASP198 4.6 16.5 1.0
CA A:TYR199 4.7 21.5 1.0
CZ3 A:TRP224 4.9 27.8 1.0
CB A:GLU222 5.0 19.1 1.0

Reference:

A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, M.Wilmanns. Differential Regulation of A Hyperthermophilic Alpha-Amylase with A Novel (Ca,Zn) Two-Metal Center By Zinc J.Biol.Chem. V. 278 9875 2003.
ISSN: ISSN 0021-9258
PubMed: 12482867
DOI: 10.1074/JBC.M211339200
Page generated: Wed Oct 16 17:02:48 2024

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