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Zinc in PDB 1mxd: Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei

Enzymatic activity of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei

All present enzymatic activity of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei:
3.2.1.1;

Protein crystallography data

The structure of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei, PDB code: 1mxd 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.837, 77.207, 106.569, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.5

Other elements in 1mxd:

The structure of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei (pdb code 1mxd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei, PDB code: 1mxd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1mxd

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Zinc binding site 1 out of 6 in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn725

b:27.9
occ:1.00
 NE2 A:HIS152 1.9 31.9 1.0
O A:HOH466 1.9 25.1 1.0
NE2 A:HIS147 2.1 26.6 1.0
SG A:CYS166 2.2 27.5 1.0
CE1 A:HIS152 2.8 30.4 1.0
CD2 A:HIS147 2.9 24.7 1.0
CB A:CYS166 3.0 25.3 1.0
CD2 A:HIS152 3.0 30.4 1.0
CE1 A:HIS147 3.2 24.7 1.0
CA A:CYS166 3.4 24.8 1.0
ND1 A:HIS168 3.9 31.7 1.0
ND1 A:HIS152 4.0 31.1 1.0
C A:CYS166 4.1 26.0 1.0
CG A:HIS152 4.1 30.3 1.0
CG A:HIS147 4.1 25.6 1.0
ND1 A:HIS147 4.2 24.7 1.0
O A:HOH443 4.3 21.4 1.0
N A:HIS167 4.4 24.5 1.0
CB A:HIS168 4.4 32.3 1.0
ND2 A:ASN149 4.5 29.1 1.0
N A:HIS168 4.5 29.1 1.0
CG A:HIS168 4.6 33.2 1.0
N A:CYS166 4.6 24.2 1.0
CB A:ASP155 4.7 26.2 1.0
CD2 A:LEU151 4.7 34.1 1.0
O A:CYS166 4.8 25.5 1.0
CE1 A:HIS168 4.9 33.3 1.0
O A:ILE165 4.9 24.6 1.0

Zinc binding site 2 out of 6 in 1mxd

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Zinc binding site 2 out of 6 in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn726

b:27.9
occ:1.00
 OD2 A:ASP256 1.9 26.4 1.0
OD1 A:ASP252 1.9 29.3 1.0
O A:ILE292 2.1 28.7 1.0
CG A:ASP252 2.8 29.9 1.0
CG A:ASP256 2.9 26.6 1.0
OD2 A:ASP252 3.0 32.0 1.0
C A:ILE292 3.1 28.2 1.0
CB A:ASP256 3.3 26.5 1.0
CA A:ILE293 3.6 27.4 1.0
N A:ILE293 3.8 26.9 1.0
N A:TRP294 3.9 28.2 1.0
OD1 A:ASP256 4.0 26.5 1.0
CB A:ASP252 4.2 27.9 1.0
CB A:ILE292 4.3 30.6 1.0
CA A:ILE292 4.3 28.6 1.0
C A:ILE293 4.3 28.6 1.0
O A:HOH507 4.4 31.6 1.0
CG1 A:ILE292 4.5 30.6 1.0
O A:ASP252 4.6 26.5 1.0
CA A:ASP252 4.7 27.3 1.0
CB A:ILE293 4.8 27.3 1.0
CA A:ASP256 4.8 27.9 1.0
CG1 A:ILE293 4.8 26.4 1.0
CB A:TRP294 5.0 32.1 1.0
C A:ASP252 5.0 26.7 1.0

Zinc binding site 3 out of 6 in 1mxd

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Zinc binding site 3 out of 6 in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn727

b:40.2
occ:1.00
 OE1 A:GLU36 1.9 30.7 1.0
O A:ACT737 2.0 36.4 0.5
OE2 A:GLU318 2.1 31.8 1.0
NZ A:LYS323 2.3 33.9 1.0
OE1 A:GLU318 2.6 31.5 1.0
CD A:GLU318 2.7 31.3 1.0
CD A:GLU36 2.7 34.5 1.0
OE2 A:GLU36 2.8 36.5 1.0
CE A:LYS323 3.0 30.6 1.0
C A:ACT737 3.0 35.6 0.5
CD A:LYS323 3.7 30.3 1.0
CH3 A:ACT737 3.8 35.2 0.5
OXT A:ACT737 3.9 36.6 0.5
O A:HOH698 3.9 68.8 1.0
CD A:LYS33 4.1 39.8 1.0
CG A:GLU36 4.1 32.2 1.0
NZ A:LYS33 4.2 43.0 1.0
CG A:GLU318 4.2 28.8 1.0
NE1 A:TRP37 4.2 21.8 1.0
CE2 A:PHE317 4.3 24.6 1.0
O A:HOH549 4.4 41.9 1.0
CE A:LYS33 4.6 40.5 1.0
CD2 A:PHE317 4.6 23.4 1.0
CD1 A:TRP37 4.7 20.2 1.0
CB A:GLU36 4.7 27.3 1.0
CG A:LYS323 5.0 30.5 1.0

Zinc binding site 4 out of 6 in 1mxd

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Zinc binding site 4 out of 6 in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn728

b:34.9
occ:1.00
 OD2 A:ASP347 1.9 33.8 1.0
OD1 A:ASP349 2.0 30.9 1.0
OE1 A:GLU350 2.1 27.9 1.0
O A:HOH465 2.7 24.3 1.0
CG A:ASP347 2.8 33.0 1.0
OD1 A:ASP347 3.0 33.8 1.0
CG A:ASP349 3.0 31.7 1.0
CD A:GLU350 3.1 29.0 1.0
OD2 A:ASP349 3.5 35.0 1.0
CG A:GLU350 3.5 27.4 1.0
NH2 A:ARG377 3.5 48.3 1.0
CB A:GLU350 4.1 28.7 1.0
OD1 A:ASN348 4.1 36.9 1.0
CB A:ASP347 4.1 29.7 1.0
OE2 A:GLU350 4.2 29.0 1.0
N A:GLU350 4.3 26.8 1.0
N A:ASP349 4.3 29.4 1.0
CB A:ASP349 4.4 29.2 1.0
C A:ASP349 4.5 29.0 1.0
CA A:ASP349 4.6 30.4 1.0
CZ A:ARG377 4.7 47.3 1.0
CA A:GLU350 4.9 27.4 1.0

Zinc binding site 5 out of 6 in 1mxd

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Zinc binding site 5 out of 6 in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn729

b:35.1
occ:1.00
 O A:HOH489 1.9 30.1 1.0
OE2 A:GLU88 2.0 31.1 1.0
OE2 A:GLU80 2.1 32.1 1.0
CD A:GLU88 2.8 28.6 1.0
OE1 A:GLU88 2.8 28.5 1.0
CD A:GLU80 2.8 30.1 1.0
OE1 A:GLU80 2.9 30.4 1.0
O A:GLY24 3.9 28.2 1.0
CG A:GLU88 4.2 28.3 1.0
CG A:GLU80 4.3 28.3 1.0
OG A:SER85 4.4 30.0 1.0
N A:SER85 4.5 27.4 1.0
CB A:SER85 4.6 27.2 1.0
OD2 A:ASP28 4.8 37.6 1.0
O A:HOH463 4.8 26.1 1.0
C A:GLY24 5.0 28.5 1.0
CA A:GLY84 5.0 25.8 1.0

Zinc binding site 6 out of 6 in 1mxd

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Zinc binding site 6 out of 6 in the Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn730

b:36.5
occ:0.40
 N4B A:ACR735 1.1 33.0 0.6
C1A A:ACR735 1.4 32.6 0.6
C4B A:ACR735 1.9 33.2 0.6
O3B A:ACR735 2.1 31.4 0.6
OE2 A:GLU222 2.2 29.5 1.0
C3B A:ACR735 2.3 33.1 0.6
OE1 A:GLU222 2.4 27.5 1.0
O A:HOH723 2.5 16.2 0.4
C7A A:ACR735 2.5 31.9 0.6
CD A:GLU222 2.6 27.5 1.0
C2A A:ACR735 2.9 31.1 0.6
O2A A:ACR735 3.1 32.3 0.6
C5B A:ACR735 3.3 34.1 0.6
C2B A:ACR735 3.7 34.0 0.6
C5A A:ACR735 3.8 33.1 0.6
C3A A:ACR735 3.8 32.2 0.6
OD1 A:ASP289 3.8 31.7 1.0
OD1 A:ASP198 3.9 27.3 1.0
C6B A:ACR735 4.0 34.8 0.6
CG A:GLU222 4.1 26.3 1.0
O A:HOH458 4.3 24.6 1.0
N A:TYR199 4.3 24.2 1.0
C4A A:ACR735 4.3 35.5 0.6
O5B A:ACR735 4.3 35.0 0.6
CB A:TYR199 4.4 23.5 1.0
CE3 A:TRP224 4.5 30.0 1.0
CA A:TYR199 4.5 24.1 1.0
C1B A:ACR735 4.6 34.7 0.6
O2B A:ACR735 4.6 34.6 0.6
NH2 A:ARG196 4.7 23.5 1.0
CG A:ASP198 4.7 24.6 1.0
O A:HOH479 4.8 29.7 1.0
C6A A:ACR735 4.8 32.7 0.6
CG A:ASP289 4.9 31.6 1.0
CZ3 A:TRP224 4.9 31.0 1.0
CB A:GLU222 5.0 25.0 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 Dec 16 02:57:24 2020

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