Zinc in PDB 5too: Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant

Enzymatic activity of Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant

All present enzymatic activity of Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant:
3.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant, PDB code: 5too was solved by A.Y.Lyubimov, F.Sunden, I.Alsadhan, D.Herschlag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.01 / 2.03
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 113.329, 113.329, 69.790, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.9

Other elements in 5too:

The structure of Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant (pdb code 5too). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant, PDB code: 5too:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5too

Go back to Zinc Binding Sites List in 5too
Zinc binding site 1 out of 4 in the Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant


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 Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:31.2
occ:1.00
 OD1 A:ASP38 2.0 29.1 1.0
NE2 A:HIS353 2.1 30.0 1.0
OD2 A:ASP352 2.1 31.4 1.0
CG A:ASP38 2.7 30.5 1.0
CD2 A:HIS353 2.8 30.5 1.0
HD2 A:HIS353 2.8 36.6 1.0
OD2 A:ASP38 2.9 32.3 1.0
CG A:ASP352 2.9 29.9 1.0
OD1 A:ASP352 3.1 28.8 1.0
CL A:CL605 3.1 38.4 1.0
CE1 A:HIS353 3.2 32.2 1.0
HE1 A:HIS83 3.5 37.5 1.0
HA A:SER79 3.5 37.9 1.0
HE1 A:HIS353 3.5 38.6 1.0
HE1 A:HIS486 3.8 39.7 1.0
O A:HOH778 3.8 33.1 1.0
OD1 A:ASP305 3.9 35.0 1.0
H A:GLN39 3.9 32.9 1.0
HG A:SER79 3.9 39.4 1.0
CG A:HIS353 4.0 31.1 1.0
ZN A:ZN602 4.1 35.1 1.0
O A:HOH834 4.1 37.7 1.0
CB A:ASP38 4.1 31.1 1.0
ND1 A:HIS353 4.1 31.6 1.0
CE1 A:HIS486 4.2 33.1 1.0
HA A:ASP38 4.2 34.4 1.0
HB2 A:ASP305 4.2 38.6 1.0
CE1 A:HIS83 4.3 31.2 1.0
CG A:ASP305 4.3 33.7 1.0
CB A:ASP352 4.4 28.6 1.0
N A:GLN39 4.4 27.4 1.0
CA A:SER79 4.4 31.6 1.0
NE2 A:HIS486 4.4 33.8 1.0
HB2 A:ASP352 4.5 34.3 1.0
HB3 A:SER79 4.5 38.9 1.0
HB3 A:ASP38 4.6 37.4 1.0
CA A:ASP38 4.6 28.7 1.0
OG A:SER79 4.6 32.8 1.0
HB2 A:GLN39 4.6 34.5 1.0
HB2 A:ASP38 4.7 37.4 1.0
CB A:SER79 4.7 32.4 1.0
CB A:ASP305 4.8 32.2 1.0
C A:ASP38 4.8 27.6 1.0
OD2 A:ASP305 4.8 34.0 1.0
HB3 A:ASP352 4.8 34.3 1.0
H A:ALA80 4.9 31.8 1.0
ND1 A:HIS83 4.9 30.2 1.0
N A:SER79 4.9 30.8 1.0
ND1 A:HIS486 4.9 31.2 1.0
HD1 A:HIS353 4.9 37.9 1.0

Zinc binding site 2 out of 4 in 5too

Go back to Zinc Binding Sites List in 5too
Zinc binding site 2 out of 4 in the Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant


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 Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:35.1
occ:1.00
 NE2 A:HIS309 2.0 36.4 1.0
OD1 A:ASP305 2.1 35.0 1.0
NE2 A:HIS486 2.1 33.8 1.0
CG A:ASP305 2.7 33.7 1.0
OD2 A:ASP305 2.8 34.0 1.0
CD2 A:HIS309 2.9 33.5 1.0
CL A:CL605 2.9 38.4 1.0
HD2 A:HIS309 3.0 40.2 1.0
CE1 A:HIS486 3.0 33.1 1.0
CE1 A:HIS309 3.1 36.4 1.0
CD2 A:HIS486 3.1 31.0 1.0
HE1 A:HIS486 3.2 39.7 1.0
HE1 A:HIS309 3.3 43.6 1.0
HD2 A:HIS486 3.3 37.2 1.0
HE1 A:HIS353 3.4 38.6 1.0
HE21 A:GLN39 3.4 38.1 1.0
HG A:SER79 3.6 39.4 1.0
CE1 A:HIS353 3.8 32.2 1.0
NE2 A:HIS353 3.8 30.0 1.0
CG A:HIS309 4.1 36.0 1.0
ZN A:ZN601 4.1 31.2 1.0
OG A:SER79 4.1 32.8 1.0
ND1 A:HIS309 4.1 34.9 1.0
NE2 A:GLN39 4.2 31.8 1.0
ND1 A:HIS486 4.2 31.2 1.0
CB A:ASP305 4.2 32.2 1.0
CG A:HIS486 4.3 31.7 1.0
HB2 A:ASP305 4.4 38.6 1.0
HE22 A:GLN39 4.4 38.1 1.0
OD1 A:ASP38 4.5 29.1 1.0
HB2 A:GLN39 4.6 34.5 1.0
HB3 A:ASP305 4.7 38.6 1.0
HG3 A:GLN39 4.7 36.4 1.0
HA A:ASP305 4.9 39.3 1.0
HD1 A:HIS309 4.9 41.9 1.0
HD1 A:HIS486 4.9 37.5 1.0

Zinc binding site 3 out of 4 in 5too

Go back to Zinc Binding Sites List in 5too
Zinc binding site 3 out of 4 in the Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant


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 Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:69.3
occ:1.00
 O A:ASP233 2.4 63.2 1.0
OE2 A:GLU238 2.5 51.9 1.0
O A:PRO247 2.5 62.1 1.0
O A:HOH712 2.5 34.8 1.0
OD1 A:ASP233 2.6 58.6 1.0
OE1 A:GLU317 2.6 43.3 1.0
OE2 A:GLU317 2.7 50.6 1.0
CD A:GLU317 3.0 46.5 1.0
HA A:ASP233 3.2 72.8 1.0
CD A:GLU238 3.3 48.8 1.0
C A:ASP233 3.4 64.1 1.0
OE1 A:GLU238 3.5 43.3 1.0
HA A:THR248 3.5 77.4 1.0
CG A:ASP233 3.7 61.0 1.0
C A:PRO247 3.7 65.6 1.0
CA A:ASP233 3.8 60.7 1.0
HB2 A:PRO247 3.8 83.6 1.0
HB A:ILE316 3.9 46.2 1.0
HB2 A:SER315 4.1 46.2 1.0
HH A:TYR251 4.2 64.7 1.0
H A:GLU317 4.2 45.5 1.0
HD1 A:PHE311 4.3 54.7 1.0
H A:ILE316 4.3 43.5 1.0
CB A:ASP233 4.4 63.1 1.0
CA A:THR248 4.4 64.5 1.0
HD2 A:PHE249 4.4 62.7 1.0
HE2 A:PHE249 4.4 58.5 1.0
N A:THR248 4.5 66.8 1.0
HG22 A:THR248 4.5 82.4 1.0
CG A:GLU317 4.5 44.3 1.0
HA A:ASN234 4.5 85.9 1.0
OD2 A:ASP233 4.6 63.4 1.0
O A:GLU232 4.6 55.1 1.0
N A:ASN234 4.6 66.1 1.0
CB A:PRO247 4.7 69.7 1.0
HG22 A:VAL235 4.7 63.6 1.0
HG2 A:PRO247 4.7 87.9 1.0
HE1 A:PHE311 4.7 58.1 1.0
OH A:TYR251 4.7 53.9 1.0
CG A:GLU238 4.7 49.6 1.0
CD1 A:PHE311 4.8 45.6 1.0
HB3 A:GLU238 4.8 60.6 1.0
CA A:PRO247 4.8 71.4 1.0
H A:PHE249 4.8 70.1 1.0
HD12 A:ILE316 4.9 54.3 1.0
CB A:ILE316 4.9 38.5 1.0
N A:ILE316 4.9 36.3 1.0
HG3 A:GLU317 4.9 53.1 1.0
HB2 A:GLU238 4.9 60.6 1.0
HB2 A:ASP233 4.9 75.7 1.0
HG2 A:GLU317 5.0 53.1 1.0
N A:GLU317 5.0 38.0 1.0
CD2 A:PHE249 5.0 52.2 1.0
CE2 A:PHE249 5.0 48.8 1.0
HB3 A:ASP233 5.0 75.7 1.0

Zinc binding site 4 out of 4 in 5too

Go back to Zinc Binding Sites List in 5too
Zinc binding site 4 out of 4 in the Crystal Structure of Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant


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 Alkaline Phosphatase Pafa T79S, N100A, K162A, R164A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:67.2
occ:1.00
 O A:HOH832 2.2 32.0 1.0
OD2 A:ASP295 2.4 36.6 1.0
O A:ILE293 2.5 36.6 1.0
OD1 A:ASP291 2.6 46.6 1.0
OD1 A:ASP295 2.7 30.2 1.0
O A:HOH772 2.7 30.3 1.0
CG A:ASP295 2.8 34.5 1.0
O A:HOH708 2.9 31.8 1.0
HB A:ILE293 3.3 47.7 1.0
H A:GLY289 3.3 44.4 1.0
CG A:ASP291 3.4 45.5 1.0
C A:ILE293 3.6 37.2 1.0
H A:ASP291 3.7 54.4 1.0
OD2 A:ASP291 3.8 46.6 1.0
H A:ILE293 4.0 51.8 1.0
CB A:ILE293 4.1 39.7 1.0
HG22 A:ILE293 4.1 44.5 1.0
N A:GLY289 4.2 37.0 1.0
CB A:ASP295 4.2 34.1 1.0
H A:VAL290 4.2 49.2 1.0
HA2 A:GLY289 4.2 44.4 1.0
CA A:ILE293 4.2 40.7 1.0
N A:ILE293 4.3 43.2 1.0
HG2 A:LYS155 4.3 41.6 1.0
O A:ASP291 4.4 42.3 1.0
N A:ASP295 4.4 29.9 1.0
H A:ASP295 4.4 35.9 1.0
H A:LYS155 4.4 36.8 1.0
HB2 A:ASP295 4.4 40.9 1.0
N A:ASP291 4.4 45.4 1.0
HA A:MET288 4.5 41.8 1.0
C A:THR294 4.5 30.0 1.0
HG3 A:LYS155 4.6 41.6 1.0
C A:ASP291 4.6 43.4 1.0
O A:LYS30 4.6 31.6 1.0
O A:GLN287 4.6 38.0 1.0
CB A:ASP291 4.7 44.4 1.0
CA A:GLY289 4.7 37.0 1.0
CG2 A:ILE293 4.7 37.1 1.0
N A:THR294 4.7 36.0 1.0
N A:VAL290 4.7 41.0 1.0
CA A:ASP291 4.8 46.1 1.0
CA A:ASP295 4.8 28.1 1.0
HG22 A:VAL290 4.8 55.7 1.0
HB2 A:LYS155 4.8 39.9 1.0
HB3 A:ASP295 4.8 40.9 1.0
HA A:SER154 4.8 39.0 1.0
HA A:THR294 4.8 38.7 1.0
CG A:LYS155 4.8 34.6 1.0
O A:THR294 4.9 30.3 1.0
O A:HOH711 4.9 42.1 1.0
HA A:ASP295 4.9 33.7 1.0
CA A:THR294 5.0 32.3 1.0

Reference:

F.Sunden, I.Alsadhan, A.Lyubimov, T.Doukov, J.Swan, D.Herschlag. Differential Catalytic Promiscuity of the Alkaline Phosphatase Superfamily Bimetallo Core Reveals Mechanistic Features Underlying Enzyme Evolution. J. Biol. Chem. V. 292 20960 2017.
ISSN: ESSN 1083-351X
PubMed: 29070681
DOI: 10.1074/JBC.M117.788240
Page generated: Wed Dec 16 10:56:28 2020

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