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Zinc in PDB 7yiv: The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH

Enzymatic activity of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH

All present enzymatic activity of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH:
3.1.3.1; 3.9.1.1;

Protein crystallography data

The structure of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH, PDB code: 7yiv was solved by Y.Cao, A.Qin, Y.T.Yu, D.Q.Yao, Q.Zhang, B.Rao, Y.Xia, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.05 / 3.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 158.622, 167.348, 188.783, 90, 90, 90
R / Rfree (%) 17.2 / 23.4

Other elements in 7yiv:

The structure of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH also contains other interesting chemical elements:

Calcium (Ca) 8 atoms
Magnesium (Mg) 8 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH (pdb code 7yiv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH, PDB code: 7yiv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 7yiv

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Zinc binding site 1 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:67.8
occ:1.00
 OD1 A:ASP337 2.1 58.1 1.0
NE2 A:HIS454 2.3 68.8 1.0
NE2 A:HIS341 2.3 53.0 1.0
OD2 A:ASP337 2.4 67.4 1.0
CG A:ASP337 2.6 61.8 1.0
CE1 A:HIS454 2.9 65.5 1.0
CD2 A:HIS341 3.0 61.8 1.0
OG A:SER110 3.2 68.0 1.0
CE1 A:HIS341 3.4 60.9 1.0
CD2 A:HIS454 3.5 63.6 1.0
ZN A:ZN606 3.9 91.5 1.0
CE1 A:HIS379 4.1 65.3 1.0
CB A:ASP337 4.1 58.9 1.0
ND1 A:HIS454 4.2 60.5 1.0
NE2 A:HIS379 4.2 62.1 1.0
CG A:HIS341 4.3 64.5 1.0
CB A:SER110 4.4 70.5 1.0
ND1 A:HIS341 4.4 61.2 1.0
CG A:HIS454 4.4 64.8 1.0
CE1 A:HIS381 4.8 61.0 1.0
NE2 A:HIS381 4.9 59.1 1.0

Zinc binding site 2 out of 16 in 7yiv

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Zinc binding site 2 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:91.5
occ:1.00
 OG A:SER110 2.1 68.0 1.0
NE2 A:HIS379 2.3 62.1 1.0
OD2 A:ASP378 2.5 63.0 1.0
CE1 A:HIS379 3.0 65.3 1.0
CB A:SER110 3.1 70.5 1.0
CG A:ASP60 3.1 75.2 1.0
OD1 A:ASP60 3.2 80.6 1.0
CG A:ASP378 3.2 68.5 1.0
OD1 A:ASP378 3.3 66.1 1.0
CD2 A:HIS379 3.4 62.1 1.0
OD2 A:ASP60 3.4 77.5 1.0
CB A:ASP60 3.5 67.5 1.0
OD1 A:ASP337 3.6 58.1 1.0
CG A:ASP337 3.7 61.8 1.0
CA A:SER110 3.7 72.4 1.0
CA A:ASP60 3.8 61.0 1.0
ZN A:ZN604 3.9 67.8 1.0
CB A:ASP337 4.0 58.9 1.0
N A:GLY61 4.1 60.5 1.0
ND1 A:HIS379 4.1 59.9 1.0
OD2 A:ASP337 4.2 67.4 1.0
C A:ASP60 4.2 59.5 1.0
MG A:MG603 4.3 64.7 1.0
CG A:HIS379 4.3 60.7 1.0
N A:SER110 4.5 67.5 1.0
OG1 A:THR173 4.6 60.9 1.0
CE1 A:HIS454 4.6 65.5 1.0
NE2 A:HIS454 4.7 68.8 1.0
CB A:ASP378 4.7 62.6 1.0
CA A:GLY61 4.9 58.1 1.0
C A:SER110 4.9 64.4 1.0

Zinc binding site 3 out of 16 in 7yiv

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Zinc binding site 3 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn604

b:132.9
occ:1.00
 OD2 D:ASP337 1.5 57.3 1.0
NE2 D:HIS454 2.2 59.8 1.0
NE2 D:HIS341 2.3 67.3 1.0
CE1 D:HIS454 2.6 71.7 1.0
CG D:ASP337 2.7 65.6 1.0
OG D:SER110 2.9 70.6 1.0
OD1 D:ASP337 3.2 74.4 1.0
CD2 D:HIS341 3.2 67.8 1.0
CE1 D:HIS341 3.3 73.7 1.0
CD2 D:HIS454 3.6 69.1 1.0
ND1 D:HIS454 3.9 65.5 1.0
CB D:ASP337 4.0 58.4 1.0
CB D:SER110 4.2 71.9 1.0
ZN D:ZN606 4.3 80.7 1.0
CG D:HIS454 4.4 69.9 1.0
ND1 D:HIS341 4.4 65.7 1.0
CG D:HIS341 4.4 65.2 1.0
NE2 D:HIS379 4.5 67.1 1.0
CE1 D:HIS379 4.6 67.4 1.0
N D:SER110 4.9 68.8 1.0

Zinc binding site 4 out of 16 in 7yiv

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Zinc binding site 4 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn606

b:80.7
occ:1.00
 OD1 D:ASP60 1.9 68.6 1.0
OD2 D:ASP378 2.0 70.3 1.0
NE2 D:HIS379 2.3 67.1 1.0
OG D:SER110 2.5 70.6 1.0
CB D:SER110 3.0 71.9 1.0
CG D:ASP60 3.0 65.8 1.0
CG D:ASP378 3.0 65.0 1.0
CE1 D:HIS379 3.1 67.4 1.0
CD2 D:HIS379 3.3 64.7 1.0
CA D:SER110 3.3 74.2 1.0
OD1 D:ASP378 3.4 59.6 1.0
OD2 D:ASP60 3.6 71.9 1.0
CG D:ASP337 3.7 65.6 1.0
OD1 D:ASP337 3.8 74.4 1.0
OD2 D:ASP337 3.8 57.3 1.0
N D:GLY61 4.1 62.3 1.0
N D:SER110 4.1 68.8 1.0
CB D:ASP337 4.1 58.4 1.0
ND1 D:HIS379 4.2 63.7 1.0
CB D:ASP60 4.2 64.0 1.0
ZN D:ZN604 4.3 132.9 1.0
CE1 D:HIS454 4.3 71.7 1.0
CG D:HIS379 4.3 60.3 1.0
CA D:ASP60 4.3 63.8 1.0
C D:ASP60 4.4 63.1 1.0
CB D:ASP378 4.4 56.2 1.0
NE2 D:HIS454 4.4 59.8 1.0
C D:SER110 4.5 76.8 1.0
MG D:MG603 4.7 62.4 1.0
O D:SER110 4.7 71.8 1.0
CA D:GLY61 4.8 56.7 1.0
C D:ASP109 4.9 73.5 1.0
OG1 D:THR173 4.9 64.6 1.0

Zinc binding site 5 out of 16 in 7yiv

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Zinc binding site 5 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn604

b:76.2
occ:1.00
 OD2 C:ASP337 1.6 67.4 1.0
NE2 C:HIS454 2.3 67.5 1.0
NE2 C:HIS341 2.3 49.8 1.0
CG C:ASP337 2.5 66.4 1.0
OD1 C:ASP337 2.7 64.3 1.0
CE1 C:HIS454 3.0 62.8 1.0
OG C:SER110 3.0 60.5 1.0
CD2 C:HIS341 3.1 61.4 1.0
CE1 C:HIS341 3.4 54.4 1.0
CD2 C:HIS454 3.4 62.0 1.0
CB C:ASP337 4.0 56.5 1.0
ZN C:ZN606 4.1 76.8 1.0
NE2 C:HIS379 4.2 56.2 1.0
ND1 C:HIS454 4.2 53.5 1.0
CE1 C:HIS379 4.3 62.0 1.0
CG C:HIS341 4.4 59.1 1.0
ND1 C:HIS341 4.4 54.5 1.0
CG C:HIS454 4.5 55.2 1.0
CB C:SER110 4.5 65.2 1.0
OD1 C:ASP60 4.8 61.5 1.0

Zinc binding site 6 out of 16 in 7yiv

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Zinc binding site 6 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn606

b:76.8
occ:1.00
 OD2 C:ASP378 1.9 57.3 1.0
OD1 C:ASP60 1.9 61.5 1.0
NE2 C:HIS379 2.3 56.2 1.0
OG C:SER110 2.8 60.5 1.0
CG C:ASP378 2.9 58.0 1.0
CD2 C:HIS379 3.0 57.8 1.0
CG C:ASP60 3.1 61.2 1.0
CB C:SER110 3.1 65.2 1.0
OD1 C:ASP378 3.3 59.8 1.0
CE1 C:HIS379 3.4 62.0 1.0
CA C:SER110 3.4 55.4 1.0
OD2 C:ASP60 3.6 60.0 1.0
OD2 C:ASP337 3.9 67.4 1.0
CG C:ASP337 4.0 66.4 1.0
ZN C:ZN604 4.1 76.2 1.0
N C:SER110 4.2 57.6 1.0
CB C:ASP378 4.2 59.4 1.0
CG C:HIS379 4.2 56.6 1.0
OD1 C:ASP337 4.2 64.3 1.0
CB C:ASP60 4.3 63.7 1.0
CE1 C:HIS454 4.3 62.8 1.0
CB C:ASP337 4.3 56.5 1.0
ND1 C:HIS379 4.4 56.8 1.0
NE2 C:HIS454 4.4 67.5 1.0
CA C:ASP60 4.5 53.8 1.0
N C:GLY61 4.5 57.7 1.0
MG C:MG603 4.5 55.8 1.0
C C:SER110 4.6 48.9 1.0
OG1 C:THR173 4.7 57.8 1.0
C C:ASP60 4.7 54.0 1.0
C C:ASP109 4.7 52.9 1.0
O C:ASP109 4.8 50.1 1.0
O C:SER110 4.8 49.2 1.0

Zinc binding site 7 out of 16 in 7yiv

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Zinc binding site 7 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:54.0
occ:1.00
 OD2 B:ASP337 1.9 53.6 1.0
NE2 B:HIS454 2.2 52.4 1.0
NE2 B:HIS341 2.2 47.1 1.0
CE1 B:HIS454 2.8 58.4 1.0
CG B:ASP337 2.8 51.6 1.0
OD1 B:ASP337 2.9 57.8 1.0
CD2 B:HIS341 3.1 52.5 1.0
CE1 B:HIS341 3.3 56.2 1.0
OG B:SER110 3.4 64.1 1.0
CD2 B:HIS454 3.4 57.2 1.0
ZN B:ZN606 3.9 90.8 1.0
ND1 B:HIS454 4.0 60.4 1.0
NE2 B:HIS379 4.0 60.7 1.0
CE1 B:HIS379 4.1 59.6 1.0
CB B:ASP337 4.2 49.6 1.0
CG B:HIS341 4.3 50.4 1.0
ND1 B:HIS341 4.3 56.9 1.0
CG B:HIS454 4.3 60.1 1.0
CB B:SER110 4.8 72.5 1.0
OD1 B:ASP60 5.0 65.8 1.0

Zinc binding site 8 out of 16 in 7yiv

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Zinc binding site 8 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn606

b:90.8
occ:1.00
 OD2 B:ASP378 1.8 52.9 1.0
OD1 B:ASP60 1.9 65.8 1.0
NE2 B:HIS379 2.3 60.7 1.0
OG B:SER110 2.5 64.1 1.0
CG B:ASP378 2.8 54.0 1.0
CD2 B:HIS379 3.0 57.4 1.0
CG B:ASP60 3.1 60.9 1.0
CB B:SER110 3.1 72.5 1.0
OD1 B:ASP378 3.3 53.2 1.0
CE1 B:HIS379 3.3 59.6 1.0
OD2 B:ASP60 3.6 56.1 1.0
CA B:SER110 3.7 63.6 1.0
CG B:ASP337 3.7 51.6 1.0
OD1 B:ASP337 3.8 57.8 1.0
OD2 B:ASP337 3.8 53.6 1.0
ZN B:ZN604 3.9 54.0 1.0
CB B:ASP378 4.1 50.5 1.0
CG B:HIS379 4.2 54.9 1.0
N B:SER110 4.2 61.1 1.0
CB B:ASP60 4.3 54.5 1.0
ND1 B:HIS379 4.3 55.9 1.0
CB B:ASP337 4.3 49.6 1.0
CE1 B:HIS454 4.3 58.4 1.0
CA B:ASP60 4.4 49.4 1.0
N B:GLY61 4.4 46.5 1.0
C B:ASP60 4.5 46.5 1.0
NE2 B:HIS454 4.6 52.4 1.0
C B:ASP109 4.8 60.9 1.0
OG1 B:THR173 4.8 54.6 1.0
MG B:MG603 4.9 50.1 1.0
C B:SER110 5.0 55.9 1.0

Zinc binding site 9 out of 16 in 7yiv

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Zinc binding site 9 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn604

b:102.5
occ:1.00
 OD2 G:ASP337 1.7 63.9 1.0
NE2 G:HIS454 2.2 63.3 1.0
NE2 G:HIS341 2.3 66.3 1.0
CG G:ASP337 2.5 64.4 1.0
OD1 G:ASP337 2.6 66.5 1.0
CE1 G:HIS454 2.8 63.7 1.0
CD2 G:HIS341 3.2 72.4 1.0
CE1 G:HIS341 3.3 73.5 1.0
CD2 G:HIS454 3.4 69.9 1.0
OG G:SER110 3.5 70.1 1.0
CB G:ASP337 4.0 62.5 1.0
ND1 G:HIS454 4.1 61.6 1.0
CE1 G:HIS379 4.1 70.4 1.0
ZN G:ZN606 4.1 83.8 1.0
NE2 G:HIS379 4.1 66.6 1.0
ND1 G:HIS341 4.4 75.6 1.0
CG G:HIS454 4.4 69.2 1.0
CG G:HIS341 4.4 72.4 1.0
CB G:SER110 4.5 70.7 1.0

Zinc binding site 10 out of 16 in 7yiv

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Zinc binding site 10 out of 16 in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn606

b:83.8
occ:1.00
 OD2 G:ASP378 1.9 68.6 1.0
OG G:SER110 2.0 70.1 1.0
NE2 G:HIS379 2.3 66.6 1.0
CE1 G:HIS379 2.8 70.4 1.0
CG G:ASP378 2.9 65.8 1.0
CB G:SER110 3.1 70.7 1.0
CG G:ASP60 3.2 73.0 1.0
OD1 G:ASP378 3.3 60.7 1.0
OD1 G:ASP60 3.3 76.6 1.0
CD2 G:HIS379 3.4 65.5 1.0
OD2 G:ASP60 3.6 74.1 1.0
CB G:ASP60 3.6 70.8 1.0
OD1 G:ASP337 3.7 66.5 1.0
CG G:ASP337 3.7 64.4 1.0
CA G:ASP60 3.8 64.0 1.0
CA G:SER110 3.9 71.1 1.0
N G:GLY61 3.9 64.2 1.0
CB G:ASP337 3.9 62.5 1.0
ND1 G:HIS379 4.0 61.9 1.0
C G:ASP60 4.0 65.8 1.0
ZN G:ZN604 4.1 102.5 1.0
OD2 G:ASP337 4.2 63.9 1.0
CG G:HIS379 4.2 62.8 1.0
CB G:ASP378 4.2 58.6 1.0
OG1 G:THR173 4.5 66.0 1.0
MG G:MG603 4.6 61.2 1.0
N G:SER110 4.6 68.1 1.0
CE1 G:HIS454 4.6 63.7 1.0
NE2 G:HIS454 4.6 63.3 1.0
CA G:GLY61 4.6 58.8 1.0
O G:ASP60 4.8 64.0 1.0

Reference:

Y.Yu, K.Rong, D.Yao, Q.Zhang, X.Cao, B.Rao, Y.Xia, Y.Lu, Y.Shen, Y.Yao, H.Xu, P.Ma, Y.Cao, A.Qin. The Structural Pathology For Hypophosphatasia Caused By Malfunctional Tissue Non-Specific Alkaline Phosphatase. Nat Commun V. 14 4048 2023.
ISSN: ESSN 2041-1723
PubMed: 37422472
DOI: 10.1038/S41467-023-39833-3
Page generated: Wed Oct 30 15:53:46 2024

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