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Calcium 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:

Magnesium (Mg) 8 atoms
Zinc (Zn) 16 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 8 binding sites of Calcium where determined in the The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (Alpl) at Basic pH, PDB code: 7yiv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7yiv

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Calcium binding site 1 out of 8 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 Calcium with other atoms in the Ca 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:Ca605

b:88.4
occ:1.00
 OD1 A:ASP306 2.4 86.6 1.0
OE2 A:GLU235 2.6 87.3 1.0
O A:PHE290 2.7 77.3 1.0
OE1 A:GLU235 2.8 95.3 1.0
CD A:GLU235 2.8 96.4 1.0
CG A:ASP306 3.0 82.4 1.0
OD2 A:ASP306 3.0 84.8 1.0
OE1 A:GLU291 3.2 76.7 1.0
NH2 A:ARG223 3.7 82.2 1.0
C A:PHE290 3.7 74.4 1.0
O A:TRP270 3.8 80.8 1.0
O A:THR305 3.8 81.6 1.0
CG A:GLU235 4.0 94.0 1.0
CA A:PHE290 4.3 74.2 1.0
C A:THR305 4.4 81.5 1.0
CB A:ASP306 4.4 74.0 1.0
OG1 A:THR305 4.4 69.1 1.0
CB A:GLU235 4.4 93.2 1.0
CD A:GLU291 4.4 85.3 1.0
CB A:THR305 4.5 70.7 1.0
CB A:PHE290 4.5 69.5 1.0
CA A:ASP306 4.7 77.6 1.0
CE3 A:TRP270 4.7 92.7 1.0
N A:GLU291 4.8 70.2 1.0
N A:ASP306 4.8 85.5 1.0
CA A:GLU291 4.9 75.8 1.0
CZ3 A:TRP270 4.9 88.7 1.0
C A:TRP270 5.0 81.0 1.0
CA A:ASN271 5.0 81.6 1.0
CZ A:ARG223 5.0 79.8 1.0

Calcium binding site 2 out of 8 in 7yiv

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Calcium binding site 2 out of 8 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 Calcium with other atoms in the Ca 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
D:Ca605

b:70.8
occ:1.00
 OD1 D:ASP306 2.3 70.3 1.0
O D:PHE290 2.4 63.1 1.0
OE2 D:GLU235 2.4 77.1 1.0
OE1 D:GLU235 2.5 73.5 1.0
OE2 D:GLU291 2.6 64.8 1.0
OD2 D:ASP306 2.6 69.9 1.0
CD D:GLU235 2.7 75.7 1.0
CG D:ASP306 2.7 69.9 1.0
O D:THR305 3.5 70.7 1.0
C D:PHE290 3.6 62.4 1.0
CD D:GLU291 3.7 69.0 1.0
CG D:GLU291 4.0 68.7 1.0
O D:TRP270 4.1 67.4 1.0
CB D:ASP306 4.1 61.9 1.0
CG D:GLU235 4.1 69.4 1.0
C D:THR305 4.3 71.7 1.0
CA D:PHE290 4.3 63.9 1.0
OH D:TYR236 4.3 78.7 1.0
OG1 D:THR305 4.4 68.9 1.0
NH2 D:ARG223 4.4 60.0 1.0
CB D:PHE290 4.5 64.2 1.0
CA D:ASP306 4.5 69.3 1.0
N D:GLU291 4.6 61.5 1.0
NH1 D:ARG223 4.6 67.3 1.0
CB D:THR305 4.6 65.3 1.0
CA D:GLU291 4.7 63.7 1.0
N D:ASP306 4.8 72.7 1.0
OE1 D:GLU291 4.8 70.2 1.0
CE1 D:TYR236 4.9 75.6 1.0
CB D:GLU291 5.0 68.0 1.0

Calcium binding site 3 out of 8 in 7yiv

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Calcium binding site 3 out of 8 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 Calcium with other atoms in the Ca 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
C:Ca605

b:82.6
occ:1.00
 OE2 C:GLU235 2.2 94.5 1.0
OD2 C:ASP306 2.3 81.0 1.0
OD1 C:ASP306 2.3 83.3 1.0
O C:PHE290 2.4 75.3 1.0
OE1 C:GLU235 2.4 84.4 1.0
OE1 C:GLU291 2.5 68.7 1.0
CG C:ASP306 2.6 78.8 1.0
CD C:GLU235 2.7 85.9 1.0
C C:PHE290 3.6 65.4 1.0
CD C:GLU291 3.6 77.3 1.0
OH C:TYR236 3.7 82.2 1.0
NH2 C:ARG223 4.1 74.0 1.0
CB C:ASP306 4.1 68.7 1.0
CG C:GLU235 4.2 81.4 1.0
OE2 C:GLU291 4.2 89.3 1.0
O C:THR305 4.2 73.6 1.0
CA C:GLU291 4.4 68.0 1.0
O C:TRP270 4.4 68.4 1.0
CE2 C:TYR236 4.4 81.1 1.0
N C:GLU291 4.4 62.0 1.0
CZ C:TYR236 4.5 73.3 1.0
CA C:PHE290 4.5 66.1 1.0
OG1 C:THR305 4.6 64.2 1.0
C C:THR305 4.7 72.9 1.0
CB C:PHE290 4.7 63.0 1.0
CB C:GLU291 4.8 69.0 1.0
CB C:THR305 4.8 75.2 1.0
CG C:GLU291 4.8 67.0 1.0
CA C:ASP306 4.8 70.8 1.0
CB C:GLU235 5.0 86.6 1.0

Calcium binding site 4 out of 8 in 7yiv

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Calcium binding site 4 out of 8 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 Calcium with other atoms in the Ca 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
B:Ca605

b:62.7
occ:1.00
 OE1 B:GLU235 2.3 59.9 1.0
O B:PHE290 2.4 50.8 1.0
OD1 B:ASP306 2.5 57.5 1.0
OD2 B:ASP306 2.5 49.4 1.0
CG B:ASP306 2.7 56.0 1.0
OE2 B:GLU291 2.8 48.9 1.0
CD B:GLU235 2.9 64.3 1.0
OE2 B:GLU235 3.1 65.8 1.0
C B:PHE290 3.5 50.0 1.0
O B:THR305 3.5 48.9 1.0
O B:TRP270 3.8 56.6 1.0
CD B:GLU291 3.9 58.8 1.0
CB B:ASP306 4.0 55.1 1.0
C B:THR305 4.0 56.8 1.0
CA B:PHE290 4.0 50.6 1.0
CB B:PHE290 4.0 50.9 1.0
CG B:GLU235 4.1 57.9 1.0
CB B:THR305 4.2 50.9 1.0
CA B:ASP306 4.2 51.7 1.0
CG B:GLU291 4.3 55.3 1.0
N B:ASP306 4.4 53.0 1.0
NH1 B:ARG223 4.4 58.0 1.0
OG1 B:THR305 4.5 47.8 1.0
N B:GLU291 4.6 52.3 1.0
CA B:THR305 4.7 57.6 1.0
CA B:ASN271 4.8 57.2 1.0
CA B:GLU291 4.8 51.6 1.0
C B:TRP270 4.9 56.0 1.0
NH2 B:ARG223 4.9 56.8 1.0

Calcium binding site 5 out of 8 in 7yiv

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Calcium binding site 5 out of 8 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 Calcium with other atoms in the Ca 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
G:Ca605

b:77.6
occ:1.00
 OD1 G:ASP306 2.0 73.4 1.0
OE2 G:GLU235 2.2 83.2 1.0
O G:PHE290 2.6 75.5 1.0
OE1 G:GLU235 2.6 80.4 1.0
CD G:GLU235 2.7 83.4 1.0
CG G:ASP306 2.9 74.1 1.0
OD2 G:ASP306 3.2 81.1 1.0
OE2 G:GLU291 3.3 75.7 1.0
O G:THR305 3.5 78.5 1.0
C G:PHE290 3.7 71.7 1.0
OG1 G:THR305 3.7 78.8 1.0
O G:TRP270 3.9 70.2 1.0
OE1 G:GLU291 3.9 84.2 1.0
CD G:GLU291 3.9 78.5 1.0
C G:THR305 3.9 81.4 1.0
CB G:THR305 4.0 77.9 1.0
CB G:ASP306 4.1 72.4 1.0
CG G:GLU235 4.2 87.7 1.0
CA G:PHE290 4.3 65.8 1.0
CA G:ASP306 4.3 78.1 1.0
N G:ASP306 4.4 78.9 1.0
OH G:TYR236 4.4 71.2 1.0
CB G:PHE290 4.5 67.2 1.0
CA G:THR305 4.6 79.8 1.0
N G:GLU291 4.7 69.9 1.0
CA G:GLU291 5.0 70.7 1.0

Calcium binding site 6 out of 8 in 7yiv

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Calcium binding site 6 out of 8 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 Calcium with other atoms in the Ca 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
H:Ca605

b:74.6
occ:1.00
 O H:PHE290 2.2 74.1 1.0
OD1 H:ASP306 2.2 77.1 1.0
OE1 H:GLU235 2.7 82.5 1.0
OE2 H:GLU291 2.9 73.4 1.0
CG H:ASP306 2.9 79.3 1.0
CD H:GLU235 3.1 84.6 1.0
OE2 H:GLU235 3.2 80.7 1.0
OD2 H:ASP306 3.3 86.5 1.0
C H:PHE290 3.3 72.7 1.0
O H:TRP270 3.5 74.6 1.0
O H:THR305 3.6 78.8 1.0
CA H:PHE290 3.9 70.6 1.0
CD H:GLU291 4.0 77.9 1.0
CB H:PHE290 4.0 66.6 1.0
C H:THR305 4.1 79.9 1.0
CB H:ASP306 4.1 71.7 1.0
CA H:ASP306 4.1 76.2 1.0
CG H:GLU235 4.2 91.7 1.0
OG1 H:THR305 4.3 76.3 1.0
N H:ASP306 4.3 83.2 1.0
CG H:GLU291 4.4 80.6 1.0
N H:GLU291 4.4 72.2 1.0
NH1 H:ARG223 4.5 88.3 1.0
CA H:ASN271 4.6 76.3 1.0
C H:TRP270 4.6 79.9 1.0
CB H:THR305 4.7 76.4 1.0
CA H:GLU291 4.8 79.2 1.0
NH2 H:ARG223 4.8 86.2 1.0
CD1 H:PHE290 4.9 68.7 1.0
CB H:ASN271 5.0 82.0 1.0

Calcium binding site 7 out of 8 in 7yiv

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Calcium binding site 7 out of 8 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 Calcium with other atoms in the Ca 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
F:Ca605

b:73.6
occ:1.00
 O F:PHE290 2.2 75.0 1.0
OE2 F:GLU235 2.4 82.7 1.0
OD2 F:ASP306 2.4 79.6 1.0
OE1 F:GLU235 2.4 86.5 1.0
OE2 F:GLU291 2.5 67.9 1.0
OD1 F:ASP306 2.6 84.3 1.0
CD F:GLU235 2.7 81.6 1.0
CG F:ASP306 2.8 79.9 1.0
C F:PHE290 3.4 74.4 1.0
O F:THR305 3.5 77.6 1.0
CD F:GLU291 3.6 78.6 1.0
OG1 F:THR305 4.0 66.3 1.0
NH2 F:ARG223 4.0 76.6 1.0
C F:THR305 4.1 80.3 1.0
CB F:ASP306 4.2 73.5 1.0
CG F:GLU235 4.2 81.2 1.0
O F:TRP270 4.2 71.5 1.0
CA F:PHE290 4.2 78.2 1.0
CG F:GLU291 4.2 76.7 1.0
CB F:PHE290 4.3 73.8 1.0
CB F:THR305 4.3 70.5 1.0
OH F:TYR236 4.4 81.6 1.0
N F:GLU291 4.4 71.7 1.0
CA F:ASP306 4.5 72.5 1.0
CA F:GLU291 4.6 71.7 1.0
OE1 F:GLU291 4.7 85.0 1.0
CE2 F:TYR236 4.7 80.5 1.0
N F:ASP306 4.7 78.1 1.0
CA F:THR305 4.9 78.7 1.0
CB F:GLU235 4.9 82.3 1.0
CZ F:TYR236 4.9 79.0 1.0
CB F:GLU291 5.0 73.8 1.0

Calcium binding site 8 out of 8 in 7yiv

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Calcium binding site 8 out of 8 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 Calcium with other atoms in the Ca 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
E:Ca605

b:90.9
occ:1.00
 OD2 E:ASP306 2.1 80.9 1.0
O E:PHE290 2.3 90.1 1.0
OD1 E:ASP306 2.3 95.2 1.0
OE1 E:GLU235 2.4 95.7 1.0
CG E:ASP306 2.5 87.2 1.0
OE2 E:GLU291 2.5 92.1 1.0
OE2 E:GLU235 2.5 98.0 1.0
CD E:GLU235 2.8 94.2 1.0
C E:PHE290 3.4 85.8 1.0
CD E:GLU291 3.5 90.6 1.0
CG E:GLU291 3.8 87.0 1.0
O E:THR305 3.8 88.5 1.0
OH E:TYR236 3.8 98.6 1.0
CB E:ASP306 3.9 81.6 1.0
CA E:PHE290 4.3 82.9 1.0
N E:GLU291 4.3 81.6 1.0
CG E:GLU235 4.3 93.5 1.0
C E:THR305 4.4 93.6 1.0
CB E:PHE290 4.4 80.2 1.0
CA E:GLU291 4.4 81.2 1.0
CA E:ASP306 4.5 86.3 1.0
O E:TRP270 4.5 87.3 1.0
OG1 E:THR305 4.6 83.2 1.0
OE1 E:GLU291 4.7 90.2 1.0
CB E:THR305 4.7 90.4 1.0
CB E:GLU291 4.7 86.9 1.0
CZ E:TYR236 4.7 104.7 1.0
N E:ASP306 4.7 92.3 1.0
NH1 E:ARG223 4.8 79.8 1.0
NH2 E:ARG223 4.9 82.4 1.0
CE2 E:TYR236 4.9 98.7 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: Fri Jul 19 06:14:11 2024

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