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Magnesium 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
Zinc (Zn) 16 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:64.7
occ:1.00
 OD2 A:ASP60 1.9 77.5 1.0
OE2 A:GLU332 2.6 64.3 1.0
OG1 A:THR173 2.7 60.9 1.0
CG A:ASP60 3.0 75.2 1.0
ND1 A:HIS171 3.0 82.3 1.0
CB A:THR173 3.3 58.5 1.0
OD1 A:ASP60 3.4 80.6 1.0
CE1 A:HIS171 3.4 84.2 1.0
CD A:GLU332 3.7 70.3 1.0
N A:THR173 3.8 71.0 1.0
OE1 A:GLU332 4.1 81.3 1.0
CA A:THR173 4.1 64.1 1.0
CG A:HIS171 4.3 69.9 1.0
CB A:ASP60 4.3 67.5 1.0
CB A:SER110 4.3 70.5 1.0
CB A:ALA172 4.3 63.2 1.0
ZN A:ZN606 4.3 91.5 1.0
OG A:SER110 4.4 68.0 1.0
CG2 A:THR173 4.5 59.6 1.0
OG1 A:THR167 4.6 65.5 1.0
CG2 A:THR167 4.6 75.3 1.0
NE2 A:HIS171 4.7 74.1 1.0
CA A:GLY334 4.8 62.6 1.0
C A:ALA172 4.8 63.2 1.0
O A:GLY334 4.8 68.5 1.0
CB A:HIS171 4.9 69.6 1.0
CA A:ALA172 5.0 69.4 1.0

Magnesium binding site 2 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:62.4
occ:1.00
 OD2 D:ASP60 2.2 71.9 1.0
OG1 D:THR173 2.3 64.6 1.0
OE2 D:GLU332 2.5 67.8 1.0
CB D:THR173 3.1 64.6 1.0
ND1 D:HIS171 3.2 74.7 1.0
CG D:ASP60 3.2 65.8 1.0
CE1 D:HIS171 3.5 76.0 1.0
N D:THR173 3.5 65.5 1.0
CD D:GLU332 3.5 65.2 1.0
OD1 D:ASP60 3.8 68.6 1.0
OE1 D:GLU332 3.9 69.1 1.0
CA D:THR173 3.9 65.0 1.0
CB D:SER110 4.2 71.9 1.0
CB D:ASP60 4.3 64.0 1.0
CG2 D:THR173 4.4 55.5 1.0
CB D:ALA172 4.4 62.7 1.0
CG D:HIS171 4.5 73.5 1.0
CG2 D:THR167 4.5 66.9 1.0
C D:ALA172 4.6 62.6 1.0
OG D:SER110 4.6 70.6 1.0
ZN D:ZN606 4.7 80.7 1.0
N D:ALA172 4.7 64.0 1.0
NE2 D:HIS171 4.8 69.9 1.0
CA D:ALA172 4.8 61.7 1.0
O D:GLY334 4.8 56.9 1.0
CG D:GLU332 4.8 58.6 1.0
OG1 D:THR167 4.9 69.3 1.0
CD D:PRO174 5.0 61.6 1.0

Magnesium binding site 3 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:55.8
occ:1.00
 OD2 C:ASP60 2.0 60.0 1.0
OE2 C:GLU332 2.4 50.4 1.0
OG1 C:THR173 3.0 57.8 1.0
CG C:ASP60 3.2 61.2 1.0
CE1 C:HIS171 3.2 74.2 1.0
ND1 C:HIS171 3.2 64.1 1.0
CB C:THR173 3.3 53.0 1.0
CD C:GLU332 3.5 60.8 1.0
N C:THR173 3.5 55.7 1.0
OE1 C:GLU332 3.8 67.5 1.0
OD1 C:ASP60 3.8 61.5 1.0
CB C:ALA172 4.0 54.9 1.0
CA C:THR173 4.1 54.9 1.0
CB C:SER110 4.3 65.2 1.0
CB C:ASP60 4.3 63.7 1.0
NE2 C:HIS171 4.5 63.9 1.0
ZN C:ZN606 4.5 76.8 1.0
CG C:HIS171 4.6 61.4 1.0
C C:ALA172 4.6 54.8 1.0
CG2 C:THR173 4.6 49.8 1.0
OG C:SER110 4.7 60.5 1.0
O C:GLY334 4.7 62.0 1.0
CA C:ALA172 4.7 59.2 1.0
CG C:GLU332 4.8 55.4 1.0
CD C:PRO174 4.9 56.0 1.0
CG2 C:THR167 4.9 62.3 1.0
OG1 C:THR167 4.9 60.1 1.0
N C:ALA172 4.9 59.4 1.0
OD2 C:ASP378 5.0 57.3 1.0

Magnesium binding site 4 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:50.1
occ:1.00
 OD2 B:ASP60 2.1 56.1 1.0
OE2 B:GLU332 2.4 59.9 1.0
OG1 B:THR173 2.6 54.6 1.0
ND1 B:HIS171 2.8 65.4 1.0
CE1 B:HIS171 3.2 71.9 1.0
CB B:THR173 3.2 50.2 1.0
CD B:GLU332 3.3 59.5 1.0
CG B:ASP60 3.4 60.9 1.0
N B:THR173 3.4 56.2 1.0
OE1 B:GLU332 3.5 57.9 1.0
CA B:THR173 3.9 52.3 1.0
OD1 B:ASP60 4.1 65.8 1.0
CG B:HIS171 4.1 58.1 1.0
CB B:SER110 4.2 72.5 1.0
CB B:ALA172 4.4 59.1 1.0
CB B:ASP60 4.4 54.5 1.0
CG2 B:THR167 4.4 53.6 1.0
NE2 B:HIS171 4.5 67.5 1.0
C B:ALA172 4.5 50.7 1.0
CG2 B:THR173 4.5 40.3 1.0
OG B:SER110 4.5 64.1 1.0
OG1 B:THR167 4.5 52.7 1.0
CD B:PRO174 4.6 48.1 1.0
N B:ALA172 4.6 57.6 1.0
CG B:GLU332 4.7 55.2 1.0
CA B:ALA172 4.7 54.2 1.0
CB B:HIS171 4.8 57.8 1.0
CB B:THR167 4.9 53.0 1.0
O B:GLY334 4.9 54.0 1.0
ZN B:ZN606 4.9 90.8 1.0
CD2 B:HIS171 4.9 59.1 1.0

Magnesium binding site 5 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:61.2
occ:1.00
 OD2 G:ASP60 1.9 74.1 1.0
OG1 G:THR173 2.3 66.0 1.0
OE2 G:GLU332 2.7 71.3 1.0
ND1 G:HIS171 2.8 85.9 1.0
CG G:ASP60 2.9 73.0 1.0
CB G:THR173 3.0 65.1 1.0
OD1 G:ASP60 3.1 76.6 1.0
CE1 G:HIS171 3.4 87.5 1.0
N G:THR173 3.6 59.6 1.0
CD G:GLU332 3.7 69.8 1.0
CA G:THR173 3.9 63.4 1.0
OE1 G:GLU332 4.0 73.4 1.0
CG G:HIS171 4.1 74.8 1.0
CG2 G:THR173 4.1 57.8 1.0
CB G:SER110 4.2 70.7 1.0
CB G:ASP60 4.3 70.8 1.0
OG G:SER110 4.3 70.1 1.0
CG2 G:THR167 4.5 68.8 1.0
ZN G:ZN606 4.6 83.8 1.0
OG1 G:THR167 4.6 70.2 1.0
NE2 G:HIS171 4.6 83.5 1.0
CB G:HIS171 4.6 68.0 1.0
C G:ALA172 4.8 62.2 1.0
O G:GLY334 4.8 66.1 1.0
N G:ALA172 4.9 71.0 1.0
CD G:PRO174 4.9 63.9 1.0
CG G:GLU332 4.9 58.5 1.0
CB G:THR167 5.0 68.1 1.0

Magnesium binding site 6 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:73.7
occ:1.00
 OD2 H:ASP60 2.2 79.7 1.0
ND1 H:HIS171 3.0 93.2 1.0
CE1 H:HIS171 3.0 94.9 1.0
OE2 H:GLU332 3.2 76.5 1.0
CG H:ASP60 3.3 77.2 1.0
OG1 H:THR173 3.4 63.7 1.0
OG H:SER110 3.8 77.2 1.0
OD1 H:ASP60 3.9 79.0 1.0
CB H:SER110 4.0 86.6 1.0
CB H:THR173 4.2 69.4 1.0
NE2 H:HIS338 4.2 82.8 1.0
O H:GLY334 4.2 72.2 1.0
CB H:ASP60 4.3 74.1 1.0
CD H:GLU332 4.3 75.7 1.0
NE2 H:HIS171 4.3 82.1 1.0
CG H:HIS171 4.3 84.7 1.0
OD2 H:ASP337 4.3 85.0 1.0
N H:THR173 4.4 79.1 1.0
CG2 H:THR167 4.4 77.2 1.0
ZN H:ZN606 4.5 82.0 1.0
OE1 H:GLU332 4.6 80.5 1.0
CG H:ASP337 4.8 78.9 1.0
CB H:ASP337 4.8 71.9 1.0
OG1 H:THR167 4.9 78.5 1.0
CD2 H:HIS338 4.9 77.1 1.0
CB H:ALA172 4.9 75.0 1.0
CD2 H:HIS171 4.9 81.8 1.0
CA H:THR173 5.0 75.5 1.0
CB H:THR167 5.0 79.1 1.0

Magnesium binding site 7 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:54.4
occ:1.00
 OE2 F:GLU332 2.1 65.9 1.0
OD2 F:ASP60 2.2 76.0 1.0
OG1 F:THR173 2.9 72.3 1.0
CB F:THR173 3.0 66.0 1.0
CD F:GLU332 3.3 66.4 1.0
CG F:ASP60 3.4 75.1 1.0
ND1 F:HIS171 3.4 77.0 1.0
N F:THR173 3.6 73.1 1.0
CA F:THR173 3.9 67.6 1.0
OE1 F:GLU332 4.0 67.2 1.0
CG2 F:THR173 4.1 60.8 1.0
CE1 F:HIS171 4.1 71.8 1.0
OD1 F:ASP60 4.2 75.2 1.0
CG2 F:THR167 4.2 61.7 1.0
CB F:ASP60 4.4 69.0 1.0
CG F:GLU332 4.4 62.8 1.0
CD F:PRO174 4.5 70.2 1.0
OG1 F:THR167 4.5 67.4 1.0
CG F:HIS171 4.5 70.9 1.0
CB F:SER110 4.7 78.4 1.0
CA F:GLY334 4.7 61.9 1.0
CB F:ALA172 4.8 69.9 1.0
C F:ALA172 4.8 71.9 1.0
CB F:HIS171 4.8 67.5 1.0
O F:GLY334 4.8 58.8 1.0
CB F:THR167 4.9 62.3 1.0

Magnesium binding site 8 out of 8 in 7yiv

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:58.2
occ:1.00
 OD2 E:ASP60 2.3 81.1 1.0
OE2 E:GLU332 2.7 72.3 1.0
ND1 E:HIS171 2.8 88.2 1.0
OG1 E:THR173 2.8 73.2 1.0
CB E:THR173 3.3 68.9 1.0
CE1 E:HIS171 3.3 91.8 1.0
N E:THR173 3.5 74.2 1.0
CG E:ASP60 3.5 79.9 1.0
CD E:GLU332 3.7 71.9 1.0
CA E:THR173 4.0 67.9 1.0
OE1 E:GLU332 4.0 80.4 1.0
CG E:HIS171 4.0 82.1 1.0
CB E:ALA172 4.1 73.4 1.0
OD1 E:ASP60 4.2 74.5 1.0
CG2 E:THR167 4.3 76.1 1.0
OG1 E:THR167 4.5 76.6 1.0
C E:ALA172 4.5 70.3 1.0
N E:ALA172 4.5 84.7 1.0
NE2 E:HIS171 4.6 82.3 1.0
CG2 E:THR173 4.6 66.2 1.0
CA E:ALA172 4.6 78.6 1.0
CB E:HIS171 4.6 78.3 1.0
CB E:ASP60 4.6 76.7 1.0
CD E:PRO174 4.7 71.5 1.0
CB E:SER110 4.7 77.1 1.0
O E:GLY334 4.8 78.0 1.0
CB E:THR167 4.9 78.3 1.0
CA E:GLY334 4.9 73.3 1.0
CD2 E:HIS171 4.9 78.4 1.0
ZN E:ZN606 5.0 68.8 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: Thu Oct 3 14:47:10 2024

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