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Magnesium in PDB 4toq: Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity

Enzymatic activity of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity

All present enzymatic activity of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity:
3.2.1.14;

Protein crystallography data

The structure of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity, PDB code: 4toq was solved by T.Masuda, G.Zhao, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.60 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.462, 79.969, 97.532, 90.00, 102.97, 90.00
R / Rfree (%) 15.5 / 19.2

Other elements in 4toq:

The structure of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity (pdb code 4toq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity, PDB code: 4toq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 4toq

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Magnesium binding site 1 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:12.5
occ:1.00
 OG1 A:THR56 3.0 18.1 1.0
O A:HOH494 3.1 20.8 1.0
O A:HOH461 3.5 19.7 1.0
CA A:CYS50 3.6 8.8 1.0
CB A:THR56 3.7 15.5 1.0
N A:ASP51 3.9 10.7 1.0
C A:CYS50 4.1 14.3 1.0
CB A:CYS50 4.2 10.6 1.0
CG2 A:THR56 4.3 15.1 1.0
O A:HIS49 4.5 13.2 1.0
N A:CYS50 4.5 10.8 1.0
CB A:ASP51 4.7 11.2 1.0
C A:HIS49 4.9 10.8 1.0
O A:THR56 4.9 15.5 1.0
CA A:ASP51 4.9 14.4 1.0

Magnesium binding site 2 out of 13 in 4toq

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Magnesium binding site 2 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:13.2
occ:0.48
 O A:HOH724 2.1 25.1 1.0
O A:HOH725 2.1 27.2 1.0
O A:HOH672 2.1 25.3 1.0
O A:HOH548 2.1 29.7 1.0
O A:HOH590 2.1 16.6 1.0
OE1 A:GLN158 4.1 18.6 1.0
O A:HOH516 4.2 20.8 1.0
O A:HOH495 4.3 22.1 1.0
O A:HOH645 4.3 18.3 1.0
CD A:GLN158 4.4 16.7 1.0
OE1 A:GLU127 4.5 12.4 1.0
O A:HOH655 4.5 24.8 1.0
O A:HOH561 4.6 21.5 1.0
O A:HOH654 4.6 21.2 1.0
CB A:ASN184 4.6 6.7 1.0
NE2 A:GLN158 4.6 17.4 1.0
O A:ASN184 4.7 11.5 1.0
O A:HOH668 4.8 30.9 1.0

Magnesium binding site 3 out of 13 in 4toq

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Magnesium binding site 3 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:44.0
occ:1.00
 O A:HOH744 2.0 26.5 1.0
O A:HOH728 2.1 29.6 1.0
O A:HOH625 2.1 23.8 1.0
O A:HOH727 2.1 35.4 1.0
O A:HOH528 4.0 22.5 1.0
O A:HOH530 4.3 31.1 1.0
O A:HOH743 4.4 27.9 1.0
OD2 A:ASP167 4.4 16.1 1.0
OD1 A:ASP167 4.4 10.7 1.0
OD1 A:ASN171 4.6 24.5 1.0
ND2 A:ASN171 4.6 25.8 1.0
CG A:PRO162 4.8 23.8 1.0
CG A:ASP167 4.9 11.8 1.0

Magnesium binding site 4 out of 13 in 4toq

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Magnesium binding site 4 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:23.8
occ:1.00
 O A:HOH415 2.1 27.2 1.0
O A:HOH539 2.1 18.9 1.0
O A:HOH512 2.1 30.1 1.0
O A:HOH536 4.1 28.3 1.0
O A:HOH491 4.2 16.4 1.0
OD1 A:ASN198 4.2 23.9 1.0
O A:HOH434 4.3 13.5 1.0
ND2 A:ASN198 4.5 27.8 1.0
CG A:ASN198 4.8 27.0 1.0
O A:GLY195 4.8 12.3 1.0

Magnesium binding site 5 out of 13 in 4toq

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Magnesium binding site 5 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:31.9
occ:1.00
 O A:HOH408 2.1 26.6 1.0
OG A:SER248 2.4 9.1 0.6
OG1 A:THR208 2.5 10.6 1.0
OG A:SER248 3.1 10.0 0.4
CB A:SER248 3.3 10.1 0.6
CB A:SER248 3.3 10.1 0.4
CB A:THR208 3.4 7.3 1.0
OD1 A:ASN205 4.0 14.7 1.0
CG2 A:THR208 4.0 10.2 1.0
CA A:SER248 4.1 7.8 0.6
CA A:SER248 4.1 7.8 0.4
NE1 A:TRP204 4.2 7.8 1.0
O A:HOH404 4.3 26.6 1.0
CA A:ASN205 4.4 9.4 1.0
CD1 A:TRP204 4.5 7.4 1.0
OG A:SER209 4.6 9.9 0.4
O A:ASN205 4.6 10.6 1.0
CA A:THR208 4.7 8.2 1.0
O A:TRP204 4.8 9.2 1.0
CG A:ASN205 4.8 14.1 1.0

Magnesium binding site 6 out of 13 in 4toq

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Magnesium binding site 6 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:13.2
occ:0.55
 O B:HOH456 2.1 20.3 1.0
O B:HOH459 2.1 18.9 1.0
O B:HOH511 2.1 27.6 1.0
O B:HOH558 2.1 15.4 1.0
O B:HOH474 4.0 13.4 1.0
O B:PHE36 4.2 9.2 1.0
O B:GLY37 4.2 9.3 1.0
O B:HOH442 4.2 21.7 1.0
O B:HOH478 4.3 18.0 1.0
O B:HOH501 4.4 21.5 1.0
O B:HOH581 4.5 15.0 1.0
O B:ASP84 4.5 10.7 1.0
C B:PHE36 4.6 10.9 1.0
C B:GLY37 4.8 11.8 1.0
CG B:ARG40 4.9 18.9 1.0

Magnesium binding site 7 out of 13 in 4toq

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Magnesium binding site 7 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:33.0
occ:1.00
 O B:HOH692 2.1 29.0 1.0
O B:HOH696 2.1 25.4 1.0
O B:HOH596 2.1 20.5 1.0
OD1 B:ASN185 4.1 12.3 1.0
O B:ASN184 4.1 12.3 1.0
OE1 B:GLN158 4.2 15.5 1.0
O B:HOH565 4.2 17.3 1.0
O B:HOH637 4.4 26.2 1.0
CD B:GLN158 4.7 14.5 1.0
CG B:ASN185 4.7 10.6 1.0
ND2 B:ASN185 4.8 11.9 1.0
CG B:GLN158 4.9 16.6 1.0

Magnesium binding site 8 out of 13 in 4toq

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Magnesium binding site 8 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:24.1
occ:1.00
 O C:PRO113 2.6 19.2 1.0
N C:CYS57 3.0 15.4 1.0
O C:PRO52 3.1 20.5 1.0
C C:GLY55 3.3 22.6 1.0
CA C:GLY55 3.3 21.2 1.0
CB C:CYS57 3.4 13.1 1.0
N C:THR56 3.5 16.1 1.0
CA C:PRO52 3.5 13.8 1.0
CA C:CYS57 3.5 15.6 1.0
C C:PRO113 3.6 15.2 1.0
N C:THR58 3.7 23.2 1.0
C C:PRO52 3.7 16.7 1.0
O C:GLY55 3.7 20.9 1.0
O C:HOH569 3.8 30.1 1.0
C C:CYS57 3.8 18.6 1.0
N C:GLY55 3.9 18.5 1.0
CG2 C:THR58 4.0 21.3 1.0
C C:THR56 4.1 16.0 1.0
CA C:PRO113 4.1 13.5 1.0
O C:ASP51 4.1 17.0 1.0
SG C:CYS57 4.3 13.8 1.0
CA C:THR56 4.3 16.1 1.0
CB C:PRO52 4.5 9.4 1.0
N C:PRO52 4.5 13.9 1.0
CA C:THR58 4.7 21.7 1.0
C C:ASP51 4.7 18.8 1.0
O C:CYS57 4.7 18.3 1.0
O C:ARG112 4.7 14.1 1.0
N C:LEU114 4.8 11.5 1.0
CB C:THR58 4.9 22.4 1.0

Magnesium binding site 9 out of 13 in 4toq

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Magnesium binding site 9 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:16.4
occ:0.49
 O C:HOH427 2.1 25.7 1.0
O C:HOH713 2.1 35.0 1.0
O C:ALA47 3.9 14.5 1.0
O C:HOH677 4.6 29.7 1.0
O C:HOH594 4.7 23.8 1.0
C C:ALA47 4.7 16.6 1.0
CA C:GLY48 4.8 15.3 1.0

Magnesium binding site 10 out of 13 in 4toq

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Magnesium binding site 10 out of 13 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:11.7
occ:0.64
 O C:HOH662 2.1 19.1 1.0
O C:HOH645 2.1 21.8 1.0
O C:HOH513 2.1 24.1 1.0
O C:HOH578 2.1 21.3 1.0
O C:HOH577 2.1 20.6 1.0
OE1 C:GLN158 4.1 15.2 1.0
O C:HOH667 4.2 24.7 1.0
O C:HOH575 4.2 15.3 1.0
O C:HOH697 4.2 28.0 1.0
O C:HOH411 4.3 27.9 1.0
CD C:GLN158 4.3 17.6 1.0
O C:ASN184 4.4 12.1 1.0
OE1 C:GLU127 4.4 16.3 1.0
O C:HOH527 4.5 20.7 1.0
NE2 C:GLN158 4.6 12.7 1.0
CB C:ASN184 4.6 13.2 1.0
O C:HOH615 4.6 20.1 1.0
O C:HOH612 5.0 21.7 1.0

Reference:

T.Masuda, G.Zhao, B.Mikami. Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity. Biosci.Biotechnol.Biochem. 1 2014.
ISSN: ISSN 0916-8451
PubMed: 25252615
DOI: 10.1080/09168451.2014.962475
Page generated: Tue Aug 12 00:09:09 2025

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