Magnesium in PDB 5a1a: 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor

Enzymatic activity of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor

All present enzymatic activity of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor:
3.2.1.23;

Other elements in 5a1a:

The structure of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor (pdb code 5a1a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor, PDB code: 5a1a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5a1a

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Magnesium binding site 1 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:16.1
occ:1.00
 OE1 A:GLU461 2.2 13.9 1.0
O A:HOH5078 2.2 30.0 1.0
O A:HOH5036 2.4 30.0 1.0
O A:HOH5037 2.5 30.0 1.0
OE2 A:GLU416 2.6 11.7 1.0
ND1 A:HIS418 2.7 11.4 1.0
CD A:GLU461 3.1 19.5 1.0
OE2 A:GLU461 3.3 13.7 1.0
CE1 A:HIS418 3.4 12.3 1.0
CD A:GLU416 3.5 15.4 1.0
CG A:HIS418 3.7 15.0 1.0
OE1 A:GLU416 3.9 11.8 1.0
ND2 A:ASN460 4.0 13.9 1.0
CB A:HIS418 4.1 13.0 1.0
OD1 A:ASN102 4.2 16.2 1.0
O4 A:PTQ2001 4.2 20.0 1.0
O A:ASN102 4.3 13.8 1.0
O A:ASP199 4.3 15.8 1.0
CG A:GLU461 4.4 9.5 1.0
N A:ASP201 4.4 10.8 1.0
O A:HOH5079 4.5 30.0 1.0
NE2 A:HIS418 4.5 11.3 1.0
CB A:ASP201 4.5 12.1 1.0
C2 A:PTQ2001 4.6 20.0 1.0
CD2 A:HIS418 4.7 12.0 1.0
O3 A:PTQ2001 4.7 20.0 1.0
CB A:GLU461 4.7 10.0 1.0
CG A:GLU416 4.8 8.0 1.0

Magnesium binding site 2 out of 8 in 5a1a

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Magnesium binding site 2 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:30.0
occ:1.00
 O A:ASP15 2.4 14.8 1.0
OD1 A:ASP193 2.5 15.4 1.0
NE2 A:GLN163 2.5 13.3 1.0
OD2 A:ASP193 2.6 14.7 1.0
O A:VAL21 2.7 15.5 1.0
O A:ASN18 2.7 15.7 1.0
CG A:ASP193 2.9 19.2 1.0
CD A:GLN163 3.3 15.2 1.0
OE1 A:GLN163 3.4 13.8 1.0
C A:ASP15 3.5 15.9 1.0
C A:ASN18 3.6 18.4 1.0
OH A:TYR161 3.7 13.2 1.0
C A:TRP16 3.8 14.6 1.0
CA A:TRP16 3.8 11.8 1.0
C A:VAL21 3.9 13.9 1.0
N A:ASN18 3.9 18.5 1.0
N A:GLU17 4.0 13.8 1.0
O A:TRP16 4.1 15.0 1.0
N A:TRP16 4.1 11.4 1.0
OG A:SER192 4.2 15.0 1.0
CA A:ASN18 4.3 18.4 1.0
CB A:ASP193 4.3 13.9 1.0
C A:GLU17 4.4 22.4 1.0
N A:PRO19 4.5 19.0 1.0
CA A:THR22 4.6 12.3 1.0
CG A:GLN163 4.6 16.7 1.0
CZ A:TYR161 4.6 14.2 1.0
CE2 A:TYR161 4.6 11.6 1.0
N A:THR22 4.7 11.3 1.0
CA A:GLU17 4.7 16.5 1.0
CA A:PRO19 4.7 14.3 1.0
CA A:ASP15 4.8 15.4 1.0
CA A:VAL21 4.9 11.2 1.0
N A:ASP193 4.9 12.7 1.0
CB A:ASN18 5.0 14.5 1.0

Magnesium binding site 3 out of 8 in 5a1a

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Magnesium binding site 3 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:16.1
occ:1.00
 OE1 B:GLU461 2.2 13.9 1.0
O B:HOH5078 2.2 30.0 1.0
O B:HOH5036 2.4 30.0 1.0
O B:HOH5037 2.5 30.0 1.0
OE2 B:GLU416 2.6 11.7 1.0
ND1 B:HIS418 2.7 11.4 1.0
CD B:GLU461 3.1 19.5 1.0
OE2 B:GLU461 3.3 13.7 1.0
CE1 B:HIS418 3.4 12.3 1.0
CD B:GLU416 3.5 15.4 1.0
CG B:HIS418 3.7 15.0 1.0
OE1 B:GLU416 3.9 11.8 1.0
ND2 B:ASN460 4.0 13.9 1.0
CB B:HIS418 4.1 13.0 1.0
OD1 B:ASN102 4.2 16.2 1.0
O4 B:PTQ2001 4.2 20.0 1.0
O B:ASN102 4.3 13.8 1.0
O B:ASP199 4.3 15.8 1.0
CG B:GLU461 4.4 9.5 1.0
N B:ASP201 4.4 10.8 1.0
O B:HOH5079 4.5 30.0 1.0
NE2 B:HIS418 4.5 11.3 1.0
CB B:ASP201 4.5 12.1 1.0
C2 B:PTQ2001 4.6 20.0 1.0
CD2 B:HIS418 4.7 12.0 1.0
O3 B:PTQ2001 4.7 20.0 1.0
CB B:GLU461 4.7 10.0 1.0
CG B:GLU416 4.8 8.0 1.0

Magnesium binding site 4 out of 8 in 5a1a

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Magnesium binding site 4 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:30.0
occ:1.00
 O B:ASP15 2.4 14.8 1.0
OD1 B:ASP193 2.5 15.4 1.0
NE2 B:GLN163 2.5 13.3 1.0
OD2 B:ASP193 2.6 14.7 1.0
O B:VAL21 2.7 15.5 1.0
O B:ASN18 2.7 15.7 1.0
CG B:ASP193 2.9 19.2 1.0
CD B:GLN163 3.3 15.2 1.0
OE1 B:GLN163 3.4 13.8 1.0
C B:ASP15 3.5 15.9 1.0
C B:ASN18 3.6 18.4 1.0
OH B:TYR161 3.7 13.2 1.0
C B:TRP16 3.8 14.6 1.0
CA B:TRP16 3.8 11.8 1.0
C B:VAL21 3.9 13.9 1.0
N B:ASN18 3.9 18.5 1.0
N B:GLU17 4.0 13.8 1.0
O B:TRP16 4.1 15.0 1.0
N B:TRP16 4.1 11.4 1.0
OG B:SER192 4.2 15.0 1.0
CA B:ASN18 4.3 18.4 1.0
CB B:ASP193 4.3 13.9 1.0
C B:GLU17 4.4 22.4 1.0
N B:PRO19 4.5 19.0 1.0
CA B:THR22 4.6 12.3 1.0
CG B:GLN163 4.6 16.7 1.0
CZ B:TYR161 4.6 14.2 1.0
CE2 B:TYR161 4.6 11.6 1.0
N B:THR22 4.7 11.3 1.0
CA B:GLU17 4.7 16.5 1.0
CA B:PRO19 4.7 14.3 1.0
CA B:ASP15 4.8 15.4 1.0
CA B:VAL21 4.9 11.2 1.0
N B:ASP193 4.9 12.7 1.0
CB B:ASN18 5.0 14.5 1.0

Magnesium binding site 5 out of 8 in 5a1a

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Magnesium binding site 5 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:16.1
occ:1.00
 OE1 C:GLU461 2.2 13.9 1.0
O C:HOH5078 2.2 30.0 1.0
O C:HOH5036 2.4 30.0 1.0
O C:HOH5037 2.5 30.0 1.0
OE2 C:GLU416 2.6 11.7 1.0
ND1 C:HIS418 2.7 11.4 1.0
CD C:GLU461 3.1 19.5 1.0
OE2 C:GLU461 3.3 13.7 1.0
CE1 C:HIS418 3.4 12.3 1.0
CD C:GLU416 3.5 15.4 1.0
CG C:HIS418 3.7 15.0 1.0
OE1 C:GLU416 3.9 11.8 1.0
ND2 C:ASN460 4.0 13.9 1.0
CB C:HIS418 4.1 13.0 1.0
OD1 C:ASN102 4.2 16.2 1.0
O4 C:PTQ2001 4.2 20.0 1.0
O C:ASN102 4.3 13.8 1.0
O C:ASP199 4.3 15.8 1.0
CG C:GLU461 4.4 9.5 1.0
N C:ASP201 4.4 10.8 1.0
O C:HOH5079 4.5 30.0 1.0
NE2 C:HIS418 4.5 11.3 1.0
CB C:ASP201 4.5 12.1 1.0
C2 C:PTQ2001 4.6 20.0 1.0
CD2 C:HIS418 4.7 12.0 1.0
O3 C:PTQ2001 4.7 20.0 1.0
CB C:GLU461 4.7 10.0 1.0
CG C:GLU416 4.8 8.0 1.0

Magnesium binding site 6 out of 8 in 5a1a

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Magnesium binding site 6 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:30.0
occ:1.00
 O C:ASP15 2.4 14.8 1.0
OD1 C:ASP193 2.5 15.4 1.0
NE2 C:GLN163 2.5 13.3 1.0
OD2 C:ASP193 2.6 14.7 1.0
O C:VAL21 2.7 15.5 1.0
O C:ASN18 2.7 15.7 1.0
CG C:ASP193 2.9 19.2 1.0
CD C:GLN163 3.3 15.2 1.0
OE1 C:GLN163 3.4 13.8 1.0
C C:ASP15 3.5 15.9 1.0
C C:ASN18 3.6 18.4 1.0
OH C:TYR161 3.7 13.2 1.0
C C:TRP16 3.8 14.6 1.0
CA C:TRP16 3.8 11.8 1.0
C C:VAL21 3.9 13.9 1.0
N C:ASN18 3.9 18.5 1.0
N C:GLU17 4.0 13.8 1.0
O C:TRP16 4.1 15.0 1.0
N C:TRP16 4.1 11.4 1.0
OG C:SER192 4.2 15.0 1.0
CA C:ASN18 4.3 18.4 1.0
CB C:ASP193 4.3 13.9 1.0
C C:GLU17 4.4 22.4 1.0
N C:PRO19 4.5 19.0 1.0
CA C:THR22 4.6 12.3 1.0
CG C:GLN163 4.6 16.7 1.0
CZ C:TYR161 4.6 14.2 1.0
CE2 C:TYR161 4.6 11.6 1.0
N C:THR22 4.7 11.3 1.0
CA C:GLU17 4.7 16.5 1.0
CA C:PRO19 4.7 14.3 1.0
CA C:ASP15 4.8 15.4 1.0
CA C:VAL21 4.9 11.2 1.0
N C:ASP193 4.9 12.7 1.0
CB C:ASN18 5.0 14.5 1.0

Magnesium binding site 7 out of 8 in 5a1a

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Magnesium binding site 7 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:16.1
occ:1.00
 OE1 D:GLU461 2.2 13.9 1.0
O D:HOH5078 2.2 30.0 1.0
O D:HOH5036 2.4 30.0 1.0
O D:HOH5037 2.5 30.0 1.0
OE2 D:GLU416 2.6 11.7 1.0
ND1 D:HIS418 2.7 11.4 1.0
CD D:GLU461 3.1 19.5 1.0
OE2 D:GLU461 3.3 13.7 1.0
CE1 D:HIS418 3.4 12.3 1.0
CD D:GLU416 3.5 15.4 1.0
CG D:HIS418 3.7 15.0 1.0
OE1 D:GLU416 3.9 11.8 1.0
ND2 D:ASN460 4.0 13.9 1.0
CB D:HIS418 4.1 13.0 1.0
OD1 D:ASN102 4.2 16.2 1.0
O4 D:PTQ2001 4.2 20.0 1.0
O D:ASN102 4.3 13.8 1.0
O D:ASP199 4.3 15.8 1.0
CG D:GLU461 4.4 9.5 1.0
N D:ASP201 4.4 10.8 1.0
O D:HOH5079 4.5 30.0 1.0
NE2 D:HIS418 4.5 11.3 1.0
CB D:ASP201 4.5 12.1 1.0
C2 D:PTQ2001 4.6 20.0 1.0
CD2 D:HIS418 4.7 12.0 1.0
O3 D:PTQ2001 4.7 20.0 1.0
CB D:GLU461 4.7 10.0 1.0
CG D:GLU416 4.8 8.0 1.0

Magnesium binding site 8 out of 8 in 5a1a

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Magnesium binding site 8 out of 8 in the 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:30.0
occ:1.00
 O D:ASP15 2.4 14.8 1.0
OD1 D:ASP193 2.5 15.4 1.0
NE2 D:GLN163 2.5 13.3 1.0
OD2 D:ASP193 2.6 14.7 1.0
O D:VAL21 2.7 15.5 1.0
O D:ASN18 2.7 15.7 1.0
CG D:ASP193 2.9 19.2 1.0
CD D:GLN163 3.3 15.2 1.0
OE1 D:GLN163 3.4 13.8 1.0
C D:ASP15 3.5 15.9 1.0
C D:ASN18 3.6 18.4 1.0
OH D:TYR161 3.7 13.2 1.0
C D:TRP16 3.8 14.6 1.0
CA D:TRP16 3.8 11.8 1.0
C D:VAL21 3.9 13.9 1.0
N D:ASN18 3.9 18.5 1.0
N D:GLU17 4.0 13.8 1.0
O D:TRP16 4.1 15.0 1.0
N D:TRP16 4.1 11.4 1.0
OG D:SER192 4.2 15.0 1.0
CA D:ASN18 4.3 18.4 1.0
CB D:ASP193 4.3 13.9 1.0
C D:GLU17 4.4 22.4 1.0
N D:PRO19 4.5 19.0 1.0
CA D:THR22 4.6 12.3 1.0
CG D:GLN163 4.6 16.7 1.0
CZ D:TYR161 4.6 14.2 1.0
CE2 D:TYR161 4.6 11.6 1.0
N D:THR22 4.7 11.3 1.0
CA D:GLU17 4.7 16.5 1.0
CA D:PRO19 4.7 14.3 1.0
CA D:ASP15 4.8 15.4 1.0
CA D:VAL21 4.9 11.2 1.0
N D:ASP193 4.9 12.7 1.0
CB D:ASN18 5.0 14.5 1.0

Reference:

A.Bartesaghi, A.Merk, S.Banerjee, D.Matthies, X.Wu, J.Milne, S.Subramaniam. 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with A Cell-Permeant Inhibitor Science 2015.
ISSN: ESSN 1095-9203
PubMed: 25953817
DOI: 10.1126/SCIENCE.AAB1576
Page generated: Mon Dec 14 19:59:01 2020

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