Magnesium in PDB 6tsk: Beta-Galactosidase in Complex with L-Ribose

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Beta-Galactosidase in Complex with L-Ribose (pdb code 6tsk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Beta-Galactosidase in Complex with L-Ribose, PDB code: 6tsk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6tsk

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Magnesium binding site 1 out of 4 in the Beta-Galactosidase in Complex with L-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Galactosidase in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:3.9
occ:1.00
 OE2 A:GLU416 2.1 11.8 1.0
O A:HOH3136 2.2 1.5 1.0
O A:HOH3208 2.3 1.1 1.0
OE1 A:GLU461 2.4 22.0 1.0
ND1 A:HIS418 2.4 9.3 1.0
O A:HOH3114 2.4 0.5 1.0
CE1 A:HIS418 3.3 10.2 1.0
CD A:GLU416 3.3 11.0 1.0
CD A:GLU461 3.3 31.7 1.0
CG A:HIS418 3.4 9.4 1.0
CB A:HIS418 3.7 6.4 1.0
OE1 A:GLU416 3.8 12.5 1.0
OE2 A:GLU461 4.0 43.4 1.0
OD1 A:ASN102 4.2 11.1 1.0
O A:ASP199 4.3 4.9 1.0
CB A:ASP201 4.3 10.3 1.0
CG A:GLU461 4.4 23.6 1.0
O2 A:0MK3002 4.4 14.9 1.0
CB A:GLU461 4.4 12.2 1.0
N A:ASP201 4.4 9.3 1.0
O3 A:0MK3002 4.5 12.1 1.0
NE2 A:HIS418 4.5 11.1 1.0
CG A:GLU416 4.5 8.2 1.0
CD2 A:HIS418 4.5 9.0 1.0
ND2 A:ASN460 4.5 11.8 1.0
C1 A:0MK3002 4.7 18.2 1.0
O A:ASN102 4.8 8.9 1.0
O1 A:0MK3002 4.8 16.9 1.0
CA A:ASP201 5.0 9.7 1.0

Magnesium binding site 2 out of 4 in 6tsk

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Magnesium binding site 2 out of 4 in the Beta-Galactosidase in Complex with L-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Galactosidase in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:3.9
occ:1.00
 OE2 B:GLU416 2.1 11.8 1.0
O B:HOH3136 2.2 1.5 1.0
O B:HOH3208 2.3 1.1 1.0
OE1 B:GLU461 2.4 22.0 1.0
ND1 B:HIS418 2.4 9.3 1.0
O B:HOH3114 2.4 0.5 1.0
CE1 B:HIS418 3.3 10.2 1.0
CD B:GLU416 3.3 11.0 1.0
CD B:GLU461 3.3 31.7 1.0
CG B:HIS418 3.4 9.4 1.0
CB B:HIS418 3.7 6.4 1.0
OE1 B:GLU416 3.8 12.5 1.0
OE2 B:GLU461 4.0 43.4 1.0
OD1 B:ASN102 4.2 11.1 1.0
O B:ASP199 4.3 4.9 1.0
CB B:ASP201 4.3 10.3 1.0
CG B:GLU461 4.4 23.6 1.0
O2 B:0MK3002 4.4 14.9 1.0
CB B:GLU461 4.4 12.2 1.0
N B:ASP201 4.4 9.3 1.0
O3 B:0MK3002 4.5 12.1 1.0
NE2 B:HIS418 4.5 11.1 1.0
CG B:GLU416 4.5 8.2 1.0
CD2 B:HIS418 4.5 9.0 1.0
ND2 B:ASN460 4.5 11.8 1.0
C1 B:0MK3002 4.7 18.2 1.0
O B:ASN102 4.8 8.9 1.0
O1 B:0MK3002 4.8 16.9 1.0
CA B:ASP201 5.0 9.7 1.0

Magnesium binding site 3 out of 4 in 6tsk

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Magnesium binding site 3 out of 4 in the Beta-Galactosidase in Complex with L-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Galactosidase in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:3.9
occ:1.00
 OE2 C:GLU416 2.1 11.8 1.0
O C:HOH3136 2.2 1.5 1.0
O C:HOH3208 2.3 1.1 1.0
OE1 C:GLU461 2.4 22.0 1.0
ND1 C:HIS418 2.4 9.3 1.0
O C:HOH3114 2.4 0.5 1.0
CE1 C:HIS418 3.3 10.2 1.0
CD C:GLU416 3.3 11.0 1.0
CD C:GLU461 3.3 31.7 1.0
CG C:HIS418 3.4 9.4 1.0
CB C:HIS418 3.7 6.4 1.0
OE1 C:GLU416 3.8 12.5 1.0
OE2 C:GLU461 4.0 43.4 1.0
OD1 C:ASN102 4.2 11.1 1.0
O C:ASP199 4.3 4.9 1.0
CB C:ASP201 4.4 10.3 1.0
CG C:GLU461 4.4 23.6 1.0
O2 C:0MK3002 4.4 14.9 1.0
CB C:GLU461 4.4 12.2 1.0
N C:ASP201 4.4 9.3 1.0
O3 C:0MK3002 4.5 12.1 1.0
NE2 C:HIS418 4.5 11.1 1.0
CG C:GLU416 4.5 8.2 1.0
CD2 C:HIS418 4.5 9.0 1.0
ND2 C:ASN460 4.5 11.8 1.0
C1 C:0MK3002 4.7 18.2 1.0
O C:ASN102 4.8 8.9 1.0
O1 C:0MK3002 4.8 16.9 1.0
CA C:ASP201 5.0 9.7 1.0

Magnesium binding site 4 out of 4 in 6tsk

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Magnesium binding site 4 out of 4 in the Beta-Galactosidase in Complex with L-Ribose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beta-Galactosidase in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:3.9
occ:1.00
 OE2 D:GLU416 2.1 11.8 1.0
O D:HOH3135 2.2 1.5 1.0
O D:HOH3208 2.3 1.1 1.0
OE1 D:GLU461 2.4 22.0 1.0
ND1 D:HIS418 2.4 9.3 1.0
O D:HOH3114 2.4 0.5 1.0
CE1 D:HIS418 3.3 10.2 1.0
CD D:GLU416 3.3 11.0 1.0
CD D:GLU461 3.3 31.7 1.0
CG D:HIS418 3.4 9.4 1.0
CB D:HIS418 3.7 6.4 1.0
OE1 D:GLU416 3.8 12.5 1.0
OE2 D:GLU461 4.0 43.4 1.0
OD1 D:ASN102 4.2 11.1 1.0
O D:ASP199 4.3 4.9 1.0
CB D:ASP201 4.3 10.3 1.0
CG D:GLU461 4.4 23.6 1.0
O2 D:0MK3002 4.4 14.9 1.0
CB D:GLU461 4.4 12.2 1.0
N D:ASP201 4.4 9.3 1.0
O3 D:0MK3002 4.5 12.1 1.0
NE2 D:HIS418 4.5 11.1 1.0
CG D:GLU416 4.5 8.2 1.0
CD2 D:HIS418 4.5 9.0 1.0
ND2 D:ASN460 4.5 11.8 1.0
C1 D:0MK3002 4.7 18.2 1.0
O D:ASN102 4.8 8.9 1.0
O1 D:0MK3002 4.8 16.9 1.0
CA D:ASP201 5.0 9.7 1.0

Reference:

M.Saur, M.J.Hartshorn, J.Dong, J.Reeks, G.Bunkoczi, H.Jhoti, P.A.Williams. Fragment-Based Drug Discovery Using Cryo-Em Drug Discov Today 2019.
ISSN: ESSN 1878-5832
PubMed: 31877353
DOI: 10.1016/J.DRUDIS.2019.12.006
Page generated: Tue Dec 15 00:37:25 2020

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