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Magnesium in PDB 6cvm: Atomic Resolution Cryo-Em Structure of Beta-Galactosidase

Enzymatic activity of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase

All present enzymatic activity of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase:
3.2.1.23;

Other elements in 6cvm:

The structure of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 6cvm

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Magnesium binding site 1 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2002

b:67.2
occ:1.00
OE1 A:GLU461 2.1 66.1 1.0
O A:HOH2226 2.1 64.6 1.0
O A:HOH2136 2.1 66.1 1.0
OE2 A:GLU416 2.1 62.8 1.0
O A:HOH2283 2.1 63.9 1.0
ND1 A:HIS418 2.4 66.4 1.0
CD A:GLU461 3.2 66.1 1.0
CD A:GLU416 3.3 62.8 1.0
CE1 A:HIS418 3.3 66.4 1.0
CG A:HIS418 3.4 66.4 1.0
CB A:HIS418 3.7 66.4 1.0
OE2 A:GLU461 3.8 66.1 1.0
OE1 A:GLU416 3.9 62.8 1.0
OD1 A:ASN102 3.9 69.9 1.0
O A:ASP199 4.1 65.6 1.0
C6 A:PTQ2001 4.2 70.6 1.0
N A:ASP201 4.3 68.8 1.0
CB A:ASP201 4.3 68.8 1.0
C5 A:PTQ2001 4.3 70.6 1.0
O A:ASN102 4.3 69.9 1.0
O5 A:PTQ2001 4.3 70.6 1.0
CG A:GLU461 4.4 66.1 1.0
CB A:GLU461 4.4 66.1 1.0
CG A:GLU416 4.4 62.8 1.0
NE2 A:HIS418 4.4 66.4 1.0
ND2 A:ASN460 4.5 62.9 1.0
CD2 A:HIS418 4.5 66.4 1.0
O1 A:PTQ2001 4.8 70.6 1.0
CA A:ASP201 4.8 68.8 1.0
C A:GLN200 4.9 64.6 1.0
CA A:GLN200 4.9 64.6 1.0

Magnesium binding site 2 out of 8 in 6cvm

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Magnesium binding site 2 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2003

b:68.3
occ:1.00
O A:VAL21 2.1 64.8 1.0
O A:ASN18 2.2 66.7 1.0
OD2 A:ASP193 2.2 66.8 1.0
O A:ASP15 2.4 68.1 1.0
NE2 A:GLN163 2.6 62.8 1.0
CG A:ASP193 3.0 66.8 1.0
C A:ASN18 3.1 66.7 1.0
OD1 A:ASP193 3.2 66.8 1.0
C A:VAL21 3.3 64.8 1.0
CD A:GLN163 3.5 62.8 1.0
C A:ASP15 3.6 68.1 1.0
OE1 A:GLN163 3.7 62.8 1.0
N A:ASN18 3.7 66.7 1.0
CA A:ASN18 3.9 66.7 1.0
OH A:TYR161 4.0 58.5 1.0
N A:PRO19 4.0 65.1 1.0
CA A:VAL21 4.1 64.8 1.0
N A:VAL21 4.2 64.8 1.0
CB A:ASN18 4.2 66.7 1.0
CA A:PRO19 4.2 65.1 1.0
CA A:TRP16 4.2 64.8 1.0
N A:THR22 4.2 63.6 1.0
CB A:ASP193 4.3 66.8 1.0
CB A:VAL21 4.3 64.8 1.0
N A:TRP16 4.4 64.8 1.0
CA A:THR22 4.4 63.6 1.0
C A:TRP16 4.4 64.8 1.0
CE2 A:TYR161 4.4 58.5 1.0
CA A:ASP15 4.6 68.1 1.0
N A:GLU17 4.6 69.2 1.0
C A:PRO19 4.7 65.1 1.0
CZ A:TYR161 4.7 58.5 1.0
CG A:GLN163 4.7 62.8 1.0
CG1 A:VAL21 4.8 64.8 1.0
O A:TRP16 4.9 64.8 1.0
C A:GLU17 4.9 69.2 1.0

Magnesium binding site 3 out of 8 in 6cvm

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Magnesium binding site 3 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:67.1
occ:1.00
OE1 B:GLU461 2.1 66.2 1.0
O B:HOH2227 2.1 64.7 1.0
O B:HOH2139 2.1 66.1 1.0
OE2 B:GLU416 2.1 62.7 1.0
O B:HOH2282 2.1 63.9 1.0
ND1 B:HIS418 2.4 66.3 1.0
CD B:GLU461 3.2 66.2 1.0
CD B:GLU416 3.3 62.7 1.0
CE1 B:HIS418 3.3 66.3 1.0
CG B:HIS418 3.4 66.3 1.0
CB B:HIS418 3.7 66.3 1.0
OE2 B:GLU461 3.8 66.2 1.0
OE1 B:GLU416 3.9 62.7 1.0
OD1 B:ASN102 3.9 69.9 1.0
O B:ASP199 4.1 65.5 1.0
C6 B:PTQ2001 4.2 70.5 1.0
N B:ASP201 4.3 68.8 1.0
CB B:ASP201 4.3 68.8 1.0
C5 B:PTQ2001 4.3 70.5 1.0
O B:ASN102 4.3 69.9 1.0
O5 B:PTQ2001 4.3 70.5 1.0
CG B:GLU461 4.4 66.2 1.0
CB B:GLU461 4.4 66.2 1.0
CG B:GLU416 4.4 62.7 1.0
NE2 B:HIS418 4.4 66.3 1.0
ND2 B:ASN460 4.5 62.9 1.0
CD2 B:HIS418 4.5 66.3 1.0
O1 B:PTQ2001 4.8 70.5 1.0
CA B:ASP201 4.8 68.8 1.0
C B:GLN200 4.9 64.7 1.0
CA B:GLN200 4.9 64.7 1.0

Magnesium binding site 4 out of 8 in 6cvm

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Magnesium binding site 4 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:68.3
occ:1.00
O B:VAL21 2.1 64.7 1.0
O B:ASN18 2.2 66.7 1.0
OD2 B:ASP193 2.2 66.7 1.0
O B:ASP15 2.4 68.0 1.0
NE2 B:GLN163 2.6 62.8 1.0
CG B:ASP193 3.0 66.7 1.0
C B:ASN18 3.1 66.7 1.0
OD1 B:ASP193 3.2 66.7 1.0
C B:VAL21 3.3 64.7 1.0
CD B:GLN163 3.5 62.8 1.0
C B:ASP15 3.6 68.0 1.0
OE1 B:GLN163 3.7 62.8 1.0
N B:ASN18 3.7 66.7 1.0
CA B:ASN18 3.9 66.7 1.0
OH B:TYR161 4.0 58.4 1.0
N B:PRO19 4.0 65.1 1.0
CA B:VAL21 4.1 64.7 1.0
N B:VAL21 4.2 64.7 1.0
CB B:ASN18 4.2 66.7 1.0
CA B:PRO19 4.2 65.1 1.0
CA B:TRP16 4.2 64.8 1.0
N B:THR22 4.2 63.5 1.0
CB B:ASP193 4.3 66.7 1.0
CB B:VAL21 4.3 64.7 1.0
N B:TRP16 4.4 64.8 1.0
CA B:THR22 4.4 63.5 1.0
C B:TRP16 4.4 64.8 1.0
CE2 B:TYR161 4.4 58.4 1.0
CA B:ASP15 4.6 68.0 1.0
N B:GLU17 4.6 69.4 1.0
C B:PRO19 4.7 65.1 1.0
CZ B:TYR161 4.7 58.4 1.0
CG B:GLN163 4.7 62.8 1.0
CG1 B:VAL21 4.8 64.7 1.0
O B:TRP16 4.9 64.8 1.0
C B:GLU17 4.9 69.4 1.0

Magnesium binding site 5 out of 8 in 6cvm

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Magnesium binding site 5 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2002

b:67.0
occ:1.00
OE1 C:GLU461 2.1 65.9 1.0
O C:HOH2225 2.1 64.4 1.0
O C:HOH2139 2.1 66.0 1.0
OE2 C:GLU416 2.1 62.5 1.0
O C:HOH2283 2.1 63.8 1.0
ND1 C:HIS418 2.4 66.2 1.0
CD C:GLU461 3.2 65.9 1.0
CD C:GLU416 3.3 62.5 1.0
CE1 C:HIS418 3.3 66.2 1.0
CG C:HIS418 3.4 66.2 1.0
CB C:HIS418 3.7 66.2 1.0
OE2 C:GLU461 3.8 65.9 1.0
OE1 C:GLU416 3.9 62.5 1.0
OD1 C:ASN102 3.9 69.9 1.0
O C:ASP199 4.1 65.3 1.0
C6 C:PTQ2001 4.2 70.6 1.0
N C:ASP201 4.3 68.8 1.0
CB C:ASP201 4.3 68.8 1.0
C5 C:PTQ2001 4.3 70.6 1.0
O C:ASN102 4.3 69.9 1.0
O5 C:PTQ2001 4.3 70.6 1.0
CG C:GLU461 4.4 65.9 1.0
CB C:GLU461 4.4 65.9 1.0
CG C:GLU416 4.4 62.5 1.0
NE2 C:HIS418 4.4 66.2 1.0
ND2 C:ASN460 4.5 62.6 1.0
CD2 C:HIS418 4.5 66.2 1.0
O1 C:PTQ2001 4.8 70.6 1.0
CA C:ASP201 4.8 68.8 1.0
C C:GLN200 4.9 64.6 1.0
CA C:GLN200 4.9 64.6 1.0

Magnesium binding site 6 out of 8 in 6cvm

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Magnesium binding site 6 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2003

b:68.4
occ:1.00
O C:VAL21 2.1 64.7 1.0
O C:ASN18 2.2 66.7 1.0
OD2 C:ASP193 2.2 66.6 1.0
O C:ASP15 2.4 68.0 1.0
NE2 C:GLN163 2.6 62.7 1.0
CG C:ASP193 3.0 66.6 1.0
C C:ASN18 3.1 66.7 1.0
OD1 C:ASP193 3.2 66.6 1.0
C C:VAL21 3.3 64.7 1.0
CD C:GLN163 3.5 62.7 1.0
C C:ASP15 3.6 68.0 1.0
OE1 C:GLN163 3.7 62.7 1.0
N C:ASN18 3.7 66.7 1.0
CA C:ASN18 3.9 66.7 1.0
OH C:TYR161 4.0 58.4 1.0
N C:PRO19 4.0 65.2 1.0
CA C:VAL21 4.1 64.7 1.0
N C:VAL21 4.2 64.7 1.0
CB C:ASN18 4.2 66.7 1.0
CA C:PRO19 4.2 65.2 1.0
CA C:TRP16 4.2 64.8 1.0
N C:THR22 4.2 63.5 1.0
CB C:ASP193 4.3 66.6 1.0
CB C:VAL21 4.3 64.7 1.0
N C:TRP16 4.4 64.8 1.0
CA C:THR22 4.4 63.5 1.0
C C:TRP16 4.4 64.8 1.0
CE2 C:TYR161 4.4 58.4 1.0
CA C:ASP15 4.6 68.0 1.0
N C:GLU17 4.6 69.2 1.0
C C:PRO19 4.7 65.2 1.0
CZ C:TYR161 4.7 58.4 1.0
CG C:GLN163 4.7 62.7 1.0
CG1 C:VAL21 4.8 64.7 1.0
O C:TRP16 4.9 64.8 1.0
C C:GLU17 4.9 69.2 1.0

Magnesium binding site 7 out of 8 in 6cvm

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Magnesium binding site 7 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2002

b:67.0
occ:1.00
OE1 D:GLU461 2.1 66.1 1.0
O D:HOH2225 2.1 64.7 1.0
O D:HOH2135 2.1 66.0 1.0
OE2 D:GLU416 2.1 62.7 1.0
O D:HOH2281 2.1 63.8 1.0
ND1 D:HIS418 2.4 66.2 1.0
CD D:GLU461 3.2 66.1 1.0
CD D:GLU416 3.3 62.7 1.0
CE1 D:HIS418 3.3 66.2 1.0
CG D:HIS418 3.4 66.2 1.0
CB D:HIS418 3.7 66.2 1.0
OE2 D:GLU461 3.8 66.1 1.0
OE1 D:GLU416 3.9 62.7 1.0
OD1 D:ASN102 3.9 69.8 1.0
O D:ASP199 4.1 65.5 1.0
C6 D:PTQ2001 4.2 70.5 1.0
N D:ASP201 4.3 68.8 1.0
CB D:ASP201 4.3 68.8 1.0
O D:ASN102 4.3 69.8 1.0
C5 D:PTQ2001 4.3 70.5 1.0
O5 D:PTQ2001 4.3 70.5 1.0
CG D:GLU461 4.4 66.1 1.0
CB D:GLU461 4.4 66.1 1.0
CG D:GLU416 4.4 62.7 1.0
NE2 D:HIS418 4.4 66.2 1.0
ND2 D:ASN460 4.5 62.9 1.0
CD2 D:HIS418 4.5 66.2 1.0
O1 D:PTQ2001 4.8 70.5 1.0
CA D:ASP201 4.8 68.8 1.0
C D:GLN200 4.9 64.6 1.0
CA D:GLN200 4.9 64.6 1.0

Magnesium binding site 8 out of 8 in 6cvm

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Magnesium binding site 8 out of 8 in the Atomic Resolution Cryo-Em Structure of Beta-Galactosidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Atomic Resolution Cryo-Em Structure of Beta-Galactosidase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:68.4
occ:1.00
O D:VAL21 2.1 64.7 1.0
O D:ASN18 2.2 66.8 1.0
OD2 D:ASP193 2.2 66.7 1.0
O D:ASP15 2.4 68.0 1.0
NE2 D:GLN163 2.6 62.9 1.0
CG D:ASP193 3.0 66.7 1.0
C D:ASN18 3.1 66.8 1.0
OD1 D:ASP193 3.2 66.7 1.0
C D:VAL21 3.3 64.7 1.0
CD D:GLN163 3.5 62.9 1.0
C D:ASP15 3.6 68.0 1.0
OE1 D:GLN163 3.7 62.9 1.0
N D:ASN18 3.7 66.8 1.0
CA D:ASN18 3.9 66.8 1.0
OH D:TYR161 4.0 58.5 1.0
N D:PRO19 4.0 65.2 1.0
CA D:VAL21 4.1 64.7 1.0
N D:VAL21 4.2 64.7 1.0
CB D:ASN18 4.2 66.8 1.0
CA D:PRO19 4.2 65.2 1.0
CA D:TRP16 4.2 64.9 1.0
N D:THR22 4.2 63.5 1.0
CB D:ASP193 4.3 66.7 1.0
CB D:VAL21 4.3 64.7 1.0
N D:TRP16 4.4 64.9 1.0
CA D:THR22 4.4 63.5 1.0
C D:TRP16 4.4 64.9 1.0
CE2 D:TYR161 4.4 58.5 1.0
CA D:ASP15 4.6 68.0 1.0
N D:GLU17 4.6 69.4 1.0
C D:PRO19 4.7 65.2 1.0
CZ D:TYR161 4.7 58.5 1.0
CG D:GLN163 4.7 62.9 1.0
CG1 D:VAL21 4.8 64.7 1.0
O D:TRP16 4.9 64.9 1.0
C D:GLU17 4.9 69.4 1.0

Reference:

A.Bartesaghi, C.Aguerrebere, V.Falconieri, S.Banerjee, L.A.Earl, X.Zhu, N.Grigorieff, J.L.S.Milne, G.Sapiro, X.Wu, S.Subramaniam. Atomic Resolution Cryo-Em Structure of Beta-Galactosidase. Structure V. 26 848 2018.
ISSN: ISSN 1878-4186
PubMed: 29754826
DOI: 10.1016/J.STR.2018.04.004
Page generated: Mon Sep 30 22:46:39 2024

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