Magnesium in PDB 8vt0: Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface

Enzymatic activity of Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface

All present enzymatic activity of Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface:
3.2.1.23;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface (pdb code 8vt0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface, PDB code: 8vt0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8vt0

Go back to Magnesium Binding Sites List in 8vt0
Magnesium binding site 1 out of 4 in the Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:71.1
occ:1.00
 ND1 A:HIS418 2.2 92.9 1.0
OE2 A:GLU416 2.6 94.2 1.0
CE1 A:HIS418 2.9 92.9 1.0
CG A:HIS418 3.2 92.9 1.0
CB A:HIS418 3.7 92.9 1.0
CD A:GLU416 3.8 94.2 1.0
CG A:GLU461 3.8 93.9 1.0
NE2 A:HIS418 4.0 92.9 1.0
CB A:GLU461 4.1 93.9 1.0
CD2 A:HIS418 4.2 92.9 1.0
CD A:GLU461 4.7 93.9 1.0
CG A:GLU416 4.7 94.2 1.0
OE1 A:GLU416 4.7 94.2 1.0
O A:ASP199 4.8 95.7 1.0
OE1 A:GLU461 4.9 93.9 1.0

Magnesium binding site 2 out of 4 in 8vt0

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Magnesium binding site 2 out of 4 in the Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:62.8
occ:1.00
 ND1 B:HIS418 2.2 97.5 1.0
OE2 B:GLU416 2.7 97.8 1.0
CE1 B:HIS418 2.9 97.5 1.0
CG B:HIS418 3.2 97.5 1.0
CB B:HIS418 3.8 97.5 1.0
CG B:GLU461 3.8 96.9 1.0
CD B:GLU416 3.9 97.8 1.0
NE2 B:HIS418 4.0 97.5 1.0
CB B:GLU461 4.0 96.9 1.0
CD2 B:HIS418 4.2 97.5 1.0
CD B:GLU461 4.6 96.9 1.0
CG B:GLU416 4.7 97.8 1.0
OE1 B:GLU416 4.8 97.8 1.0
OE1 B:GLU461 4.8 96.9 1.0
O B:ASP199 4.9 99.7 1.0

Magnesium binding site 3 out of 4 in 8vt0

Go back to Magnesium Binding Sites List in 8vt0
Magnesium binding site 3 out of 4 in the Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:55.8
occ:1.00
 ND1 C:HIS418 2.2 97.9 1.0
OE2 C:GLU416 2.6 98.5 1.0
CE1 C:HIS418 2.9 97.9 1.0
CG C:HIS418 3.2 97.9 1.0
CB C:HIS418 3.7 97.9 1.0
CG C:GLU461 3.8 96.1 1.0
CD C:GLU416 3.8 98.5 1.0
CB C:GLU461 4.0 96.1 1.0
NE2 C:HIS418 4.0 97.9 1.0
CD2 C:HIS418 4.2 97.9 1.0
CD C:GLU461 4.6 96.1 1.0
CG C:GLU416 4.6 98.5 1.0
OE1 C:GLU416 4.7 98.5 1.0
OE1 C:GLU461 4.8 96.1 1.0
O C:ASP199 4.8 99.3 1.0

Magnesium binding site 4 out of 4 in 8vt0

Go back to Magnesium Binding Sites List in 8vt0
Magnesium binding site 4 out of 4 in the Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Spot-Rastr - A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:57.3
occ:1.00
 ND1 D:HIS418 2.2 95.8 1.0
OE2 D:GLU416 2.6 95.8 1.0
CE1 D:HIS418 3.0 95.8 1.0
CG D:HIS418 3.2 95.8 1.0
CB D:HIS418 3.7 95.8 1.0
CD D:GLU416 3.8 95.8 1.0
CG D:GLU461 3.9 94.9 1.0
NE2 D:HIS418 4.1 95.8 1.0
CB D:GLU461 4.1 94.9 1.0
CD2 D:HIS418 4.2 95.8 1.0
CG D:GLU416 4.6 95.8 1.0
OE1 D:GLU416 4.7 95.8 1.0
CD D:GLU461 4.7 94.9 1.0
O D:ASP199 4.8 96.7 1.0
OE1 D:GLU461 4.9 94.9 1.0

Reference:

B.G.Esfahani, P.S.Randolph, R.Peng, T.Grant, M.E.Stroupe, S.M.Stagg. Spot-Rastr-A Cryo-Em Specimen Preparation Technique That Overcomes Problems with Preferred Orientation and the Air/Water Interface. PNAS Nexus V. 3 AE284 2024.
ISSN: ESSN 2752-6542
PubMed: 39108302
DOI: 10.1093/PNASNEXUS/PGAE284
Page generated: Fri Oct 4 22:14:04 2024

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