Magnesium in PDB 8fax: Fab 1249A8-Mers Stem Helix Complex

Protein crystallography data

The structure of Fab 1249A8-Mers Stem Helix Complex, PDB code: 8fax was solved by A.Deshpande, N.Schormann, M.S.Piepenbrink, L.Martinez-Sobrido, J.J.Kobie, M.R.Walter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.76 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.714, 56.308, 76.124, 90, 91.19, 90
R / Rfree (%) 18.2 / 24

Other elements in 8fax:

The structure of Fab 1249A8-Mers Stem Helix Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Fab 1249A8-Mers Stem Helix Complex (pdb code 8fax). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Fab 1249A8-Mers Stem Helix Complex, PDB code: 8fax:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 8fax

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Magnesium binding site 1 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:14.4
occ:1.00
 NE2 A:HIS107 2.0 32.5 1.0
O A:HOH492 2.0 22.6 1.0
O A:HOH477 2.1 19.1 1.0
CD2 A:HIS107 2.9 33.3 1.0
CE1 A:HIS107 3.0 33.4 1.0
NH2 A:ARG98 3.7 22.6 1.0
OD2 A:ASP106 4.0 30.0 1.0
ND1 A:HIS107 4.1 30.6 1.0
CG A:HIS107 4.1 29.2 1.0
CG A:ASP106 4.5 30.8 1.0
CG2 A:VAL2 4.6 31.7 1.0
CZ A:ARG98 4.7 30.7 1.0
CB A:ASP106 4.8 24.0 1.0
OG1 B:THR57 5.0 36.4 1.0
O A:ASP106 5.0 26.3 1.0
CB B:THR57 5.0 23.7 1.0

Magnesium binding site 2 out of 9 in 8fax

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Magnesium binding site 2 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:47.6
occ:1.00
 OE2 A:GLU10 2.0 42.5 1.0
O A:LYS19 2.1 34.7 1.0
O A:HOH411 2.6 31.6 1.0
CD A:GLU10 3.0 35.6 1.0
OE1 A:GLU10 3.3 40.7 1.0
C A:LYS19 3.3 28.4 1.0
N A:LYS19 3.9 36.8 1.0
CA A:LYS19 4.0 31.5 1.0
O A:HOH415 4.0 28.3 1.0
CB A:LYS19 4.1 40.8 1.0
CG A:GLU10 4.3 40.0 1.0
N A:VAL20 4.4 30.1 1.0
CA A:VAL20 4.7 26.8 1.0

Magnesium binding site 3 out of 9 in 8fax

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Magnesium binding site 3 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:5.8
occ:1.00
 OD2 A:ASP213 1.9 29.6 1.0
CG A:ASP213 2.5 25.6 1.0
OD1 A:ASP213 2.6 29.0 1.0
CB A:ASP213 4.0 22.7 1.0
ND2 A:ASN202 4.4 21.3 1.0
CB A:ASN202 4.8 27.5 1.0
O A:VAL212 4.8 24.6 1.0
CA A:ASP213 5.0 22.0 1.0

Magnesium binding site 4 out of 9 in 8fax

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Magnesium binding site 4 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:19.7
occ:1.00
 NE2 A:HIS169 1.9 37.2 1.0
O B:HOH477 2.1 20.1 1.0
O A:HOH445 2.1 36.0 1.0
CD2 A:HIS169 2.7 32.6 1.0
CE1 A:HIS169 3.0 46.5 1.0
CG A:HIS169 4.0 36.7 1.0
CB B:THR167 4.0 29.1 1.0
ND1 A:HIS169 4.1 43.9 1.0
N B:GLU168 4.1 32.0 1.0
O A:THR170 4.2 29.8 1.0
O B:GLU168 4.5 34.0 1.0
CB B:GLU168 4.5 37.0 1.0
CG2 B:THR167 4.5 30.6 1.0
O A:HOH500 4.6 42.0 1.0
CA B:THR167 4.7 33.1 1.0
O A:HOH471 4.7 38.4 1.0
CA B:GLU168 4.8 33.7 1.0
OG1 B:THR167 4.8 30.5 1.0
C B:THR167 4.9 30.1 1.0
C B:GLU168 5.0 32.9 1.0
CG B:GLU168 5.0 33.3 1.0

Magnesium binding site 5 out of 9 in 8fax

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Magnesium binding site 5 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:28.4
occ:1.00
 NZ A:LYS148 1.8 24.6 1.0
OD2 A:ASP149 1.8 33.8 1.0
O A:HOH484 2.1 39.1 1.0
O B:HOH481 2.4 30.1 1.0
CG A:ASP149 2.7 29.5 1.0
CE A:LYS148 2.7 30.3 1.0
OD1 A:ASP149 2.9 29.8 1.0
CD A:LYS148 3.1 29.5 1.0
O A:HOH426 3.7 40.7 1.0
CG A:LYS148 3.8 33.0 1.0
O A:HOH425 3.8 46.2 1.0
CB A:ASP149 4.1 21.5 1.0
CG2 B:THR132 4.3 34.2 1.0
NE2 B:GLN127 4.6 23.5 1.0
CB A:LYS148 4.8 26.5 1.0
OG1 B:THR132 4.8 35.0 1.0
CB B:THR132 4.9 26.8 1.0
OE1 A:GLN176 5.0 43.4 1.0

Magnesium binding site 6 out of 9 in 8fax

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Magnesium binding site 6 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:53.3
occ:1.00
 O A:HOH409 2.1 33.1 1.0
O A:HOH463 2.2 39.3 1.0
O A:HOH512 2.5 54.4 1.0
OE1 A:GLU153 3.7 43.4 1.0
O A:VAL155 4.0 30.1 1.0
OE2 A:GLU153 4.1 35.5 1.0
CD A:GLU153 4.3 35.3 1.0
CB A:PRO154 4.5 25.4 1.0
CD2 A:LEU183 4.6 25.1 1.0
N A:VAL155 4.7 22.1 1.0
CA A:PRO154 4.9 28.9 1.0

Magnesium binding site 7 out of 9 in 8fax

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Magnesium binding site 7 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:58.9
occ:1.00
 O L:HOH1404 2.3 37.4 1.0
CG A:PRO53 4.1 37.4 1.0
NE2 L:GLN1232 4.2 32.4 1.0
CB A:PRO53 4.5 38.0 1.0
O A:ASP31 4.5 35.5 1.0
OD2 L:ASP1236 4.6 40.6 1.0
O A:THR30 4.7 39.8 1.0
CA A:ASP31 4.8 29.3 1.0
C A:ASP31 4.9 34.1 1.0
OD1 L:ASP1236 4.9 34.8 1.0
OD1 A:ASP31 5.0 47.1 1.0

Magnesium binding site 8 out of 9 in 8fax

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Magnesium binding site 8 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:8.4
occ:1.00
 NZ A:LYS211 1.8 21.5 1.0
O A:HOH449 1.9 27.3 1.0
CE A:LYS211 2.9 23.5 1.0
CD A:LYS211 3.3 27.0 1.0
CG A:LYS211 4.0 25.5 1.0
OD1 A:ASN204 4.0 29.5 1.0
CG A:ASN204 4.4 34.3 1.0
CB A:LYS211 4.8 23.4 1.0
CB A:ASN204 4.9 28.3 1.0

Magnesium binding site 9 out of 9 in 8fax

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Magnesium binding site 9 out of 9 in the Fab 1249A8-Mers Stem Helix Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Fab 1249A8-Mers Stem Helix Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1301

b:39.0
occ:1.00
 OE2 L:GLU1237 2.3 48.7 1.0
CD L:GLU1237 3.0 50.4 1.0
OE1 L:GLU1237 3.0 54.4 1.0
O L:HOH1402 4.1 48.1 1.0
CG L:GLU1237 4.5 41.7 1.0

Reference:

A.Deshpande, N.Schormann, M.S.Piepenbrink, L.Martinez Sobrido, J.J.Kobie, M.R.Walter. Structure and Epitope of A Neutralizing Monoclonal Antibody That Targets the Stem Helix of Beta Coronaviruses. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37014961
DOI: 10.1111/FEBS.16777
Page generated: Fri Oct 4 02:26:05 2024

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