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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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

Go back to Magnesium Binding Sites List in 8fax
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: Thu Jul 27 23:43:52 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy