Sodium in PDB 7nab: Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165

Protein crystallography data

The structure of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165, PDB code: 7nab was solved by Y.Chen, W.D.Tolbert, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.56 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.762, 85.241, 87.067, 90, 114.77, 90
R / Rfree (%) 18.5 / 23.9

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 (pdb code 7nab). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165, PDB code: 7nab:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 7nab

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Sodium binding site 1 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:42.9
occ:1.00
 O H:HOH487 2.5 42.0 1.0
OD1 H:ASP86 2.7 36.6 1.0
NH1 H:ARG38 2.8 41.1 1.0
OH H:TYR90 2.9 32.6 1.0
CD H:ARG38 3.4 35.5 1.0
CG H:ASP86 3.7 39.8 1.0
O H:HOH417 3.8 43.7 1.0
CZ H:ARG38 3.8 38.3 1.0
CA H:ASP86 3.8 40.8 1.0
CZ H:TYR90 3.9 32.2 1.0
CB H:ASP86 3.9 34.8 1.0
NE H:ARG38 4.0 37.3 1.0
CE2 H:TYR90 4.1 29.9 1.0
CE2 H:PHE63 4.2 35.5 1.0
NE1 H:TRP82 4.2 39.5 1.0
O H:ASP86 4.5 32.9 1.0
CD2 H:PHE63 4.5 33.4 1.0
O H:SER85 4.5 39.4 1.0
C H:ASP86 4.6 36.6 1.0
CZ2 H:TRP82 4.7 30.8 1.0
CG H:ARG38 4.7 34.0 1.0
CE H:MET48 4.8 28.1 1.0
CE2 H:TRP82 4.8 38.6 1.0
OD2 H:ASP86 4.8 38.6 1.0
N H:ASP86 4.8 43.4 1.0
CD2 H:HIS66 4.9 30.0 1.0
NH2 H:ARG38 5.0 36.7 1.0

Sodium binding site 2 out of 16 in 7nab

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Sodium binding site 2 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:46.4
occ:1.00
 O H:LEU45 2.6 31.3 1.0
O L:HOH492 2.6 31.8 1.0
O H:HOH472 3.2 39.4 1.0
C H:LEU45 3.6 32.3 1.0
O L:PHE98 3.7 31.3 1.0
CB L:PHE98 4.1 28.3 1.0
CA H:GLU46 4.3 36.2 1.0
CG H:GLU46 4.3 36.9 1.0
N H:GLU46 4.4 29.9 1.0
N H:LEU45 4.4 32.4 1.0
C L:PHE98 4.4 33.9 1.0
N L:PHE98 4.5 31.6 1.0
CA L:PHE98 4.6 32.8 1.0
CA H:LEU45 4.6 29.0 1.0
O H:HOH441 4.7 37.0 1.0
CB H:GLU46 4.8 34.7 1.0
O L:HOH472 4.8 48.4 1.0
O L:GLY99 4.8 32.2 1.0
CD1 L:PHE98 5.0 31.9 1.0

Sodium binding site 3 out of 16 in 7nab

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Sodium binding site 3 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:30.0
occ:1.00
 OE1 H:GLN81 2.7 50.2 1.0
OG1 H:THR68 3.1 36.0 1.0
O H:GLN81 3.2 42.4 1.0
ND2 H:ASN82A 3.2 44.2 1.0
N H:ASN82A 3.3 41.7 1.0
CG H:ASN82A 3.5 49.8 1.0
CA H:TRP82 3.7 40.1 1.0
C H:TRP82 3.7 43.5 1.0
C H:GLN81 3.8 44.0 1.0
OD1 H:ASN82A 3.9 45.9 1.0
CB H:THR68 3.9 39.5 1.0
CD H:GLN81 3.9 53.0 1.0
N H:THR68 4.0 38.4 1.0
CB H:ASN82A 4.0 43.4 1.0
N H:TRP82 4.1 38.9 1.0
O H:HIS66 4.2 48.5 1.0
CA H:ASN82A 4.2 43.9 1.0
C H:VAL67 4.4 40.0 1.0
O H:HOH451 4.4 45.3 1.0
CA H:VAL67 4.5 45.1 1.0
CA H:THR68 4.6 36.6 1.0
O H:TRP82 4.6 41.5 1.0
CB H:GLN81 4.8 41.6 1.0
CG H:GLN81 4.8 47.8 1.0
C H:HIS66 4.8 47.5 1.0
NE2 H:GLN81 4.8 61.7 1.0
CA H:GLN81 4.9 44.5 1.0
N H:VAL67 5.0 43.4 1.0

Sodium binding site 4 out of 16 in 7nab

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Sodium binding site 4 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:44.5
occ:1.00
 OG L:SER14 2.5 43.8 1.0
O L:HOH440 2.6 42.2 1.0
CB L:SER14 3.5 40.5 1.0
CD L:LYS107 3.5 47.0 1.0
CG L:LYS107 3.8 47.4 1.0
CB L:LYS107 3.9 40.0 1.0
OD2 L:ASP17 4.0 42.7 1.0
O L:HOH418 4.2 32.5 1.0
N L:SER14 4.2 39.8 1.0
CE L:LYS107 4.5 58.0 1.0
CA L:SER14 4.5 37.4 1.0
C L:ALA13 4.8 40.4 1.0
CG L:ASP17 4.8 41.5 1.0
OD1 L:ASP17 4.9 43.6 1.0
O L:LYS107 5.0 38.2 1.0

Sodium binding site 5 out of 16 in 7nab

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Sodium binding site 5 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na302

b:41.7
occ:1.00
 N L:LYS39 2.8 28.9 1.0
O L:ALA43 2.9 35.8 1.0
O L:HOH412 3.1 42.1 1.0
O L:HOH502 3.2 52.2 1.0
CB L:LYS42 3.3 39.3 1.0
CA L:GLN38 3.5 32.3 1.0
C L:GLN38 3.6 33.7 1.0
CB L:LYS39 3.7 35.4 1.0
CA L:LYS39 3.8 31.6 1.0
O L:HOH453 3.9 48.8 1.0
O L:GLN37 3.9 31.3 1.0
C L:ALA43 4.0 33.5 1.0
CG L:LYS39 4.0 35.8 1.0
O L:LYS39 4.0 34.4 1.0
NZ L:LYS45 4.1 51.6 1.0
C L:LYS42 4.2 37.0 1.0
CG L:LYS42 4.3 43.8 1.0
N L:GLN38 4.3 33.8 1.0
CG L:GLN38 4.3 31.5 1.0
CA L:LYS42 4.3 39.2 1.0
O L:LYS42 4.4 34.5 1.0
C L:LYS39 4.4 33.5 1.0
N L:ALA43 4.4 35.7 1.0
CB L:GLN38 4.4 33.1 1.0
C L:GLN37 4.5 31.3 1.0
CD L:LYS39 4.5 44.1 1.0
CA L:PRO44 4.7 29.8 1.0
N L:PRO44 4.7 32.4 1.0
O L:HOH454 4.7 52.3 1.0
O L:GLN38 4.8 33.3 1.0
CG L:LYS45 4.8 46.4 1.0
CA L:ALA43 4.8 35.2 1.0
C L:PRO44 5.0 32.4 1.0
N L:LYS45 5.0 31.0 1.0

Sodium binding site 6 out of 16 in 7nab

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Sodium binding site 6 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na303

b:50.3
occ:1.00
 OG1 L:THR180 2.4 53.5 1.0
O L:THR178 2.8 41.2 1.0
O L:HOH510 2.9 44.9 1.0
CB L:THR180 3.5 54.4 1.0
N L:THR180 3.5 47.6 1.0
N L:GLN160 3.6 42.8 1.0
C L:THR178 3.7 38.7 1.0
CA L:SER159 3.7 44.9 1.0
O L:ASN158 3.7 48.4 1.0
C L:SER159 3.9 45.2 1.0
CG L:GLN160 4.1 45.1 1.0
CA L:THR180 4.1 50.4 1.0
C L:LEU179 4.1 44.8 1.0
CB L:GLN160 4.2 41.3 1.0
CB L:THR178 4.2 44.0 1.0
OE1 L:GLN160 4.2 44.2 1.0
CA L:LEU179 4.3 44.3 1.0
CG2 L:THR178 4.3 42.0 1.0
N L:SER159 4.3 48.1 1.0
N L:LEU179 4.3 42.4 1.0
O H:HOH440 4.4 48.5 1.0
C L:ASN158 4.4 52.1 1.0
O L:HOH431 4.5 46.9 1.0
CA L:GLN160 4.5 42.6 1.0
CA L:THR178 4.6 41.7 1.0
CD L:GLN160 4.7 47.9 1.0
CG2 L:THR180 4.7 52.9 1.0
O L:SER159 4.8 46.7 1.0
CB L:SER159 4.9 45.5 1.0

Sodium binding site 7 out of 16 in 7nab

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Sodium binding site 7 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na304

b:51.6
occ:1.00
 OG L:SER93 2.4 43.3 1.0
O L:HOH482 2.7 51.0 1.0
O L:HOH429 2.7 34.3 1.0
O L:PHE94 2.8 39.3 1.0
C L:PHE94 3.5 35.9 1.0
CB L:SER93 3.6 36.3 1.0
CG1 L:ILE2 3.7 43.5 1.0
O L:SER93 3.8 34.3 1.0
C L:SER93 3.8 35.5 1.0
CD1 L:ILE2 3.9 39.4 1.0
N L:PHE94 4.1 36.6 1.0
N L:PRO95 4.1 36.7 1.0
CD L:PRO95 4.3 32.9 1.0
CA L:SER93 4.3 37.9 1.0
CA L:PHE94 4.4 35.2 1.0
N L:ILE2 4.5 41.7 1.0
O L:PRO95 4.6 29.9 1.0
CB L:ILE2 4.8 35.4 1.0
NE2 L:GLN90 4.8 31.8 1.0
CA L:GLU1 5.0 46.9 1.0

Sodium binding site 8 out of 16 in 7nab

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Sodium binding site 8 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na305

b:53.8
occ:1.00
 O L:GLN160 3.0 39.6 1.0
OG1 L:THR178 3.1 47.0 1.0
OG L:SER176 3.2 37.7 1.0
O L:SER176 3.6 38.3 1.0
O H:HOH405 3.6 40.8 1.0
O L:HOH470 3.6 42.2 1.0
N L:THR178 3.7 36.1 1.0
C L:GLN160 3.7 43.3 1.0
CB L:THR178 3.8 44.0 1.0
O H:HOH500 3.8 46.4 1.0
N L:SER162 4.0 36.0 1.0
CA L:GLU161 4.0 42.6 1.0
C L:SER176 4.1 36.8 1.0
C L:GLU161 4.1 38.2 1.0
O H:HOH432 4.2 41.7 1.0
N L:GLU161 4.2 44.4 1.0
CB L:SER176 4.3 31.5 1.0
CA L:SER177 4.3 37.2 1.0
C L:SER177 4.3 38.8 1.0
CB L:SER162 4.3 39.7 1.0
CA L:THR178 4.4 41.7 1.0
N L:SER177 4.4 36.1 1.0
CG1 H:VAL169 4.5 41.1 1.0
CG2 H:VAL169 4.6 43.5 1.0
CB L:GLN160 4.7 41.3 1.0
CA L:GLN160 4.7 42.6 1.0
O L:GLU161 4.8 44.6 1.0
CA L:SER162 4.8 37.3 1.0
CA L:SER176 4.9 35.8 1.0

Sodium binding site 9 out of 16 in 7nab

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Sodium binding site 9 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na306

b:50.3
occ:1.00
 OG1 L:THR109 2.5 35.1 1.0
NH2 L:ARG108 3.3 35.0 1.0
O L:VAL110 3.4 38.2 1.0
CB L:THR109 3.5 38.6 1.0
C L:THR109 4.4 41.4 1.0
C L:VAL110 4.5 37.5 1.0
CA L:THR109 4.5 35.5 1.0
CG2 L:THR109 4.5 40.8 1.0
O L:THR109 4.6 33.6 1.0
O L:HOH441 4.6 50.9 1.0
CZ L:ARG108 4.6 39.6 1.0
N L:VAL110 4.8 38.2 1.0

Sodium binding site 10 out of 16 in 7nab

Go back to Sodium Binding Sites List in 7nab
Sodium binding site 10 out of 16 in the Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Human Neutralizing Mab CV3-25 Binding to Sars- Cov-2 S Mper Peptide 1140-1165 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na307

b:30.0
occ:1.00
 O H:HOH464 3.6 39.3 1.0
CG L:PHE94 3.7 36.6 1.0
CB L:PHE94 3.8 35.4 1.0
CD2 L:PHE94 3.8 38.3 1.0
CD H:ARG58 3.9 56.9 0.9
CB H:ARG58 4.1 40.2 0.9
O L:HOH522 4.2 41.5 1.0
CD1 L:PHE94 4.2 36.5 1.0
CE2 L:PHE94 4.4 41.8 1.0
CG H:ARG58 4.6 48.7 0.9
O H:TYR59 4.6 40.5 1.0
O H:HOH527 4.7 54.4 1.0
CE1 L:PHE94 4.8 36.6 1.0
NE H:ARG58 4.8 58.5 0.9
O H:HOH447 4.9 49.5 1.0
CZ L:PHE94 4.9 37.7 1.0
CA H:ARG58 4.9 39.8 0.9

Reference:

I.Ullah, J.Prevost, M.S.Ladinsky, H.Stone, M.Lu, S.P.Anand, G.Beaudoin-Bussieres, M.Benlarbi, S.Ding, R.Gasser, C.Fink, Y.Chen, A.Tauzin, G.Goyette, C.Bourassa, H.Medjahed, M.Mack, K.Chung, C.B.Wilen, G.A.Dekaban, J.D.Dikeakos, E.A.Bruce, D.E.Kaufmann, L.Stamatatos, A.T.Mcguire, J.Richard, M.Pazgier, P.J.Bjorkman, W.Mothes, A.Finzi, P.Kumar, P.D.Uchil. Live Imaging of Sars-Cov-2 Infection in Mice Reveals Neutralizing Antibodies Require Fc Function For Optimal Efficacy. Biorxiv 2021.
DOI: 10.1101/2021.03.22.436337
Page generated: Fri Dec 17 11:20:39 2021

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