Sodium in PDB 8ulf: Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7

The structure of Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7, PDB code: 8ulf was solved by W.K.Tang, N.H.Tolia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 3.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	182.89, 78.62, 47.32, 90.03, 95.37, 89.88
R / Rfree (%)	27.5 / 29.5

The binding sites of Sodium atom in the Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7 (pdb code 8ulf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7, PDB code: 8ulf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7


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 Plasmodium Vivax Celtos in Complex with Antibody 7G7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:110.3 occ:1.00 OE1 A:GLU161 2.1 122.0 1.0 OD1 A:ASP170 2.2 129.3 1.0 O A:ILE168 2.2 124.7 1.0 OD1 A:ASN158 2.8 124.4 1.0 CD A:GLU161 2.9 120.9 1.0 OE2 A:GLU161 3.1 121.9 1.0 CG A:ASP170 3.2 134.4 1.0 CG A:ASN158 3.3 124.5 1.0 C A:ILE168 3.4 124.9 1.0 H A:ILE168 3.6 166.0 1.0 OD2 A:ASP170 3.6 137.0 1.0 HA A:PRO169 3.8 155.4 1.0 HA A:ASN158 3.8 139.4 1.0 HD22 A:ASN158 3.9 147.0 1.0 ND2 A:ASN158 3.9 126.7 1.0 H A:ASP170 3.9 167.5 1.0 N A:ASP170 3.9 130.4 1.0 HB3 A:ASN158 4.0 146.7 1.0 C A:PRO169 4.0 126.6 1.0 CB A:ASN158 4.1 122.5 1.0 CA A:PRO169 4.2 127.2 1.0 N A:ILE168 4.2 123.9 1.0 N A:PRO169 4.3 126.0 1.0 HA A:ASP170 4.3 172.7 1.0 CB A:ASP170 4.3 138.1 1.0 CG A:GLU161 4.4 118.7 1.0 HB A:ILE168 4.4 204.6 1.0 CA A:ILE168 4.4 124.0 1.0 CA A:ASP170 4.4 132.2 1.0 CA A:ASN158 4.5 120.3 1.0 HD21 A:ASN158 4.5 147.0 1.0 HB2 A:GLU161 4.5 150.6 1.0 O A:PRO169 4.6 125.7 1.0 HB3 A:GLU161 4.7 150.6 1.0 HB2 A:ASP170 4.7 168.9 1.0 HG2 A:GLU161 4.8 153.8 1.0 CB A:GLU161 4.8 118.0 1.0 CB A:ILE168 4.9 123.0 1.0 HG22 A:ILE168 4.9 204.8 1.0 HG3 A:GLU161 4.9 153.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7


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 Plasmodium Vivax Celtos in Complex with Antibody 7G7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:101.5 occ:1.00 OE2 B:GLU161 2.0 108.0 1.0 OD1 B:ASP170 2.1 115.7 1.0 O B:ILE168 2.1 112.6 1.0 OE1 B:GLU161 2.3 109.6 1.0 CD B:GLU161 2.5 109.4 1.0 OD1 B:ASN158 2.9 108.6 1.0 C B:ILE168 3.2 112.7 1.0 CG B:ASP170 3.3 115.5 1.0 HA B:ASP170 3.3 191.6 1.0 HB B:ILE168 3.5 242.9 1.0 C B:PRO169 3.5 111.5 1.0 O B:PRO169 3.6 110.9 1.0 N B:ASP170 3.6 114.2 1.0 H B:ILE168 3.7 181.8 1.0 CA B:ASP170 3.8 113.5 1.0 HE1 B:TRP173 3.8 180.0 1.0 HG22 B:ILE168 3.9 247.2 1.0 CG B:GLU161 4.0 111.3 1.0 HA B:ASN158 4.0 169.2 1.0 H B:ASP170 4.0 189.8 1.0 CG B:ASN158 4.1 109.9 1.0 CA B:ILE168 4.1 113.9 1.0 OD2 B:ASP170 4.1 116.7 1.0 CB B:ASP170 4.1 115.5 1.0 N B:PRO169 4.1 113.3 1.0 CB B:ILE168 4.1 113.5 1.0 HA B:PRO169 4.2 212.5 1.0 OE2 B:GLU129 4.2 116.5 1.0 CA B:PRO169 4.2 112.6 1.0 OE1 B:GLU129 4.2 114.6 1.0 N B:ILE168 4.3 115.6 1.0 HG3 B:GLU161 4.3 157.5 1.0 HG2 B:GLU161 4.3 157.5 1.0 CG2 B:ILE168 4.5 112.0 1.0 CD B:GLU129 4.6 115.5 1.0 HB3 B:PHE157 4.6 164.7 1.0 HB3 B:ASP170 4.6 171.3 1.0 NE1 B:TRP173 4.7 114.6 1.0 CA B:ASN158 4.7 112.0 1.0 HB2 B:GLU161 4.7 149.5 1.0 HB2 B:LYS154 4.7 184.9 1.0 N B:ASN158 4.7 110.9 1.0 HB2 B:ASP170 4.8 171.3 1.0 HD21 B:ASN158 4.9 155.4 1.0 H B:ASN158 4.9 169.9 1.0 CB B:GLU161 4.9 113.3 1.0 O B:LYS154 4.9 114.8 1.0 CB B:ASN158 5.0 111.9 1.0 ND2 B:ASN158 5.0 110.1 1.0 HA B:ILE168 5.0 190.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7


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 Plasmodium Vivax Celtos in Complex with Antibody 7G7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:101.7 occ:1.00 OE2 C:GLU161 2.0 107.4 1.0 OD1 C:ASP170 2.0 114.4 1.0 O C:ILE168 2.1 113.5 1.0 OE1 C:GLU161 2.3 108.8 1.0 CD C:GLU161 2.4 108.7 1.0 OD1 C:ASN158 2.9 108.6 1.0 CG C:ASP170 3.2 114.3 1.0 C C:ILE168 3.3 113.4 1.0 HA C:ASP170 3.3 189.4 1.0 C C:PRO169 3.6 110.9 1.0 HB C:ILE168 3.6 254.0 1.0 N C:ASP170 3.6 112.4 1.0 O C:PRO169 3.6 110.4 1.0 H C:ILE168 3.7 186.7 1.0 CA C:ASP170 3.8 112.0 1.0 HE1 C:TRP173 3.9 172.6 1.0 CG C:GLU161 3.9 110.7 1.0 HA C:ASN158 4.0 147.0 1.0 H C:ASP170 4.0 189.2 1.0 OD2 C:ASP170 4.0 116.8 1.0 HG22 C:ILE168 4.1 255.8 1.0 CG C:ASN158 4.1 110.2 1.0 CB C:ASP170 4.1 114.7 1.0 OE2 C:GLU129 4.1 116.0 1.0 HA C:PRO169 4.1 213.0 1.0 CA C:ILE168 4.1 114.5 1.0 N C:PRO169 4.2 112.5 1.0 CA C:PRO169 4.2 111.9 1.0 CB C:ILE168 4.2 114.2 1.0 HG3 C:GLU161 4.3 155.9 1.0 N C:ILE168 4.3 116.2 1.0 OE1 C:GLU129 4.3 113.7 1.0 HG2 C:GLU161 4.3 155.9 1.0 HB3 C:PHE157 4.6 163.5 1.0 CD C:GLU129 4.6 114.8 1.0 HB3 C:ASP170 4.6 165.1 1.0 CA C:ASN158 4.7 112.2 1.0 HB2 C:GLU161 4.7 146.8 1.0 CG2 C:ILE168 4.7 112.7 1.0 N C:ASN158 4.7 111.2 1.0 NE1 C:TRP173 4.7 114.0 1.0 HB2 C:ASP170 4.8 165.1 1.0 HB2 C:LYS154 4.8 180.4 1.0 CB C:GLU161 4.8 112.8 1.0 H C:ASN158 4.8 152.4 1.0 HB3 C:GLU161 4.9 146.8 1.0 HD22 C:ASN158 4.9 154.8 1.0 CB C:ASN158 4.9 112.3 1.0 O C:LYS154 5.0 114.2 1.0 C C:PHE157 5.0 111.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Plasmodium Vivax Celtos in Complex with Antibody 7G7


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 Plasmodium Vivax Celtos in Complex with Antibody 7G7 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:107.5 occ:1.00 O D:ILE168 2.2 130.9 1.0 OD1 D:ASP170 2.2 130.0 1.0 OE1 D:GLU161 2.4 121.9 1.0 OD1 D:ASN158 2.9 125.9 1.0 CG D:ASP170 3.2 132.6 1.0 CD D:GLU161 3.2 120.7 1.0 OE2 D:GLU161 3.3 122.5 1.0 C D:ILE168 3.4 129.3 1.0 H D:ILE168 3.4 172.6 1.0 CG D:ASN158 3.6 125.7 1.0 OD2 D:ASP170 3.7 134.1 1.0 HA D:ASN158 3.7 147.6 1.0 HA D:PRO169 3.8 159.1 1.0 N D:ASP170 3.9 133.7 1.0 H D:ASP170 3.9 165.8 1.0 C D:PRO169 4.0 129.0 1.0 N D:ILE168 4.1 122.8 1.0 CA D:PRO169 4.2 128.0 1.0 HA D:ASP170 4.2 168.9 1.0 N D:PRO169 4.2 125.3 1.0 HB D:ILE168 4.3 203.0 1.0 HB3 D:ASN158 4.3 151.4 1.0 CA D:ILE168 4.3 124.9 1.0 ND2 D:ASN158 4.3 127.9 1.0 HD21 D:ASN158 4.3 148.9 1.0 CB D:ASP170 4.3 137.5 1.0 CB D:ASN158 4.3 123.2 1.0 CA D:ASP170 4.4 134.7 1.0 CA D:ASN158 4.4 121.1 1.0 O D:PRO169 4.5 128.4 1.0 CG D:GLU161 4.6 118.2 1.0 HB2 D:GLU161 4.6 155.8 1.0 HB2 D:ASP170 4.7 163.1 1.0 CB D:ILE168 4.8 126.5 1.0 HG2 D:GLU161 4.8 158.0 1.0 HA D:PRO167 4.9 174.0 1.0 N D:ASN158 4.9 121.5 1.0 HG22 D:ILE168 4.9 211.2 1.0 HD22 D:ASN158 5.0 148.9 1.0

W.K.Tang, N.D.Salinas, S.K.Kolli, S.Xu, D.V.Urusova, H.Kumar, J.R.Jimah, P.A.Subramani, M.M.Ogbondah, S.J.Barnes, J.H.Adams, N.H.Tolia. Multistage Protective Anti-Celtos Monoclonal Antibodies with Cross-Species Sterile Protection Against Malaria. Nat Commun V. 15 7487 2024.
ISSN: ESSN 2041-1723
PubMed: 39209843
DOI: 10.1038/S41467-024-51701-2