Sodium in PDB 6b5s: Structure of Pfcsp Peptide 25 with Human Antibody CIS42

The structure of Structure of Pfcsp Peptide 25 with Human Antibody CIS42, PDB code: 6b5s was solved by M.Pancera, C.Weidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.42 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.960, 70.817, 164.901, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.4

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>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42 (pdb code 6b5s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42, PDB code: 6b5s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na323 b:58.7 occ:1.00 H13 H:IPA301 2.1 56.9 1.0 O H:HOH437 2.8 31.8 1.0 C1 H:IPA301 3.0 47.4 1.0 H12 H:IPA301 3.1 56.9 1.0 H32 H:IPA301 3.1 50.2 1.0 HB3 H:SER9 3.1 41.4 1.0 O H:HOH452 3.2 52.0 1.0 HD23 H:LEU108 3.2 35.7 1.0 H11 H:IPA301 3.7 56.9 1.0 HB2 H:SER9 3.7 41.4 1.0 CB H:SER9 3.8 34.5 1.0 C3 H:IPA301 4.0 41.9 1.0 CD2 H:LEU108 4.1 29.7 1.0 HD21 H:LEU108 4.1 35.7 1.0 C2 H:IPA301 4.1 42.4 1.0 OG H:SER9 4.3 39.3 1.0 H33 H:IPA301 4.4 50.2 1.0 HB2 H:LEU11 4.4 36.6 1.0 H2 H:IPA301 4.5 50.9 1.0 HD22 H:LEU108 4.6 35.7 1.0 HG H:LEU108 4.8 36.7 1.0 H31 H:IPA301 4.8 50.2 1.0 HB3 H:LEU108 5.0 36.0 1.0 HG H:SER9 5.0 47.2 1.0

Sodium binding site 2 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na324 b:57.6 occ:1.00 HZ3 H:LYS143 2.1 65.0 1.0 NZ H:LYS143 3.0 54.2 1.0 HG3 L:LYS130 3.0 68.7 1.0 HE2 H:PHE122 3.1 55.0 1.0 HD3 H:LYS143 3.2 56.5 1.0 HZ H:PHE122 3.2 52.7 1.0 HZ1 H:LYS143 3.3 65.0 1.0 HZ2 H:LYS143 3.4 65.0 1.0 HE2 H:LYS143 3.6 59.8 1.0 CE H:LYS143 3.7 49.8 1.0 HG H:SER120 3.8 51.8 1.0 CE2 H:PHE122 3.8 45.9 1.0 CZ H:PHE122 3.8 43.9 1.0 CD H:LYS143 3.9 47.1 1.0 HB2 L:LYS130 3.9 60.0 1.0 CG L:LYS130 4.0 57.3 1.0 HB2 H:SER120 4.0 47.6 1.0 HG3 L:GLU125 4.1 46.9 1.0 HE2 L:LYS130 4.2 81.8 1.0 HB3 H:SER120 4.3 47.6 1.0 CB L:LYS130 4.4 50.0 1.0 OD2 H:ASP144 4.4 38.0 1.0 CB H:SER120 4.5 39.7 1.0 HG2 L:LYS130 4.5 68.7 1.0 OG H:SER120 4.5 43.1 1.0 HD2 H:LYS143 4.5 56.5 1.0 HB3 L:LYS130 4.5 60.0 1.0 HE3 H:LYS143 4.6 59.8 1.0 HZ3 L:LYS130 4.7 85.7 1.0 HB3 H:LYS143 4.7 48.6 1.0 HB3 L:ALA128 4.7 58.7 1.0 HB1 L:ALA128 4.7 58.7 1.0 HG2 H:LYS143 4.7 54.0 1.0 CD L:LYS130 4.9 63.3 1.0 CG H:LYS143 4.9 45.0 1.0 HD2 L:LYS130 4.9 76.0 1.0 CE L:LYS130 4.9 68.1 1.0 O H:HOH434 4.9 40.0 1.0

Sodium binding site 3 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na325 b:61.5 occ:1.00 NA H:NA328 2.4 63.6 1.0 OE2 H:GLU46 2.5 49.5 1.0 O H:HOH528 2.7 40.0 1.0 HG3 H:GLU46 3.0 53.1 1.0 HG2 H:GLU46 3.3 53.1 1.0 CD H:GLU46 3.3 46.8 1.0 CG H:GLU46 3.4 44.2 1.0 HE2 H:PHE63 3.6 32.9 1.0 O H:PRO61 3.9 50.0 1.0 HB1 H:ALA60 4.0 38.0 1.0 O H:TRP47 4.1 24.7 1.0 CE2 H:PHE63 4.5 27.4 1.0 HB3 H:ALA60 4.5 38.0 1.0 OE1 H:GLU46 4.6 45.8 1.0 O H:HOH502 4.6 25.6 1.0 HD2 H:PHE63 4.6 32.9 1.0 CB H:ALA60 4.7 31.7 1.0 HG2 H:PRO61 4.7 56.5 1.0 O L:HOH421 4.9 30.6 1.0 CB H:GLU46 4.9 36.3 1.0 H H:TRP47 5.0 29.6 1.0 HD2 H:PRO61 5.0 52.7 1.0 CD2 H:PHE63 5.0 27.4 1.0

Sodium binding site 4 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na326 b:56.6 occ:1.00 O H:GLY55 2.7 29.2 1.0 O H:HOH440 2.8 35.1 1.0 H12 H:IPA302 3.1 56.6 1.0 HD3 H:PRO57 3.4 43.5 1.0 H13 H:IPA302 3.4 56.6 1.0 HN2 H:NH4308 3.6 49.1 1.0 C H:GLY55 3.7 29.8 1.0 HA3 H:GLY55 3.7 35.6 1.0 C1 H:IPA302 3.7 47.2 1.0 HD11 H:ILE51 3.7 35.4 1.0 HN4 H:NH4308 3.8 49.1 1.0 HG3 H:PRO57 4.1 41.6 1.0 CA H:GLY55 4.1 29.7 1.0 N H:NH4308 4.1 40.9 1.0 H32 H:IPA302 4.2 32.2 1.0 HA2 H:GLY55 4.2 35.6 1.0 H2 H:IPA302 4.2 49.2 1.0 CD H:PRO57 4.3 36.3 1.0 C2 H:IPA302 4.4 41.0 1.0 HD12 H:ILE51 4.4 35.4 1.0 HN3 H:NH4308 4.5 49.1 1.0 H33 H:IPA302 4.5 32.2 1.0 CD1 H:ILE51 4.5 29.5 1.0 HA H:ASN56 4.6 36.6 1.0 C3 H:IPA302 4.6 26.8 1.0 H11 H:IPA302 4.7 56.6 1.0 CG H:PRO57 4.7 34.6 1.0 N H:ASN56 4.8 29.0 1.0 HD2 H:PRO57 4.8 43.5 1.0 O H:PHE69 4.9 24.1 1.0 HN1 H:NH4308 5.0 49.1 1.0 HG13 H:ILE51 5.0 32.7 1.0

Sodium binding site 5 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na327 b:63.3 occ:1.00 HA3 H:GLY15 3.1 40.7 1.0 O H:PRO14 3.2 28.9 1.0 C H:GLY15 3.7 33.3 1.0 CA H:GLY15 3.8 33.9 1.0 O H:HOH447 3.8 52.7 1.0 N H:ALA16 3.9 31.2 1.0 H H:ALA16 4.1 37.4 1.0 O H:GLY15 4.1 35.0 1.0 C H:PRO14 4.2 30.5 1.0 HA H:ALA16 4.2 37.2 1.0 N H:GLY15 4.4 32.3 1.0 HB2 H:LYS13 4.5 45.7 1.0 HB2 H:ALA16 4.5 37.4 1.0 HA2 H:GLY15 4.6 40.7 1.0 CA H:ALA16 4.6 31.0 1.0 HB3 H:LYS13 4.7 45.7 1.0

Sodium binding site 6 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na328 b:63.6 occ:1.00 O H:PRO61 2.2 50.0 1.0 HG2 H:PRO61 2.4 56.5 1.0 NA H:NA325 2.4 61.5 1.0 HB1 H:ALA60 3.2 38.0 1.0 HD2 H:PRO61 3.2 52.7 1.0 C H:PRO61 3.2 45.5 1.0 CG H:PRO61 3.2 47.1 1.0 CD H:PRO61 3.6 43.9 1.0 N H:PRO61 3.7 39.7 1.0 HB2 H:PRO61 3.8 56.1 1.0 CA H:PRO61 3.8 44.8 1.0 CB H:PRO61 3.9 46.8 1.0 HG3 H:PRO61 4.0 56.5 1.0 CB H:ALA60 4.1 31.7 1.0 O H:HOH528 4.1 40.0 1.0 HA3 H:GLY62 4.1 46.3 1.0 HB3 H:ALA60 4.1 38.0 1.0 OE2 H:GLU46 4.3 49.5 1.0 C H:ALA60 4.3 32.8 1.0 N H:GLY62 4.3 41.1 1.0 HD3 H:PRO61 4.5 52.7 1.0 HD2 H:PHE63 4.6 32.9 1.0 HE2 H:PHE63 4.6 32.9 1.0 HB2 H:ALA60 4.7 38.0 1.0 CA H:GLY62 4.7 38.6 1.0 CA H:ALA60 4.7 31.6 1.0 HA H:PRO61 4.8 53.7 1.0 HB3 H:PRO61 4.8 56.1 1.0 HA H:ALA60 5.0 38.0 1.0 O L:HOH421 5.0 30.6 1.0 O H:ALA60 5.0 30.5 1.0

Sodium binding site 7 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na329 b:60.1 occ:1.00 HB3 H:LYS206 2.6 48.1 1.0 HB3 H:ASN197 2.7 43.9 1.0 OD1 H:ASP208 3.0 44.5 1.0 O H:VAL198 3.1 34.3 1.0 H H:VAL198 3.2 39.9 1.0 HA H:ASN197 3.2 43.4 1.0 H H:VAL207 3.4 40.9 1.0 O H:VAL207 3.4 35.5 1.0 HD3 H:LYS206 3.4 55.6 1.0 N H:VAL198 3.4 33.2 1.0 CB H:ASN197 3.5 36.6 1.0 C H:ASN197 3.6 34.7 1.0 CB H:LYS206 3.6 40.1 1.0 CA H:ASN197 3.6 36.1 1.0 C H:VAL198 3.7 33.6 1.0 N H:VAL207 3.8 34.1 1.0 C H:VAL207 3.9 36.9 1.0 CG H:ASP208 3.9 43.5 1.0 HB2 H:ASN197 4.0 43.9 1.0 HD22 H:ASN197 4.0 49.2 1.0 HB2 H:LYS206 4.1 48.1 1.0 HA H:LYS206 4.2 44.9 1.0 CD H:LYS206 4.2 46.3 1.0 CA H:VAL198 4.2 33.9 1.0 HB2 H:ASN199 4.3 53.2 1.0 HG2 H:LYS206 4.3 53.4 1.0 CG H:LYS206 4.3 44.5 1.0 CA H:LYS206 4.3 37.4 1.0 OD2 H:ASP208 4.3 47.7 1.0 O H:ASN197 4.3 34.6 1.0 C H:LYS206 4.3 36.3 1.0 N H:ASP208 4.5 36.8 1.0 HD2 H:LYS206 4.5 55.6 1.0 HA H:ASP208 4.5 44.4 1.0 CA H:VAL207 4.5 34.5 1.0 HA H:ASN199 4.6 45.2 1.0 N H:ASN199 4.6 35.0 1.0 CG H:ASN197 4.6 39.1 1.0 ND2 H:ASN197 4.7 41.0 1.0 HA H:VAL198 4.8 40.6 1.0 CA H:ASP208 4.9 37.0 1.0 H H:ASP208 4.9 44.2 1.0 HA H:VAL207 5.0 41.4 1.0

Sodium binding site 8 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na314 b:71.9 occ:1.00 HZ2 L:LYS157 1.8 0.5 1.0 NZ L:LYS157 2.5 0.1 1.0 HZ3 L:LYS157 2.6 0.5 1.0 HD2 L:LYS157 3.0 0.8 1.0 HZ1 L:LYS157 3.1 0.5 1.0 CE L:LYS157 3.5 0.2 1.0 CD L:LYS157 3.5 97.3 1.0 HD3 L:LYS157 3.6 0.8 1.0 HE3 L:LYS157 3.8 0.1 1.0 HE2 L:LYS157 4.3 0.1 1.0 CG L:LYS157 5.0 83.5 1.0

Sodium binding site 9 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na315 b:59.9 occ:1.00 HN2 L:NH4306 2.2 46.6 1.0 HN1 L:NH4306 2.2 46.6 1.0 OG1 L:THR117 2.4 34.0 1.0 N L:NH4306 2.6 38.9 1.0 HN3 L:NH4306 3.0 46.6 1.0 HB2 L:SER115 3.3 53.4 1.0 HN4 L:NH4306 3.4 46.6 1.0 CB L:THR117 3.5 34.3 1.0 HB L:THR117 3.6 41.1 1.0 N L:THR117 3.6 29.0 1.0 OG L:SER115 3.7 52.2 1.0 HG L:SER115 3.7 62.7 1.0 C L:VAL116 3.7 29.1 1.0 H L:THR117 3.7 34.8 1.0 N L:VAL116 3.8 29.8 1.0 C L:SER115 3.9 33.6 1.0 CB L:SER115 3.9 44.5 1.0 H L:VAL116 4.0 35.7 1.0 O L:VAL116 4.0 30.9 1.0 O L:SER115 4.1 34.1 1.0 CA L:THR117 4.1 30.7 1.0 HA L:VAL116 4.2 33.6 1.0 CA L:VAL116 4.2 28.0 1.0 OG L:SER138 4.2 36.4 1.0 HG L:SER138 4.4 43.6 1.0 HA L:THR117 4.4 36.9 1.0 CA L:SER115 4.5 36.0 1.0 O L:LEU136 4.7 32.8 1.0 CG2 L:THR117 4.8 39.5 1.0 HB3 L:SER115 4.8 53.4 1.0 HG21 L:THR117 4.8 47.4 1.0 HA L:SER115 5.0 43.1 1.0 HG23 L:THR117 5.0 47.4 1.0

Sodium binding site 10 out of 13 in the Structure of Pfcsp Peptide 25 with Human Antibody CIS42


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Pfcsp Peptide 25 with Human Antibody CIS42 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na316 b:59.8 occ:1.00 NA L:NA317 3.3 55.6 1.0 HB2 L:PRO55 3.3 45.7 1.0 HB3 L:PRO55 3.6 45.7 1.0 H L:SER56 3.7 48.2 1.0 CB L:PRO55 3.8 38.1 1.0 OG L:SER56 3.9 50.6 1.0 H33 H:IPA305 4.1 53.7 1.0 HA L:PRO55 4.2 42.5 1.0 HG L:SER56 4.2 60.7 1.0 H12 H:IPA305 4.2 55.3 1.0 N L:SER56 4.3 40.2 1.0 O L:SER56 4.3 47.5 1.0 H31 H:IPA305 4.3 53.7 1.0 CA L:PRO55 4.5 35.4 1.0 H11 H:IPA305 4.5 55.3 1.0 C3 H:IPA305 4.7 44.8 1.0 C1 H:IPA305 4.8 46.1 1.0 C L:PRO55 4.8 34.0 1.0 O L:HOH509 4.9 42.7 1.0 O L:HOH523 4.9 49.3 1.0 O2 H:IPA305 5.0 46.7 1.0 CB L:SER56 5.0 51.2 1.0

N.K.Kisalu, A.H.Idris, C.Weidle, Y.Flores-Garcia, B.J.Flynn, B.K.Sack, S.Murphy, A.Schon, E.Freire, J.R.Francica, A.B.Miller, J.Gregory, S.March, H.X.Liao, B.F.Haynes, K.Wiehe, A.M.Trama, K.O.Saunders, M.A.Gladden, A.Monroe, M.Bonsignori, M.Kanekiyo, A.K.Wheatley, A.B.Mcdermott, S.K.Farney, G.Y.Chuang, B.Zhang, N.Kc, S.Chakravarty, P.D.Kwong, P.Sinnis, S.N.Bhatia, S.H.I.Kappe, B.K.L.Sim, S.L.Hoffman, F.Zavala, M.Pancera, R.A.Seder. A Human Monoclonal Antibody Prevents Malaria Infection By Targeting A New Site of Vulnerability on the Parasite. Nat. Med. V. 24 408 2018.
ISSN: ISSN 1546-170X
PubMed: 29554083
DOI: 10.1038/NM.4512