Zinc in PDB 5w23: Crystal Structure of Rsv F in Complex with 5C4 Fab

The structure of Crystal Structure of Rsv F in Complex with 5C4 Fab, PDB code: 5w23 was solved by M.B.Battles, J.S.Mclellan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 3.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	183.360, 183.360, 275.900, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.9

The binding sites of Zinc atom in the Crystal Structure of Rsv F in Complex with 5C4 Fab (pdb code 5w23). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Rsv F in Complex with 5C4 Fab, PDB code: 5w23:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.3 occ:1.00 N A:TYR458 3.1 51.6 1.0 CD1 A:TYR458 3.6 54.3 1.0 O A:LEU456 3.7 54.9 1.0 CE C:MET370 3.7 79.3 1.0 CA A:TYR457 3.8 52.7 1.0 NE1 C:TRP52 3.8 41.6 1.0 CB A:TYR458 3.9 50.8 1.0 C A:TYR457 3.9 53.3 1.0 O C:SER146 4.0 64.0 1.0 CA A:TYR458 4.0 52.0 1.0 CD1 C:TRP52 4.1 48.2 1.0 CG A:TYR458 4.3 51.9 1.0 O A:TYR458 4.4 49.7 1.0 C A:LEU456 4.6 54.5 1.0 CE1 A:TYR458 4.7 55.4 1.0 N A:TYR457 4.7 54.7 1.0 NH2 C:ARG49 4.7 55.4 1.0 O C:ALA147 4.7 51.0 1.0 C A:TYR458 4.8 51.4 1.0 CB A:TYR457 4.8 52.7 1.0 C C:SER146 4.8 56.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.2 occ:1.00 OD1 B:ASN496 3.7 98.7 1.0 CE2 B:TYR478 4.2 82.0 1.0 CZ B:TYR478 4.3 80.0 1.0 CG B:ASN496 4.4 0.2 1.0 O B:PHE477 4.4 96.1 1.0 OH B:TYR478 4.4 78.6 1.0 CE1 B:PHE387 4.5 79.3 1.0 ND2 B:ASN496 4.6 98.8 1.0 CD2 B:TYR478 4.7 84.8 1.0 CB B:PHE477 4.8 84.4 1.0 CZ B:PHE387 4.8 78.7 1.0 CE1 B:TYR478 4.9 79.3 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:0.6 occ:1.00 ND2 C:ASN175 3.6 54.6 1.0 OD1 C:ASN175 4.0 55.6 1.0 CG C:ASN175 4.1 51.9 1.0 O C:LYS191 4.1 45.3 1.0 N C:LEU193 4.6 35.9 1.0 N C:ASP194 4.6 50.7 1.0 C C:VAL192 4.7 36.4 1.0 CB C:ASP194 4.7 58.3 1.0 CA C:LEU193 4.7 44.1 1.0 O C:VAL192 4.8 37.8 1.0 C C:LEU193 4.8 35.6 1.0 C C:LYS191 5.0 37.2 1.0 CG C:LYS191 5.0 36.9 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:0.5 occ:1.00 O H:SER17 4.4 46.0 1.0 C H:SER17 4.6 43.4 1.0 CA H:VAL18 4.8 43.3 1.0 CB H:SER17 4.8 50.2 1.0 N H:VAL18 4.8 38.9 1.0 N H:LYS19 4.9 45.2 1.0 C H:VAL18 4.9 44.9 1.0 CB H:LYS19 5.0 39.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn301 b:0.5 occ:1.00 OG I:SER108 3.8 41.4 1.0 CG I:PRO41 3.8 45.0 1.0 CG2 I:THR87 4.2 48.5 1.0 OG1 I:THR110 4.5 44.5 1.0 CD I:PRO41 4.7 42.8 1.0 N I:ALA88 4.8 34.6 1.0 C I:ALA88 4.8 34.5 1.0 CB I:PRO41 4.8 49.7 1.0 CG2 I:VAL89 4.8 29.7 1.0 CA I:ALA88 4.9 37.0 1.0 O I:ALA88 4.9 36.4 1.0 O I:VAL109 4.9 46.2 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn301 b:88.3 occ:1.00 ND1 J:HIS56 2.3 56.2 1.0 OD2 J:ASP54 2.8 62.0 1.0 CE1 J:HIS56 3.1 61.9 1.0 CG J:HIS56 3.2 54.6 1.0 OD1 J:ASP54 3.5 56.6 1.0 CG J:ASP54 3.5 61.9 1.0 CB J:HIS56 3.6 51.4 1.0 OD2 J:ASP52 3.7 72.6 1.0 NE2 J:HIS56 4.0 63.9 1.0 CD2 J:HIS56 4.1 59.3 1.0 OD1 A:ASN63 4.4 75.4 1.0 ND2 A:ASN63 4.5 75.2 1.0 CG J:ASP52 4.7 69.4 1.0 CB J:ASP52 4.8 59.4 1.0 CG A:ASN63 4.8 73.0 1.0 CB J:ASP54 5.0 65.7 1.0 CA J:HIS56 5.0 50.6 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn302 b:0.2 occ:1.00 NE J:ARG50 3.2 30.7 1.0 NH2 J:ARG50 3.6 36.7 1.0 CZ J:ARG50 3.9 32.2 1.0 CD J:ARG50 4.3 28.3 1.0 CB J:PRO100C 4.4 36.8 1.0 CG J:ARG50 4.6 27.5 1.0 CG J:PRO100C 4.7 35.1 1.0 CB J:LYS58 4.8 35.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Rsv F in Complex with 5C4 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Rsv F in Complex with 5C4 Fab within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn301 b:94.9 occ:1.00 OE1 N:GLU27 2.0 0.1 1.0 OE1 N:GLU93 2.6 73.1 1.0 CD N:GLU27 3.0 0.7 1.0 OE2 N:GLU27 3.2 0.6 1.0 CD N:GLU93 3.3 70.5 1.0 OE2 N:GLU93 3.5 75.8 1.0 CG N:GLU27 4.3 78.7 1.0 CG N:GLU93 4.5 62.1 1.0 CB N:GLU27 4.8 64.3 1.0

D.Tian, M.B.Battles, S.M.Moin, M.Chen, K.Modjarrad, A.Kumar, M.Kanekiyo, K.W.Graepel, N.M.Taher, A.L.Hotard, M.L.Moore, M.Zhao, Z.Z.Zheng, N.S.Xia, J.S.Mclellan, B.S.Graham. Structural Basis of Respiratory Syncytial Virus Subtype-Dependent Neutralization By An Antibody Targeting the Fusion Glycoprotein. Nat Commun V. 8 1877 2017.
ISSN: ESSN 2041-1723
PubMed: 29187732
DOI: 10.1038/S41467-017-01858-W