Zinc in PDB 8vdl: HB3VAR03 CIDRA1.4 Domain with C7 Fab

The structure of HB3VAR03 CIDRA1.4 Domain with C7 Fab, PDB code: 8vdl was solved by N.K.Hurlburt, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.30 / 2.68
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.653, 65.353, 250.341, 90, 90, 90
R / Rfree (%)	21.7 / 26.6

The binding sites of Zinc atom in the HB3VAR03 CIDRA1.4 Domain with C7 Fab (pdb code 8vdl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the HB3VAR03 CIDRA1.4 Domain with C7 Fab, PDB code: 8vdl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the HB3VAR03 CIDRA1.4 Domain with C7 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HB3VAR03 CIDRA1.4 Domain with C7 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn801 b:86.4 occ:1.00 NE2 C:HIS702 2.3 74.7 1.0 CE1 C:HIS702 2.4 76.5 1.0 OE2 C:GLU590 2.8 72.3 1.0 OE1 C:GLU590 2.9 68.5 1.0 CD C:GLU590 3.2 69.2 1.0 ND2 C:ASN675 3.3 68.8 1.0 CD2 C:HIS702 3.7 79.0 1.0 ND1 C:HIS702 3.8 81.3 1.0 CG1 C:ILE706 4.2 78.1 1.0 CG C:HIS702 4.4 82.0 1.0 CG C:ASN675 4.4 67.3 1.0 CD1 C:ILE706 4.5 70.3 1.0 OE1 C:GLU671 4.7 78.4 1.0 CG C:GLU590 4.7 58.4 1.0 CB C:GLU671 4.9 55.9 1.0 OE1 C:GLU705 4.9 90.7 1.0

Zinc binding site 2 out of 6 in the HB3VAR03 CIDRA1.4 Domain with C7 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HB3VAR03 CIDRA1.4 Domain with C7 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn802 b:140.3 occ:1.00 OE2 C:GLU625 1.9 97.3 1.0 NZ C:LYS622 2.7 94.1 1.0 CD C:GLU625 3.1 88.2 1.0 OE1 C:GLU625 3.6 88.0 1.0 CE C:LYS622 3.9 79.9 1.0 CG C:GLU625 4.2 73.6 1.0 CB C:GLN621 4.8 74.1 1.0 CD C:LYS622 4.8 75.2 1.0 NE2 C:GLN621 4.8 77.8 1.0

Zinc binding site 3 out of 6 in the HB3VAR03 CIDRA1.4 Domain with C7 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HB3VAR03 CIDRA1.4 Domain with C7 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn301 b:76.3 occ:1.00 NE2 H:HIS32 2.3 53.8 1.0 O H:HOH430 2.7 47.7 1.0 CE1 H:HIS32 3.1 47.0 1.0 CD2 H:HIS32 3.3 47.4 1.0 ND1 H:HIS32 4.3 44.7 1.0 OG1 H:THR28 4.3 51.9 1.0 CG H:HIS32 4.4 41.4 1.0 N H:THR28 4.7 46.7 1.0 CB H:THR28 4.7 54.5 1.0 CB H:ASP31 4.8 58.9 1.0 OD2 H:ASP31 4.8 64.1 1.0 CB H:PHE27 4.9 39.2 1.0

Zinc binding site 4 out of 6 in the HB3VAR03 CIDRA1.4 Domain with C7 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of HB3VAR03 CIDRA1.4 Domain with C7 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:40.5 occ:1.00 OE2 H:GLU89 1.9 42.4 1.0 OD1 H:ASP88 2.2 26.5 1.0 OD2 H:ASP88 2.6 32.4 1.0 O H:HOH408 2.7 24.3 1.0 CG H:ASP88 2.7 28.1 1.0 CD H:GLU89 2.9 42.0 1.0 OE1 H:GLU89 3.2 38.9 1.0 CG H:GLU89 4.2 31.3 1.0 CB H:ASP88 4.3 18.9 1.0 N H:GLU89 4.7 26.3 1.0 N H:ASP88 4.8 21.5 1.0 CA H:ASP88 5.0 23.8 1.0

Zinc binding site 5 out of 6 in the HB3VAR03 CIDRA1.4 Domain with C7 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of HB3VAR03 CIDRA1.4 Domain with C7 Fab within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn303 b:82.6 occ:1.00 NE2 H:HIS180 2.2 42.4 1.0 OD2 L:ASP138 2.5 45.9 1.0 OD1 L:ASP138 2.6 44.6 1.0 CG L:ASP138 2.9 43.3 1.0 CE1 H:HIS180 3.0 37.5 1.0 CD2 H:HIS180 3.4 37.9 1.0 O L:HOH469 3.4 43.8 1.0 ND1 H:HIS180 4.2 39.2 1.0 CB L:ASP138 4.4 28.2 1.0 CG H:HIS180 4.4 36.8 1.0 O H:HOH463 4.6 31.9 1.0 OG L:SER137 4.9 24.2 1.0 CB L:SER137 4.9 22.2 1.0 ND2 L:ASN169 4.9 40.6 1.0

Zinc binding site 6 out of 6 in the HB3VAR03 CIDRA1.4 Domain with C7 Fab


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of HB3VAR03 CIDRA1.4 Domain with C7 Fab within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:54.7 occ:1.00 NE2 L:HIS188 2.3 25.7 1.0 CE1 L:HIS188 2.4 29.0 1.0 CD2 L:HIS188 3.6 32.3 1.0 ND1 L:HIS188 3.6 27.3 1.0 O L:HOH452 3.8 28.6 1.0 CB L:ALA150 4.0 22.8 1.0 CG L:HIS188 4.2 30.5 1.0 O L:HOH430 5.0 33.0 1.0

N.K.Hurlburt, M.Pancera. Broadly Inhibitory Antibodies Against Severe Malaria-Associated PFEMP1 Function Through A Structurally Convergent Mode of Binding To Be Published.