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Calcium in PDB 7b4w: Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)

Protein crystallography data

The structure of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505), PDB code: 7b4w was solved by N.Friedrich, E.Stiegeler, M.Glogl, T.Lemmin, S.Hansen, C.Kadelka, Y.Wu, P.Ernst, L.Maliqi, C.Foulkes, M.Morin, M.Eroglu, T.Liechti, B.Ivan, T.Reinberg, J.Schaefer, U.Karakus, S.Ursprung, A.Mann, P.Rusert, R.D.Kouyos, J.A.Robinson, H.F.Gunthard, A.Pluckthun, A.Trkola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.4, 67.06, 93.11, 90, 90, 90
R / Rfree (%) 18.1 / 22.7

Other elements in 7b4w:

The structure of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) (pdb code 7b4w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505), PDB code: 7b4w:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7b4w

Go back to Calcium Binding Sites List in 7b4w
Calcium binding site 1 out of 2 in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:28.1
occ:1.00
OD1 A:ASN140 2.3 31.4 1.0
O C:HOH272 2.4 23.5 1.0
OD1 A:ASP138 2.4 33.0 1.0
O C:GLY124 2.5 22.8 1.0
O A:HOH334 2.6 30.9 1.0
O C:HOH214 2.6 29.1 1.0
O C:HOH256 2.6 27.7 1.0
OD2 A:ASP138 2.6 31.6 1.0
CG A:ASP138 2.8 31.1 1.0
CG A:ASN140 3.5 31.2 1.0
C C:GLY124 3.6 22.9 1.0
CA C:GLY124 4.1 22.2 1.0
ND2 A:ASN140 4.2 32.8 1.0
O A:HOH414 4.3 36.7 1.0
CB A:ASP138 4.3 29.3 1.0
O A:HOH348 4.3 25.5 1.0
C A:ASN140 4.4 26.5 1.0
O A:ASN140 4.4 26.5 1.0
OD2 C:ASP160 4.4 34.0 1.0
N A:ALA141 4.6 24.7 1.0
O C:HOH244 4.6 31.8 1.0
N C:LEU126 4.6 25.7 1.0
N C:HIS125 4.6 21.1 1.0
CB A:ASN140 4.7 29.5 1.0
N A:ASN140 4.7 28.4 1.0
CB C:LEU126 4.8 29.0 1.0
CA A:ASN140 4.8 28.0 1.0
OD1 C:ASN158 4.9 30.7 1.0
CA C:HIS125 4.9 22.2 1.0
OD1 C:ASP160 5.0 31.8 1.0
CD1 C:ILE161 5.0 24.0 1.0

Calcium binding site 2 out of 2 in 7b4w

Go back to Calcium Binding Sites List in 7b4w
Calcium binding site 2 out of 2 in the Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Broadly Neutralizing Darpin Bnd.3 in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:47.1
occ:1.00
O A:HOH361 2.2 36.4 1.0
O A:HOH425 2.3 65.7 1.0
OE2 A:GLU61 2.5 34.8 1.0
OD2 A:ASP27 2.6 41.1 1.0
O A:HOH365 2.6 31.3 1.0
OE1 A:GLU61 2.6 33.9 1.0
CD A:GLU61 2.9 33.4 1.0
CG A:ASP27 3.7 36.1 1.0
NH1 A:ARG31 4.1 33.9 1.0
O A:HOH406 4.1 47.4 1.0
O A:HOH312 4.2 40.0 1.0
OD1 A:ASP27 4.3 39.9 1.0
OD1 A:ASP28 4.4 33.4 1.0
CG A:GLU61 4.4 31.9 1.0
NH2 A:ARG31 4.7 33.9 1.0
CB A:ASP27 4.7 31.8 1.0
CZ A:ARG31 4.8 32.9 1.0
OD2 A:ASP28 5.0 35.3 1.0
O A:HOH347 5.0 32.7 1.0

Reference:

N.Friedrich, E.Stiegeler, M.Glogl, T.Lemmin, S.Hansen, C.Kadelka, Y.Wu, P.Ernst, L.Maliqi, C.Foulkes, M.Morin, M.Eroglu, T.Liechti, B.Ivan, T.Reinberg, J.Schaefer, U.Karakus, S.Ursprung, A.Mann, P.Rusert, R.D.Kouyos, J.A.Robinson, H.F.Gunthard, A.Pluckthun, A.Trkola. Broadly Neutralizing Darpin in Complex with the Hiv-1 Envelope Variable Loop 3 Crown Mimetic Peptide V3-if (BG505) To Be Published.
Page generated: Wed Jul 9 20:55:54 2025

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