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: Thu Nov 25 08:11:35 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy