Iodine in PDB 4k1c: VCX1 Calcium/Proton Exchanger

The structure of VCX1 Calcium/Proton Exchanger, PDB code: 4k1c was solved by A.B.Waight, B.P.Pedersen, R.M.Stroud, Center For Structures Of Membraneproteins (Csmp), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.02 / 2.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	130.110, 130.110, 156.750, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 22.5

The structure of VCX1 Calcium/Proton Exchanger also contains other interesting chemical elements:

Manganese	(Mn)	3 atoms
Calcium	(Ca)	9 atoms

Pages:

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

Binding sites:

The binding sites of Iodine atom in the VCX1 Calcium/Proton Exchanger (pdb code 4k1c). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the VCX1 Calcium/Proton Exchanger, PDB code: 4k1c:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I512 b:37.5 occ:0.26 O A:HOH609 3.0 21.5 1.0 N A:ARG120 3.3 20.7 1.0 N A:VAL119 3.5 18.2 1.0 O A:GLY117 3.6 33.5 1.0 CB A:ARG120 3.7 24.9 1.0 CA A:VAL119 4.1 27.7 1.0 CB A:VAL119 4.1 29.9 1.0 C A:GLN118 4.1 33.5 1.0 CA A:ARG120 4.1 17.5 1.0 C A:VAL119 4.2 22.1 1.0 CA A:GLN118 4.2 28.0 1.0 C A:GLY117 4.6 27.8 1.0 OE1 A:GLN118 4.6 29.0 1.0 NZ A:LYS286 4.9 31.0 1.0 CG2 A:VAL119 4.9 18.6 1.0 N A:GLN118 4.9 22.2 1.0

Iodine binding site 2 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I513 b:34.1 occ:0.24 NH2 A:ARG201 3.3 36.2 1.0 C A:ASP345 3.6 44.2 1.0 O A:ASP345 3.7 45.9 1.0 N A:PRO347 3.7 33.5 1.0 C A:VAL346 3.9 34.5 1.0 CA A:ASP345 4.0 47.1 1.0 N A:VAL346 4.0 42.0 1.0 CA A:PRO347 4.0 29.4 1.0 CD A:PRO347 4.1 29.4 1.0 CB A:PRO347 4.3 28.6 1.0 CA A:VAL346 4.3 37.5 1.0 CD2 A:LEU197 4.3 49.6 1.0 CZ A:ARG201 4.3 31.9 1.0 O A:VAL346 4.3 32.0 1.0 NH1 A:ARG201 4.5 31.8 1.0 CB A:ASP345 4.6 55.8 1.0 CG A:PRO347 4.7 28.5 1.0 O A:GLY341 4.8 39.2 1.0 OD2 A:ASP345 5.0 73.7 1.0

Iodine binding site 3 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I514 b:42.7 occ:0.48 O A:HOH618 2.9 23.8 1.0 OG1 A:THR63 3.3 27.9 1.0 CD2 A:HIS60 3.5 56.0 1.0 CA A:GLN57 3.6 29.5 1.0 CB A:THR63 3.8 24.4 1.0 C A:GLN57 3.9 28.1 1.0 CA A:HIS60 3.9 32.3 1.0 N A:HIS60 4.0 26.2 1.0 CG2 A:THR63 4.0 22.9 1.0 CB A:GLN57 4.0 31.9 1.0 C A:SER59 4.1 29.2 1.0 CG2 A:THR274 4.1 38.6 1.0 CG A:HIS60 4.2 53.5 1.0 NE2 A:HIS60 4.2 59.2 1.0 N A:LEU58 4.2 29.9 1.0 O A:SER59 4.3 27.8 1.0 O A:TRP53 4.3 24.4 1.0 O A:GLN57 4.4 31.1 1.0 N A:SER59 4.4 39.6 1.0 CB A:HIS60 4.5 41.5 1.0 CG A:GLN57 4.6 37.7 1.0 CA A:SER59 4.7 33.5 1.0 N A:GLN57 4.9 32.8 1.0 C A:LEU58 4.9 46.2 1.0

Iodine binding site 4 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I515 b:29.0 occ:0.22 N A:LEU225 3.7 35.9 1.0 CB A:LEU225 3.9 44.8 1.0 CA A:HIS222 4.0 33.5 1.0 CB A:ALA224 4.2 38.9 1.0 CA A:LEU225 4.3 39.7 1.0 ND1 A:HIS222 4.3 42.0 1.0 CB A:HIS222 4.3 35.3 1.0 C A:HIS222 4.4 36.8 1.0 O A:SER221 4.4 42.7 1.0 CG A:HIS222 4.4 38.6 1.0 O A:HIS222 4.5 33.8 1.0 C A:ALA224 4.5 36.3 1.0 N A:ALA224 4.6 50.5 1.0 CA A:ALA224 4.7 38.6 1.0 CG A:LEU225 4.9 49.5 1.0 CD1 A:LEU225 5.0 49.6 1.0

Iodine binding site 5 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I516 b:23.4 occ:0.16 O A:LEU173 2.5 22.1 1.0 O A:LEU350 2.7 29.2 1.0 N A:ALA177 2.9 24.4 1.0 CB A:ALA177 3.0 19.1 1.0 CA A:LEU174 3.3 22.0 1.0 C A:LEU174 3.3 25.4 1.0 CD A:PRO176 3.4 17.1 1.0 CE2 A:PHE352 3.4 22.5 1.0 O A:LEU174 3.4 24.9 1.0 CD2 A:PHE352 3.5 20.2 1.0 C A:LEU173 3.5 25.5 1.0 CA A:ALA177 3.5 25.1 1.0 CB A:LEU350 3.6 21.2 1.0 N A:PRO176 3.7 22.9 1.0 C A:LEU350 3.8 27.1 1.0 N A:LEU174 3.8 22.8 1.0 C A:PRO176 3.9 22.2 1.0 CB A:PRO176 3.9 17.8 1.0 N A:ILE175 3.9 14.6 1.0 CG A:PRO176 4.0 16.1 1.0 CA A:PRO176 4.0 18.1 1.0 CA A:LEU350 4.2 25.5 1.0 C A:ILE175 4.4 22.1 1.0 CB A:LEU174 4.6 16.0 1.0 CZ A:PHE352 4.6 28.0 1.0 CD2 A:LEU174 4.6 18.2 1.0 CG A:LEU350 4.7 22.9 1.0 CG A:PHE352 4.7 21.5 1.0 CD1 A:LEU350 4.7 19.5 1.0 CA A:ILE175 4.8 22.1 1.0 C A:ALA177 4.8 26.1 1.0 CA A:LEU173 4.9 22.4 1.0 N A:ALA178 4.9 19.6 1.0 N A:ASN351 4.9 27.1 1.0 O A:PRO176 5.0 22.6 1.0 N A:PHE352 5.0 24.6 1.0

Iodine binding site 6 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I517 b:0.4 occ:0.65 NE2 A:HIS223 2.2 77.4 1.0 CE1 A:HIS223 2.7 78.3 1.0 CD2 A:HIS223 3.5 72.4 1.0 ND2 A:ASN91 3.8 87.4 1.0 ND1 A:HIS223 4.0 73.7 1.0 CG A:HIS223 4.4 66.4 1.0 OE2 A:GLU227 4.4 78.4 1.0 CD A:GLU227 4.7 74.5 1.0 CG A:ASN91 4.9 90.7 1.0 CA A:ASN91 4.9 79.1 1.0

Iodine binding site 7 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I518 b:0.3 occ:0.54 NE2 A:HIS246 2.6 89.9 1.0 OD1 A:ASP30 2.6 83.8 1.0 OD2 A:ASP30 3.0 78.0 1.0 CG A:ASP30 3.1 77.3 1.0 CD2 A:HIS246 3.3 88.8 1.0 CE1 A:HIS246 3.7 89.1 1.0 O A:ALA26 4.4 69.9 1.0 CG A:HIS246 4.5 89.9 1.0 O A:SER247 4.6 95.9 1.0 CB A:ASP30 4.6 69.2 1.0 ND1 A:HIS246 4.7 89.7 1.0 CB A:ALA26 4.8 79.8 1.0

Iodine binding site 8 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I519 b:61.5 occ:0.44 MN A:MN521 2.2 27.1 1.0 NZ A:LYS314 3.1 28.4 1.0 CE A:LYS314 3.9 26.4 1.0 CG2 A:VAL236 4.0 39.8 1.0 CG1 A:VAL236 4.0 28.9 1.0 OG1 A:THR239 4.1 69.3 1.0 CA A:VAL236 4.2 45.7 1.0 I A:IOD520 4.3 54.9 0.3 CB A:VAL236 4.3 38.6 1.0 CG2 A:THR239 4.3 59.9 1.0 CB A:THR239 4.3 58.5 1.0 CD A:LYS314 4.7 32.1 1.0 CG A:LYS312 4.7 29.2 1.0 CB A:LYS312 4.7 22.6 1.0 CD A:LYS312 4.8 34.2 1.0 O A:VAL236 5.0 33.4 1.0

Iodine binding site 9 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:I520 b:54.9 occ:0.28 MN A:MN521 2.2 27.1 1.0 CD A:LYS312 3.6 34.2 1.0 NZ A:LYS312 3.7 47.7 1.0 CE A:LYS312 4.1 38.9 1.0 I A:IOD519 4.3 61.5 0.4 CG A:LYS312 4.8 29.2 1.0

Iodine binding site 10 out of 11 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ B:I507 b:80.1 occ:0.37 O B:HOH612 3.3 28.7 1.0 OE1 B:GLN151 3.4 44.2 1.0 O B:VAL150 3.8 28.3 1.0 CB B:GLN151 3.9 21.5 1.0 CG1 B:VAL150 4.1 22.5 1.0 CD B:GLN151 4.3 42.7 1.0 O B:HOH605 4.4 26.1 1.0 C B:VAL150 4.5 33.4 1.0 CG B:GLN151 4.5 33.0 1.0 ND2 B:ASN377 4.6 14.1 1.0 CA B:GLN151 4.8 32.4 1.0 CB B:ASN377 4.9 14.2 1.0 N B:GLN151 4.9 32.9 1.0

A.B.Waight, B.P.Pedersen, A.Schlessinger, M.Bonomi, B.H.Chau, Z.Roe-Zurz, A.J.Risenmay, A.Sali, R.M.Stroud. Structural Basis For Alternating Access of A Eukaryotic Calcium/Proton Exchanger. Nature V. 499 107 2013.
ISSN: ISSN 0028-0836
PubMed: 23685453
DOI: 10.1038/NATURE12233