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Iodine in PDB 4k1c: VCX1 Calcium/Proton Exchanger

Protein crystallography data

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

Other elements in 4k1c:

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

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

Iodine Binding Sites:

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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

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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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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 4k1c

Go back to Iodine Binding Sites List in 4k1c
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

Reference:

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
Page generated: Sun Dec 13 19:34:09 2020

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