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Calcium 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:

Iodine (I) 11 atoms
Manganese (Mn) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 9 in 4k1c

Go back to Calcium Binding Sites List in 4k1c
Calcium binding site 1 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:59.9
occ:1.00
 OE2 A:GLU302 2.4 69.4 1.0
O A:HOH616 2.4 42.7 1.0
O A:HOH620 2.4 45.1 1.0
O A:HOH613 2.4 58.3 1.0
OE1 A:GLU302 2.4 66.1 1.0
OG A:SER325 2.4 38.8 1.0
CD A:GLU302 2.7 65.1 1.0
CB A:SER325 3.3 26.2 1.0
CA A:SER325 4.1 23.4 1.0
CG A:GLU302 4.2 57.0 1.0
O A:GLY102 4.3 34.6 1.0
ND2 A:ASN103 4.4 45.5 1.0
O A:GLY298 4.5 34.7 1.0
OE2 A:GLU106 4.7 50.8 1.0
OD1 A:ASN299 4.8 39.9 1.0
OE1 A:GLU106 4.9 42.7 1.0

Calcium binding site 2 out of 9 in 4k1c

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Calcium binding site 2 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:35.5
occ:0.82
 O A:ASP373 2.3 21.3 1.0
OE2 A:GLU375 2.4 40.3 1.0
OE1 A:GLU375 2.4 44.2 1.0
O A:HOH612 2.4 27.8 1.0
CD A:GLU375 2.7 38.5 1.0
C A:ASP373 3.5 23.5 1.0
CG A:GLU375 4.2 28.3 1.0
CA A:ASP373 4.3 21.8 1.0
OD1 A:ASN155 4.5 41.9 1.0
N A:GLY374 4.5 23.9 1.0
CB A:ASP373 4.6 33.3 1.0
N A:GLU375 4.7 18.6 1.0
CA A:GLY374 4.7 25.4 1.0
OD1 A:ASP373 4.8 38.6 1.0
CB A:GLU375 5.0 19.2 1.0

Calcium binding site 3 out of 9 in 4k1c

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Calcium binding site 3 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:63.6
occ:0.83
 OE1 A:GLU231 2.4 73.5 1.0
OE1 A:GLN228 2.4 59.0 1.0
CD A:GLU231 3.2 69.2 1.0
OE2 A:GLU231 3.4 70.7 1.0
CD A:GLN228 3.6 55.0 1.0
NE2 A:GLN228 4.1 37.9 1.0
CG A:GLU231 4.5 58.7 1.0
CA A:GLN228 4.6 37.0 1.0
CG A:GLN228 4.8 50.9 1.0
CB A:GLN228 4.8 36.0 1.0
CB A:GLU231 4.9 50.1 1.0

Calcium binding site 4 out of 9 in 4k1c

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Calcium binding site 4 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:52.9
occ:1.00
 OE2 A:GLU230 2.4 58.7 1.0
OE1 A:GLU83 2.4 78.1 1.0
O A:HOH608 2.5 43.9 1.0
OD1 A:ASP234 2.5 45.2 1.0
OE2 A:GLU83 2.6 80.2 1.0
CD A:GLU83 2.8 76.3 1.0
OE1 A:GLU230 2.8 53.3 1.0
CD A:GLU230 2.9 54.5 1.0
CG A:ASP234 3.5 47.9 1.0
OD2 A:ASP234 3.8 49.7 1.0
O A:HOH624 4.0 45.8 1.0
CA A:CA510 4.1 52.7 1.0
O A:HOH623 4.2 39.8 1.0
CG A:GLU83 4.2 70.3 1.0
CG A:GLU230 4.4 52.4 1.0
O A:GLU230 4.6 44.1 1.0
CB A:ASP234 4.8 42.0 1.0
CB A:GLU83 5.0 60.6 1.0

Calcium binding site 5 out of 9 in 4k1c

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Calcium binding site 5 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca510

b:52.7
occ:1.00
 OE2 A:GLU83 2.2 80.2 1.0
OD2 A:ASP234 2.2 49.7 1.0
OE2 A:GLU230 2.3 58.7 1.0
CD A:GLU83 3.0 76.3 1.0
CG A:GLU83 3.2 70.3 1.0
CD A:GLU230 3.3 54.5 1.0
CG A:ASP234 3.4 47.9 1.0
OD2 A:ASP87 3.5 85.6 1.0
CG A:GLU230 3.6 52.4 1.0
OD1 A:ASP234 3.8 45.2 1.0
OD1 A:ASP87 4.0 90.3 1.0
CA A:CA509 4.1 52.9 1.0
OE1 A:GLU83 4.1 78.1 1.0
CG A:ASP87 4.2 86.3 1.0
OE1 A:GLU230 4.4 53.3 1.0
CB A:ASP234 4.6 42.0 1.0
CB A:GLU83 4.8 60.6 1.0
O A:GLU230 5.0 44.1 1.0

Calcium binding site 6 out of 9 in 4k1c

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Calcium binding site 6 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:34.2
occ:0.70
 O B:ASP373 2.3 24.2 1.0
OE1 B:GLU375 2.3 46.9 1.0
O B:HOH603 2.4 24.7 1.0
OE2 B:GLU375 2.4 43.5 1.0
CD B:GLU375 2.7 40.7 1.0
C B:ASP373 3.5 25.9 1.0
CG B:GLU375 4.2 32.6 1.0
CA B:ASP373 4.3 26.4 1.0
OD1 B:ASN155 4.5 38.6 1.0
N B:GLY374 4.5 27.0 1.0
N B:GLU375 4.6 21.2 1.0
CA B:GLY374 4.6 26.4 1.0
OD1 B:ASP373 4.7 26.0 1.0
CB B:ASP373 4.7 16.7 1.0
CB B:GLU375 4.9 27.6 1.0
C B:GLY374 5.0 25.5 1.0

Calcium binding site 7 out of 9 in 4k1c

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Calcium binding site 7 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:76.5
occ:0.91
 OE2 B:GLU302 2.3 65.3 1.0
OE1 B:GLU302 2.4 60.2 1.0
O B:HOH613 2.4 58.0 1.0
O B:HOH609 2.4 65.9 1.0
OG B:SER325 2.5 45.4 1.0
CD B:GLU302 2.7 63.3 1.0
O B:HOH630 2.7 70.6 1.0
CB B:SER325 3.3 29.5 1.0
O B:GLY102 4.0 50.4 1.0
CA B:SER325 4.1 27.7 1.0
CG B:GLU302 4.2 58.4 1.0
OD1 B:ASN103 4.2 51.4 1.0
ND2 B:ASN299 4.5 42.8 1.0
O B:GLY298 4.7 37.5 1.0
OE1 B:GLU106 4.7 60.4 1.0

Calcium binding site 8 out of 9 in 4k1c

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Calcium binding site 8 out of 9 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:53.8
occ:1.00
 OE2 B:GLU230 2.4 75.1 1.0
OE2 B:GLU83 2.4 68.0 1.0
OD1 B:ASP234 2.4 50.3 1.0
CD B:GLU83 2.4 68.2 1.0
OE1 B:GLU83 2.4 68.9 1.0
CG B:ASP234 3.3 53.5 1.0
CG B:GLU83 3.5 66.4 1.0
OD2 B:ASP234 3.5 55.7 1.0
CD B:GLU230 3.5 72.9 1.0
CG B:GLU230 4.0 59.1 1.0
CA B:CA505 4.2 64.0 1.0
O B:HOH627 4.3 47.5 1.0
OE1 B:GLU230 4.5 80.2 1.0
CB B:GLU83 4.5 70.1 1.0
O B:GLU230 4.7 39.8 1.0
CB B:ASP234 4.7 45.0 1.0
CA B:ASP234 5.0 43.6 1.0

Calcium binding site 9 out of 9 in 4k1c

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of VCX1 Calcium/Proton Exchanger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:64.0
occ:1.00
 OE1 B:GLU83 2.1 68.9 1.0
OE1 B:GLU230 2.3 80.2 1.0
OD2 B:ASP234 2.4 55.7 1.0
OE2 B:GLU230 2.4 75.1 1.0
CD B:GLU230 2.6 72.9 1.0
CD B:GLU83 3.2 68.2 1.0
CG B:ASP234 3.6 53.5 1.0
CG B:GLU83 4.0 66.4 1.0
CG B:GLU230 4.1 59.1 1.0
OD1 B:ASP234 4.2 50.3 1.0
OE2 B:GLU83 4.2 68.0 1.0
CA B:CA504 4.2 53.8 1.0
O B:GLU83 4.3 93.0 1.0
CB B:ASP234 4.7 45.0 1.0
CB B:ALA86 4.9 70.7 1.0
O B:GLU230 5.0 39.8 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 Jul 14 08:45:09 2024

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