Manganese 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:

Iodine	(I)	11 atoms
Calcium	(Ca)	9 atoms

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

Manganese binding site 1 out of 3 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn511 b:14.2 occ:0.75 O A:GLU375 2.1 25.8 1.0 OE2 A:GLU380 2.2 38.5 1.0 O A:HOH614 2.2 16.2 1.0 O A:HOH627 2.2 3.4 1.0 OD1 A:ASP373 2.2 38.6 1.0 OD2 A:ASP373 2.2 41.6 1.0 OE1 A:GLU380 2.3 27.9 1.0 CG A:ASP373 2.5 36.3 1.0 CD A:GLU380 2.5 26.5 1.0 C A:GLU375 3.2 29.7 1.0 CA A:SER376 3.9 17.5 1.0 CB A:ASP373 3.9 33.3 1.0 N A:SER376 4.0 17.9 1.0 O A:LEU370 4.0 16.7 1.0 CG A:GLU380 4.1 20.4 1.0 N A:GLU375 4.3 18.6 1.0 CA A:GLU375 4.3 28.4 1.0 CD2 A:LEU370 4.5 15.9 1.0 CB A:SER376 4.7 20.1 1.0 CA A:LEU370 4.8 24.2 1.0 C A:LEU370 4.8 29.2 1.0 C A:SER376 4.9 24.7 1.0 CB A:GLU380 5.0 16.9 1.0 CB A:GLU375 5.0 19.2 1.0

Manganese binding site 2 out of 3 in the VCX1 Calcium/Proton Exchanger


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn521 b:27.1 occ:1.00 I A:IOD519 2.2 61.5 0.4 I A:IOD520 2.2 54.9 0.3 CD A:LYS312 3.9 34.2 1.0 NZ A:LYS314 4.3 28.4 1.0 CG A:LYS312 4.4 29.2 1.0 CB A:LYS312 4.5 22.6 1.0 CE A:LYS312 4.6 38.9 1.0 CE A:LYS314 4.6 26.4 1.0 CG2 A:THR239 4.8 59.9 1.0 NZ A:LYS312 4.8 47.7 1.0 O A:LYS312 4.9 32.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of VCX1 Calcium/Proton Exchanger within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn506 b:18.6 occ:0.82 O B:GLU375 2.1 19.3 1.0 OE2 B:GLU380 2.2 28.8 1.0 OD1 B:ASP373 2.2 26.0 1.0 O B:HOH614 2.2 27.7 1.0 OD2 B:ASP373 2.2 21.4 1.0 O B:HOH615 2.2 8.8 1.0 CG B:ASP373 2.5 24.5 1.0 CD B:GLU380 3.0 22.6 1.0 OE1 B:GLU380 3.1 24.8 1.0 C B:GLU375 3.2 25.3 1.0 CB B:ASP373 3.9 16.7 1.0 N B:SER376 4.0 16.3 1.0 O B:LEU370 4.0 17.0 1.0 CA B:SER376 4.0 18.6 1.0 N B:GLU375 4.2 21.2 1.0 CA B:GLU375 4.2 19.7 1.0 O B:HOH605 4.3 26.1 1.0 CG B:GLU380 4.4 16.2 1.0 O B:HOH612 4.5 28.7 1.0 CD2 B:LEU370 4.7 23.3 1.0 CB B:GLU375 4.8 27.6 1.0 C B:LEU370 4.9 23.1 1.0 CA B:LEU370 4.9 24.9 1.0 C B:SER376 4.9 21.3 1.0 C B:ASP373 4.9 25.9 1.0 CA B:ASP373 5.0 26.4 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