Chlorine in PDB 8ixu: Rat Transcobalamin in Complex with Cobalamin

The structure of Rat Transcobalamin in Complex with Cobalamin, PDB code: 8ixu was solved by M.Bokhove, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.31, 54.53, 142.87, 90, 90, 90
R / Rfree (%)	16 / 17.1

The structure of Rat Transcobalamin in Complex with Cobalamin also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Cobalt	(Co)	1 atom

The binding sites of Chlorine atom in the Rat Transcobalamin in Complex with Cobalamin (pdb code 8ixu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Rat Transcobalamin in Complex with Cobalamin, PDB code: 8ixu:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Rat Transcobalamin in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rat Transcobalamin in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:36.9 occ:1.00 H A:SER348 2.4 27.2 1.0 HH21 A:ARG361 2.6 40.1 1.0 HE A:ARG361 2.7 37.2 1.0 HA A:VAL347 2.9 21.0 1.0 HD12 A:LEU365 3.0 32.8 1.0 N A:SER348 3.2 22.7 1.0 HB2 A:SER348 3.4 36.8 1.0 HB A:VAL347 3.4 22.4 1.0 NH2 A:ARG361 3.4 33.4 1.0 NE A:ARG361 3.5 31.0 1.0 CA A:VAL347 3.7 17.5 1.0 HD13 A:LEU365 3.7 32.8 1.0 CD1 A:LEU365 3.7 27.3 1.0 HG11 A:VAL347 3.9 23.4 1.0 CZ A:ARG361 3.9 35.7 1.0 C A:VAL347 3.9 19.5 1.0 CB A:VAL347 4.0 18.6 1.0 O A:HOH737 4.0 26.1 1.0 HD11 A:LEU365 4.1 32.8 1.0 HH22 A:ARG361 4.1 40.1 1.0 CB A:SER348 4.1 30.7 1.0 O A:SER348 4.1 30.8 1.0 CA A:SER348 4.2 28.7 1.0 HG2 A:ARG361 4.2 27.7 1.0 HG3 A:ARG361 4.3 27.7 1.0 HG A:SER348 4.3 47.6 1.0 HD22 A:LEU365 4.5 38.6 1.0 CG1 A:VAL347 4.5 19.5 1.0 CG A:ARG361 4.6 23.1 1.0 O A:THR346 4.6 19.3 1.0 CD A:ARG361 4.6 27.4 1.0 C A:SER348 4.7 25.8 1.0 OG A:SER348 4.7 39.6 1.0 HB3 A:SER348 4.9 36.8 1.0 N A:VAL347 4.9 18.2 1.0 CG A:LEU365 5.0 23.0 1.0

Chlorine binding site 2 out of 4 in the Rat Transcobalamin in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rat Transcobalamin in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:19.9 occ:1.00 HG A:SER383 2.3 29.3 0.5 HG1 A:THR369 2.3 25.5 1.0 HG A:SER383 2.4 22.4 0.5 H A:GLY386 2.4 23.3 1.0 HA A:TYR370 2.9 20.3 1.0 OG A:SER383 3.1 24.4 0.5 OG1 A:THR369 3.2 21.2 1.0 OG A:SER383 3.2 18.6 0.5 N A:GLY386 3.2 19.4 1.0 HB3 A:SER383 3.3 22.8 0.5 HB2 A:SER383 3.4 22.5 0.5 HA2 A:GLY386 3.4 28.2 1.0 O A:HOH880 3.4 25.5 1.0 HB A:THR369 3.4 25.4 1.0 H A:LEU385 3.5 21.4 1.0 CA A:TYR370 3.6 16.9 1.0 N A:TYR370 3.7 16.7 1.0 C A:THR369 3.7 17.1 1.0 CB A:SER383 3.7 19.0 0.5 N A:LEU385 3.7 17.8 1.0 HA A:VAL384 3.7 19.2 1.0 CB A:SER383 3.8 18.8 0.5 C A:TYR370 3.8 16.9 1.0 O A:THR369 3.8 16.3 1.0 CB A:THR369 3.8 21.2 1.0 CA A:GLY386 3.8 23.5 1.0 C A:SER383 3.9 13.5 0.5 C A:SER383 3.9 19.1 0.5 N A:VAL384 3.9 16.6 1.0 C A:VAL384 4.0 17.7 1.0 O A:SER383 4.0 21.3 0.5 H A:GLY371 4.0 19.7 1.0 N A:GLY371 4.0 16.4 1.0 CA A:VAL384 4.1 16.0 1.0 O A:SER383 4.1 13.5 0.5 H A:TYR370 4.1 20.1 1.0 H A:VAL384 4.2 20.0 1.0 C A:LEU385 4.3 19.6 1.0 O A:TYR370 4.3 19.2 1.0 HA A:LEU385 4.3 23.4 1.0 CA A:LEU385 4.4 19.4 1.0 CA A:THR369 4.4 18.7 1.0 CA A:SER383 4.4 22.7 0.5 CA A:SER383 4.5 14.0 0.5 H A:LYS387 4.5 23.8 1.0 HB2 A:SER383 4.5 22.8 0.5 HA3 A:GLY386 4.6 28.2 1.0 HB3 A:SER383 4.6 22.5 0.5 C A:GLY386 4.6 22.3 1.0 O A:VAL384 4.6 16.8 1.0 HA3 A:GLY371 4.7 20.0 1.0 O A:HOH945 4.8 36.0 1.0 N A:LYS387 4.8 19.8 1.0 HA A:SER383 4.9 27.2 0.5 CB A:TYR370 4.9 16.4 1.0 CA A:GLY371 5.0 16.6 1.0

Chlorine binding site 3 out of 4 in the Rat Transcobalamin in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rat Transcobalamin in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:26.7 occ:1.00 H A:LYS25 2.4 28.8 1.0 N A:LYS25 3.2 24.0 1.0 HA A:PRO24 3.3 27.9 1.0 HB2 A:PRO24 3.3 31.4 1.0 HG3 A:LYS25 3.5 40.4 1.0 HB3 A:PRO24 3.7 31.4 1.0 CB A:PRO24 3.8 26.2 1.0 CA A:PRO24 3.8 23.2 1.0 HA A:LYS25 3.8 29.7 1.0 C A:PRO24 4.0 21.4 1.0 CA A:LYS25 4.1 24.7 1.0 CG A:LYS25 4.3 33.7 1.0 HG2 A:LYS25 4.5 40.4 1.0 CB A:LYS25 4.8 28.5 1.0 O A:HOH618 4.8 31.3 1.0

Chlorine binding site 4 out of 4 in the Rat Transcobalamin in Complex with Cobalamin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rat Transcobalamin in Complex with Cobalamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:25.9 occ:1.00 HH21 A:ARG345 2.3 28.6 1.0 HE A:ARG345 2.7 26.1 1.0 HE2 A:TYR343 3.1 22.3 1.0 O A:HOH650 3.1 24.5 1.0 NH2 A:ARG345 3.1 23.8 1.0 HA3 A:GLY366 3.2 26.0 1.0 NE A:ARG345 3.4 21.7 1.0 H A:GLU367 3.7 28.5 1.0 CZ A:ARG345 3.8 21.1 1.0 HH22 A:ARG345 3.8 28.6 1.0 CE2 A:TYR343 3.8 18.6 1.0 CA A:GLY366 4.2 21.7 1.0 O A:HOH633 4.2 30.9 1.0 OH A:TYR343 4.3 19.6 1.0 N A:GLU367 4.4 23.8 1.0 CZ A:TYR343 4.5 18.7 1.0 HB2 A:ARG345 4.6 21.7 1.0 H A:PHE368 4.6 26.0 1.0 HD2 A:ARG345 4.6 24.2 1.0 HA2 A:GLY366 4.6 26.0 1.0 CD A:ARG345 4.6 20.2 1.0 HD2 A:TYR343 4.7 21.1 1.0 C A:GLY366 4.7 26.7 1.0 CD2 A:TYR343 4.7 17.6 1.0 N A:GLY366 4.9 20.4 1.0 O A:LEU365 5.0 24.5 1.0 HB2 A:PHE368 5.0 23.5 1.0 HH A:TYR343 5.0 23.6 1.0

M.Bokhove, T.Kawamura, H.Okumura, S.Goto, Y.Kawano, S.Werner, F.Jarczowski, V.Klimyuk, A.Saito, T.Kumasaka. The Structure of the Rat Vitamin B 12 Transporter Tc and Its Complex with Glutathionylcobalamin. J.Biol.Chem. V. 300 07289 2024.
ISSN: ESSN 1083-351X
PubMed: 38636663
DOI: 10.1016/J.JBC.2024.107289