Chlorine in PDB 6mpx: Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers

The structure of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers, PDB code: 6mpx was solved by R.Bauer, S.P.Boudko, B.G.Hudson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.89 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.160, 121.160, 106.020, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.7

The binding sites of Chlorine atom in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers (pdb code 6mpx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers, PDB code: 6mpx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:27.1 occ:1.00 ND2 A:ASN66 3.3 27.0 1.0 OH A:TYR636 3.4 29.4 1.0 O A:HOH1034 3.6 31.9 1.0 CE1 A:TYR636 3.7 32.6 1.0 C17 A:P6G717 3.7 57.9 1.0 CE1 A:PHE64 3.9 30.6 1.0 CZ A:TYR636 4.0 31.5 1.0 CB A:ASN66 4.3 23.7 1.0 CG A:ASN66 4.3 30.2 1.0 C18 A:P6G717 4.6 56.2 1.0 CZ A:PHE64 4.6 29.2 1.0 ND2 A:ASN72 4.6 27.5 1.0 O16 A:P6G717 4.8 58.8 1.0 CD1 A:TYR636 4.9 32.4 1.0 CD1 A:PHE64 4.9 30.6 1.0

Chlorine binding site 2 out of 6 in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl702 b:23.9 occ:1.00 O A:HOH872 3.1 24.6 1.0 N A:ASP525 3.3 20.2 1.0 N A:ARG523 3.4 25.8 1.0 C A:ARG523 3.5 24.3 1.0 CA A:GLY625 3.6 26.0 1.0 O A:ARG523 3.6 24.9 1.0 CA A:ALA521 3.7 24.6 1.0 N A:ASN524 3.7 22.2 1.0 C A:ALA521 3.8 27.9 1.0 N A:SER522 3.9 23.3 1.0 CA A:ARG523 4.0 20.1 1.0 CB A:ASP525 4.0 18.7 1.0 N A:GLY625 4.1 24.4 1.0 CA A:ASP525 4.1 21.8 1.0 CA A:ASN524 4.1 19.2 1.0 C A:ASN524 4.2 20.8 1.0 O A:ASP525 4.2 19.5 1.0 CE A:MET507 4.3 20.8 1.0 O A:ALA521 4.4 26.0 1.0 C A:GLY625 4.4 29.3 1.0 C A:SER522 4.4 29.1 1.0 C A:ASP525 4.5 23.6 1.0 N A:ALA521 4.6 22.1 1.0 CB A:ARG523 4.6 20.6 1.0 O A:HOH1032 4.7 24.2 1.0 CG A:ASP525 4.7 23.9 1.0 CB A:ALA521 4.7 22.2 1.0 CA A:SER522 4.7 24.6 1.0 OD2 A:ASP525 4.7 24.6 1.0 CG A:MET507 4.7 21.0 1.0 O A:HOH920 4.8 23.6 1.0 N A:ARG626 4.9 27.1 1.0 SD A:MET507 4.9 22.2 1.0 O A:GLY625 5.0 27.7 1.0

Chlorine binding site 3 out of 6 in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl703 b:23.9 occ:1.00 OH A:TYR412 3.1 21.9 1.0 O A:HOH1043 3.3 28.0 1.0 ND2 A:ASN513 3.3 23.4 1.0 CE1 A:TYR412 3.6 22.4 1.0 CZ A:TYR412 3.8 23.2 1.0 CE1 A:PHE511 3.9 27.2 1.0 CB A:ASN513 3.9 23.9 1.0 CG A:ASN513 4.1 29.2 1.0 ND2 A:ASN519 4.2 30.7 1.0 CD1 A:PHE511 4.7 25.6 1.0 CZ A:PHE511 4.7 28.2 1.0 CD1 A:TYR412 4.9 27.1 1.0

Chlorine binding site 4 out of 6 in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl704 b:23.8 occ:1.00 OH A:TYR288 3.0 30.4 1.0 OH A:TYR189 3.2 24.6 1.0 ND2 A:ASN290 3.3 26.2 1.0 CE1 A:TYR288 3.7 24.8 1.0 CZ A:TYR189 3.8 28.5 1.0 CE2 A:TYR296 3.8 32.9 1.0 CZ A:TYR288 3.8 25.4 1.0 CE1 A:TYR189 4.0 23.6 1.0 CD2 A:TYR296 4.0 27.5 1.0 CB A:ASN290 4.1 25.0 1.0 CG A:ASN290 4.2 26.6 1.0 NH1 A:ARG300 4.4 20.6 1.0 CE2 A:TYR189 4.7 25.8 1.0 O A:HOH1170 4.8 48.7 1.0 CD1 A:TYR288 4.9 23.2 1.0 CZ A:TYR296 4.9 34.2 1.0

Chlorine binding site 5 out of 6 in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:25.7 occ:1.00 O A:HOH935 3.1 36.4 1.0 O A:HOH917 3.1 22.4 1.0 N A:ASP78 3.3 21.9 1.0 N A:ARG76 3.5 27.2 1.0 N A:ASN77 3.6 28.5 1.0 CA A:ALA74 3.6 24.9 1.0 C A:ARG76 3.6 29.6 1.0 C A:ALA74 3.6 26.4 1.0 N A:SER75 3.7 26.5 1.0 CA A:GLY178 3.8 23.6 1.0 O A:ARG76 3.9 29.9 1.0 CA A:ASN77 4.0 28.2 1.0 CB A:ASP78 4.1 21.8 1.0 CA A:ARG76 4.1 31.0 1.0 C A:ASN77 4.1 28.1 1.0 CA A:ASP78 4.2 21.7 1.0 O A:ALA74 4.2 26.0 1.0 CE A:MET60 4.2 22.3 1.0 O A:ASP78 4.4 23.4 1.0 N A:GLY178 4.4 24.2 1.0 N A:ALA74 4.4 26.1 1.0 O A:HOH1009 4.5 22.6 1.0 C A:SER75 4.5 26.7 1.0 C A:GLY178 4.5 28.9 1.0 O A:HOH926 4.6 26.2 1.0 CA A:SER75 4.6 26.7 1.0 CB A:ALA74 4.6 25.7 1.0 CG A:ASP78 4.7 21.7 1.0 C A:ASP78 4.7 23.2 1.0 CB A:ARG76 4.7 26.7 1.0 OD2 A:ASP78 4.8 24.4 1.0 CG A:MET60 4.8 25.8 1.0 SD A:MET60 4.9 23.9 1.0

Chlorine binding site 6 out of 6 in the Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Twelve Chloride Ions Induce Formation and Stabilize the NC1 Hexamer of Collagen IV Assembled From Transition State Trimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl706 b:27.2 occ:1.00 O A:HOH873 3.0 22.5 1.0 O A:HOH1001 3.1 27.3 1.0 N A:ARG300 3.3 23.8 1.0 N A:ASP302 3.4 21.9 1.0 C A:ARG300 3.5 28.7 1.0 CA A:ALA298 3.5 24.0 1.0 N A:ASN301 3.6 22.5 1.0 C A:ALA298 3.6 27.7 1.0 N A:SER299 3.6 24.6 1.0 O A:ARG300 3.7 26.6 1.0 CA A:ARG300 3.8 27.8 1.0 O A:HOH1069 4.0 22.4 1.0 CB A:ASP302 4.1 19.1 1.0 N A:ALA298 4.2 23.1 1.0 CA A:ASN301 4.2 26.1 1.0 CA A:ASP302 4.2 20.5 1.0 O A:ALA298 4.2 26.1 1.0 C A:ASN301 4.3 23.3 1.0 CE A:MET284 4.3 20.5 1.0 C A:SER299 4.3 22.0 1.0 CB A:ARG300 4.4 27.9 1.0 O A:ASP302 4.4 20.9 1.0 N A:GLY401 4.4 27.8 1.0 O A:HOH888 4.4 22.3 1.0 CA A:SER299 4.5 24.5 1.0 C A:ASP302 4.7 20.3 1.0 CB A:ALA298 4.7 24.0 1.0 CG A:ASP302 4.7 25.7 1.0 OD2 A:ASP302 4.7 25.8 1.0 CG A:MET284 4.7 22.8 1.0 SD A:MET284 4.9 24.5 1.0 CA A:GLY401 5.0 27.5 1.0

V.Pedchenko, R.Bauer, E.N.Pokidysheva, A.Al-Shaer, N.R.Forde, A.L.Fidler, B.G.Hudson, S.P.Boudko. A Chloride Ring Is An Ancient Evolutionary Innovation Mediating the Assembly of the Collagen IV Scaffold of Basement Membranes. J.Biol.Chem. V. 294 7968 2019.
ISSN: ESSN 1083-351X
PubMed: 30923125
DOI: 10.1074/JBC.RA119.007426