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Chlorine in PDB 6wku: Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain

Protein crystallography data

The structure of Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain, PDB code: 6wku was solved by 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) 45.40 / 1.76
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.42, 128.42, 104.71, 90, 90, 90
R / Rfree (%) 13.9 / 16.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain (pdb code 6wku). 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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain, PDB code: 6wku:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6wku

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Chlorine binding site 1 out of 6 in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain


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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:19.2
occ:1.00
 O A:HOH893 3.1 20.9 1.0
N A:ASP78 3.3 15.9 1.0
N A:ARG76 3.4 15.5 1.0
C A:ARG76 3.5 17.6 1.0
O A:ARG76 3.6 17.5 1.0
NH2 A:ARG179 3.6 18.4 1.0
C A:ALA74 3.6 20.4 1.0
CA A:ALA74 3.7 16.0 1.0
CA A:GLY178 3.7 15.6 1.0
N A:ASN77 3.8 19.4 1.0
N A:SER75 3.8 18.0 1.0
CA A:ARG76 4.0 17.8 1.0
O A:ALA74 4.1 20.2 1.0
CB A:ASP78 4.1 14.6 1.0
CA A:ASN77 4.1 19.4 1.0
CA A:ASP78 4.1 16.8 1.0
O A:ASP78 4.1 17.6 1.0
C A:ASN77 4.2 17.5 1.0
N A:GLY178 4.2 15.5 1.0
CE A:MET60 4.3 17.1 1.0
CZ A:ARG179 4.4 21.9 1.0
C A:SER75 4.4 16.1 1.0
C A:ASP78 4.5 18.2 1.0
C A:GLY178 4.5 18.3 1.0
O A:HOH1046 4.5 19.2 1.0
N A:ALA74 4.6 15.9 1.0
CA A:SER75 4.6 17.4 0.2
CA A:SER75 4.6 17.1 0.8
CB A:ARG76 4.7 16.0 1.0
CG A:ASP78 4.7 20.4 1.0
OD2 A:ASP78 4.7 21.0 1.0
CB A:ALA74 4.7 16.9 1.0
NH1 A:ARG179 4.8 18.9 1.0
O A:HOH978 4.9 18.3 1.0

Chlorine binding site 2 out of 6 in 6wku

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Chlorine binding site 2 out of 6 in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain


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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:19.6
occ:1.00
 O A:HOH955 3.0 22.1 1.0
O A:HOH975 3.1 18.2 1.0
N A:ARG300 3.2 20.1 1.0
N A:ASP302 3.4 16.7 1.0
C A:ARG300 3.4 20.8 1.0
N A:ASN301 3.5 18.8 1.0
CD2 A:LEU284 3.7 25.1 1.0
CA A:ARG300 3.7 19.4 1.0
CD A:ARG401 3.7 17.5 1.0
CG A:ARG401 3.7 21.2 1.0
O A:ARG300 3.7 21.3 1.0
N A:GLN299 3.8 18.7 1.0
CA A:ALA298 3.9 20.3 1.0
CB A:ASP302 4.0 19.8 1.0
O A:HOH1108 4.0 19.5 1.0
C A:ALA298 4.1 22.4 1.0
CB A:ARG300 4.2 22.8 1.0
CA A:ASN301 4.2 18.5 1.0
CA A:ASP302 4.2 17.1 1.0
C A:ASN301 4.2 18.2 1.0
C A:GLN299 4.3 21.7 1.0
N A:ALA298 4.4 18.9 1.0
O A:HOH967 4.4 19.4 1.0
O A:ASP302 4.5 18.9 1.0
CD1 A:LEU284 4.5 20.8 1.0
CG A:ASP302 4.5 21.9 1.0
OD2 A:ASP302 4.6 21.1 1.0
CA A:GLN299 4.7 25.3 1.0
CG A:LEU284 4.7 24.5 1.0
C A:ASP302 4.7 18.6 1.0
O A:ALA298 4.9 21.9 1.0
CB A:ARG401 5.0 20.6 1.0
N A:ARG401 5.0 17.0 1.0

Chlorine binding site 3 out of 6 in 6wku

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Chlorine binding site 3 out of 6 in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain


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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:19.6
occ:1.00
 O A:HOH880 3.1 20.0 1.0
N A:ASP527 3.3 15.9 1.0
N A:ARG525 3.5 18.5 1.0
C A:ARG525 3.6 21.2 1.0
CA A:ALA523 3.6 19.0 1.0
C A:ALA523 3.7 18.9 1.0
CA A:GLY627 3.7 16.8 1.0
O A:ARG525 3.7 23.1 1.0
N A:SER524 3.8 17.6 1.0
N A:ASN526 3.8 18.6 1.0
CB A:ASP527 4.1 16.5 1.0
CA A:ARG525 4.1 16.6 1.0
CA A:ASP527 4.2 16.4 1.0
O A:ALA523 4.2 20.4 1.0
CA A:ASN526 4.2 18.0 1.0
CE A:MET509 4.2 18.8 1.0
N A:GLY627 4.2 17.5 1.0
C A:ASN526 4.2 20.7 1.0
O A:ASP527 4.3 17.8 1.0
C A:GLY627 4.4 20.3 1.0
N A:ALA523 4.5 17.1 1.0
C A:SER524 4.5 19.0 1.0
O A:HOH1009 4.5 19.1 1.0
C A:ASP527 4.6 16.9 1.0
CA A:SER524 4.7 18.2 1.0
CG A:ASP527 4.7 20.2 1.0
CB A:ARG525 4.7 17.1 1.0
OD2 A:ASP527 4.7 24.8 1.0
CB A:ALA523 4.7 20.3 1.0
O A:HOH940 4.8 19.0 1.0
CG A:MET509 4.8 15.8 1.0
SD A:MET509 4.9 18.1 1.0
N A:ARG628 4.9 19.1 1.0
O A:GLY627 4.9 21.6 1.0

Chlorine binding site 4 out of 6 in 6wku

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Chlorine binding site 4 out of 6 in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain


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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:19.3
occ:1.00
 N A:SER186 3.2 16.5 1.0
CB A:SER186 3.5 15.3 0.3
C2 A:PG4756 3.5 54.6 1.0
CB A:SER186 3.6 17.2 0.7
C1 A:PG4756 3.7 56.7 1.0
CA A:SER186 4.0 17.1 0.3
OG A:SER186 4.0 15.3 0.7
CA A:SER186 4.0 17.0 0.7
CB A:TYR185 4.1 16.3 1.0
CD1 A:TYR185 4.1 20.4 1.0
O1 A:PG4756 4.1 59.0 1.0
CA A:TYR185 4.2 14.3 1.0
C A:TYR185 4.2 17.0 1.0
O2 A:PG4756 4.5 51.9 1.0
CG A:TYR185 4.6 16.3 1.0
OG A:SER186 4.8 15.3 0.3
N A:ASN187 4.9 17.1 1.0
C A:SER186 4.9 18.4 1.0

Chlorine binding site 5 out of 6 in 6wku

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Chlorine binding site 5 out of 6 in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain


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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl705

b:19.7
occ:1.00
 N A:ALA409 3.2 18.8 1.0
C1 A:PGE709 3.6 27.8 1.0
CD1 A:PHE408 3.6 15.5 1.0
CB A:ALA409 3.6 19.3 1.0
C2 A:PGE709 3.8 25.7 1.0
CB A:PHE408 3.9 16.3 1.0
CA A:ALA409 4.0 18.6 1.0
CA A:PHE408 4.0 17.5 1.0
C A:PHE408 4.1 17.8 1.0
CG A:PHE408 4.2 17.9 1.0
CE1 A:PHE408 4.7 22.7 1.0
N A:ASN410 4.8 17.5 1.0
C A:ALA409 4.9 18.5 1.0
O1 A:PGE709 4.9 29.2 1.0
O2 A:PGE709 4.9 30.8 1.0

Chlorine binding site 6 out of 6 in 6wku

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Chlorine binding site 6 out of 6 in the Twelve Chloride Ions Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain


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 Drive Assembly of Human ALPHA345 Collagen IV NC1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:19.2
occ:1.00
 N A:ALA635 3.2 17.7 1.0
O A:HOH925 3.3 22.1 1.0
CD1 A:TYR634 3.8 17.1 1.0
CB A:ALA635 3.8 17.0 1.0
CA A:TYR634 3.8 17.5 1.0
C A:TYR634 4.0 16.6 1.0
CA A:ALA635 4.1 17.2 1.0
CB A:TYR634 4.2 15.0 1.0
CG A:TYR634 4.4 16.4 1.0
CE1 A:TYR634 4.7 16.4 1.0
O A:TYR633 4.8 20.4 1.0

Reference:

S.P.Boudko, R.Bauer, S.V.Chetyrkin, S.Ivanov, J.Smith, P.A.Voziyan, B.G.Hudson. Collagen IV Alpha 345 Dysfunction in Glomerular Basement Membrane Diseases. II. Crystal Structure of the Alpha 345 Hexamer. J.Biol.Chem. 00591 2021.
ISSN: ESSN 1083-351X
PubMed: 33775698
DOI: 10.1016/J.JBC.2021.100591
Page generated: Mon Jul 29 16:47:41 2024

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