Chlorine in PDB 8txn: Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer

Protein crystallography data

The structure of Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer, PDB code: 8txn was solved by S.P.Boudko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.69 / 1.75
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 139.12, 139.12, 103.381, 90, 90, 120
R / Rfree (%) 14.2 / 16.4

Other elements in 8txn:

The structure of Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer (pdb code 8txn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer, PDB code: 8txn:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8txn

Go back to Chlorine Binding Sites List in 8txn
Chlorine binding site 1 out of 4 in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3002

b:13.5
occ:1.00
 O A:HOH4260 3.1 13.0 1.0
O A:HOH4051 3.1 15.1 1.0
N A:ARG2076 3.3 13.0 1.0
C A:ARG2076 3.4 12.4 1.0
N A:ASP2078 3.4 10.9 1.0
N A:ASN2077 3.5 12.4 1.0
O A:ARG2076 3.6 14.5 1.0
CD2 A:LEU2060 3.7 20.8 1.0
C A:ALA2074 3.7 15.6 1.0
CA A:ALA2074 3.7 14.4 1.0
N A:SER2075 3.7 13.2 1.0
CA A:ARG2076 3.8 13.2 1.0
CB A:ALA2177 4.1 13.9 1.0
CA A:ASN2077 4.1 12.8 1.0
CB A:ASP2078 4.1 13.4 1.0
NH2 D:ARG1181 4.2 16.7 1.0
O A:ALA2074 4.2 15.9 1.0
C A:ASN2077 4.3 12.8 1.0
CA A:ASP2078 4.3 10.9 1.0
C A:SER2075 4.3 17.9 1.0
O A:HOH4315 4.3 15.2 1.0
N A:ALA2177 4.4 14.3 1.0
CB A:ARG2076 4.4 12.3 1.0
OD2 A:ASP2078 4.5 17.8 1.0
N A:ALA2074 4.5 14.3 1.0
O A:ASP2078 4.5 11.8 1.0
CG A:ASP2078 4.5 15.0 1.0
CA A:SER2075 4.6 15.6 1.0
CD1 A:LEU2060 4.8 17.1 1.0
CA A:ALA2177 4.8 14.1 1.0
O A:HOH4203 4.8 16.6 1.0
CB A:ALA2074 4.8 15.3 1.0
CG A:LEU2060 4.8 21.0 1.0
C A:ASP2078 4.8 11.4 1.0

Chlorine binding site 2 out of 4 in 8txn

Go back to Chlorine Binding Sites List in 8txn
Chlorine binding site 2 out of 4 in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3003

b:20.0
occ:1.00
 O A:HOH4053 3.0 20.5 1.0
O A:HOH4150 3.1 21.6 1.0
N A:ARG76 3.2 14.8 1.0
N A:ASP78 3.3 14.6 1.0
C A:ARG76 3.4 21.5 1.0
O A:ARG76 3.6 21.9 1.0
N A:ASN77 3.6 16.5 1.0
N A:SER75 3.7 19.8 1.0
CA A:ARG76 3.7 15.7 1.0
CA A:ALA74 3.7 18.1 1.0
CD2 A:LEU60 3.8 20.9 1.0
C A:ALA74 3.8 21.7 1.0
CB A:ASP78 3.9 12.8 1.0
O A:HOH4316 4.0 17.9 1.0
CA A:ASP78 4.2 13.6 1.0
CB A:ARG76 4.2 17.2 1.0
CA A:ASN77 4.2 19.4 0.6
OD2 A:ASP78 4.2 17.5 1.0
CA A:ASN77 4.2 19.4 0.4
C A:ASN77 4.2 16.3 1.0
CG A:ASP78 4.2 15.8 1.0
CB A:ALA177 4.3 22.3 1.0
C A:SER75 4.3 21.7 1.0
N A:ALA74 4.4 15.6 1.0
O A:ASP78 4.5 14.0 1.0
O A:ALA74 4.5 19.2 1.0
CA A:SER75 4.5 18.6 1.0
N A:ALA177 4.6 19.1 1.0
O A:HOH4246 4.7 32.8 1.0
CD1 A:LEU60 4.7 20.3 1.0
C A:ASP78 4.8 13.2 1.0
CB A:ALA74 4.9 20.7 1.0
CG A:LEU60 4.9 19.7 1.0
O A:HOH4239 4.9 18.8 1.0
CA A:ALA177 5.0 18.0 1.0

Chlorine binding site 3 out of 4 in 8txn

Go back to Chlorine Binding Sites List in 8txn
Chlorine binding site 3 out of 4 in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3001

b:12.1
occ:1.00
 O D:HOH4240 3.1 13.5 1.0
O D:HOH4077 3.1 13.5 1.0
N D:ARG2076 3.3 11.6 1.0
C D:ARG2076 3.4 12.0 1.0
N D:ASP2078 3.4 10.7 1.0
N D:ASN2077 3.5 10.9 1.0
O D:ARG2076 3.6 13.9 1.0
CA D:ALA2074 3.6 13.3 1.0
C D:ALA2074 3.7 14.2 1.0
CD1 D:LEU2060 3.7 17.7 1.0
N D:SER2075 3.8 11.9 1.0
CA D:ARG2076 3.8 12.5 1.0
CA D:ASN2077 4.1 11.3 1.0
CB D:ALA2177 4.1 13.1 1.0
CB D:ASP2078 4.2 9.9 1.0
NH2 A:ARG1181 4.2 14.0 1.0
O D:ALA2074 4.2 13.6 1.0
C D:ASN2077 4.2 11.5 1.0
CA D:ASP2078 4.3 11.0 1.0
C D:SER2075 4.3 13.9 1.0
O D:HOH4185 4.4 12.2 1.0
N D:ALA2074 4.4 13.6 1.0
CB D:ARG2076 4.5 11.8 1.0
N D:ALA2177 4.5 11.9 1.0
O D:ASP2078 4.5 11.9 1.0
OD2 D:ASP2078 4.5 14.4 1.0
CG D:ASP2078 4.6 12.2 1.0
CD2 D:LEU2060 4.6 14.7 1.0
CA D:SER2075 4.6 14.5 1.0
CG D:LEU2060 4.6 21.6 1.0
CB D:ALA2074 4.7 14.4 1.0
O D:HOH4204 4.8 15.7 1.0
C D:ASP2078 4.8 11.3 1.0
CA D:ALA2177 4.8 13.2 1.0

Chlorine binding site 4 out of 4 in 8txn

Go back to Chlorine Binding Sites List in 8txn
Chlorine binding site 4 out of 4 in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3002

b:29.0
occ:1.00
 O D:HOH4022 2.9 23.7 1.0
O D:HOH4105 3.1 21.6 1.0
N D:ARG76 3.2 16.0 1.0
C D:ARG76 3.3 22.1 1.0
N D:ASP78 3.3 15.9 1.0
O D:ARG76 3.4 23.8 1.0
N D:SER75 3.7 19.4 1.0
N D:ASN77 3.7 19.6 1.0
CA D:ALA74 3.7 18.9 1.0
CA D:ARG76 3.7 15.9 1.0
CD2 D:LEU60 3.8 21.3 1.0
CB D:ASP78 3.8 13.7 1.0
C D:ALA74 3.8 21.4 1.0
O D:HOH4346 4.0 21.5 1.0
OD2 D:ASP78 4.1 20.1 1.0
CA D:ASP78 4.1 15.1 1.0
CA D:ASN77 4.2 20.1 0.6
CG D:ASP78 4.2 17.2 1.0
CB D:ALA177 4.2 27.2 1.0
CA D:ASN77 4.2 20.1 0.4
CB D:ARG76 4.2 15.2 1.0
C D:ASN77 4.3 17.4 1.0
C D:SER75 4.3 23.3 1.0
N D:ALA74 4.4 16.3 1.0
O D:ASP78 4.5 17.4 1.0
N D:ALA177 4.6 20.9 1.0
CD1 D:LEU60 4.6 17.1 1.0
O D:ALA74 4.6 21.1 1.0
CA D:SER75 4.6 21.1 1.0
C D:ASP78 4.7 15.4 1.0
O D:HOH4206 4.8 16.3 1.0
CG D:LEU60 4.8 19.7 1.0
O D:HOH4187 4.8 29.8 1.0
CB D:ALA74 4.9 22.1 1.0
CA D:ALA177 4.9 19.9 1.0

Reference:

J.A.Summers, M.Yarbrough, M.Liu, W.H.Mcdonald, B.G.Hudson, J.C.Pastor-Pareja, S.P.Boudko. Collagen IV of Basement Membranes: IV. Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila. J.Biol.Chem. 05394 2023.
ISSN: ESSN 1083-351X
PubMed: 37890775
DOI: 10.1016/J.JBC.2023.105394
Page generated: Tue Jul 30 12:57:10 2024

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