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

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

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

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Adaptive Mechanism of Collagen IV Scaffold Assembly in Drosophila: Crystal Structure of Recombinant NC1 Hexamer, PDB code: 8txn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg3004 b:15.6 occ:1.00 O A:HOH4144 2.0 16.7 1.0 OD2 A:ASP2040 2.1 15.3 1.0 O D:HOH4149 2.1 16.4 1.0 O A:HOH4088 2.1 16.3 1.0 O D:HOH4029 2.1 17.4 1.0 O A:HOH4045 2.2 20.3 1.0 CG A:ASP2040 2.9 17.0 1.0 OD1 A:ASP2040 3.1 17.4 1.0 OD2 D:ASP1079 3.8 24.8 1.0 O D:HOH4056 3.9 19.6 1.0 O D:HOH4255 4.1 23.1 1.0 O A:HOH4096 4.2 12.4 1.0 O D:HOH4088 4.2 13.2 1.0 O D:HOH4393 4.2 22.2 1.0 NZ A:LYS2079 4.2 18.2 1.0 CB A:ASP2040 4.3 10.9 1.0 O A:ASN2077 4.3 13.0 1.0 O A:HOH4170 4.4 14.5 1.0 O D:ASN1077 4.4 12.9 1.0 OD1 D:ASP1079 4.6 19.2 1.0 CB A:ASN2077 4.6 12.5 1.0 CG D:ASP1079 4.6 16.5 1.0 CG1 D:VAL1151 4.7 10.9 1.0 OG D:SER1040 4.8 15.7 1.0 N A:ASP2040 4.9 10.7 1.0 CA A:ASP2040 5.0 11.8 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 D:Mg3003 b:14.7 occ:1.00 O D:HOH4115 2.0 16.0 1.0 O D:HOH4021 2.1 15.0 1.0 O A:HOH4217 2.1 13.9 1.0 O D:HOH4152 2.1 14.7 1.0 OD2 D:ASP2040 2.1 15.9 1.0 O A:HOH4047 2.1 16.1 1.0 CG D:ASP2040 2.9 15.3 1.0 OD1 D:ASP2040 3.1 19.9 1.0 O A:HOH4062 3.8 18.1 1.0 OD2 A:ASP1079 3.8 22.3 1.0 O D:HOH4246 4.0 21.8 1.0 O A:HOH4205 4.1 10.7 1.0 O D:HOH4058 4.1 10.6 1.0 O D:HOH4401 4.2 23.7 1.0 NZ D:LYS2079 4.3 17.6 1.0 CB D:ASP2040 4.3 11.0 1.0 O D:ASN2077 4.4 10.7 1.0 O D:HOH4121 4.4 12.2 1.0 O A:ASN1077 4.4 12.8 1.0 OD1 A:ASP1079 4.5 13.9 1.0 CG A:ASP1079 4.6 14.3 1.0 CB D:ASN2077 4.6 10.8 1.0 CG1 A:VAL1151 4.8 9.1 1.0 N D:ASP2040 4.9 9.7 1.0 OG A:SER1040 4.9 14.4 1.0 CA D:ASP2040 5.0 12.1 1.0

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