Magnesium in PDB 6s4c: Crystal Structure of the VWFA2 Subdomain of Type VII Collagen

The structure of Crystal Structure of the VWFA2 Subdomain of Type VII Collagen, PDB code: 6s4c was solved by J.M.Gebauer, F.Flachsenberg, U.Baumann, K.Seeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.52 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	123.034, 123.034, 63.749, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 20.7

The binding sites of Magnesium atom in the Crystal Structure of the VWFA2 Subdomain of Type VII Collagen (pdb code 6s4c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the VWFA2 Subdomain of Type VII Collagen, PDB code: 6s4c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the VWFA2 Subdomain of Type VII Collagen


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the VWFA2 Subdomain of Type VII Collagen within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:7.8 occ:0.50 O19 A:EDT1302 1.9 14.6 1.0 O18 A:EDT1302 2.1 30.3 1.0 O A:HOH1401 2.2 37.8 0.5 N3 A:EDT1302 2.4 24.5 1.0 C5 A:EDT1302 2.8 18.4 1.0 C1 A:EDT1302 3.0 29.1 1.0 C4 A:EDT1302 3.1 21.3 1.0 C2 A:EDT1302 3.1 26.6 1.0 H062 A:EDT1302 3.3 30.8 1.0 C6 A:EDT1302 3.4 25.7 1.0 HH12 A:ARG1120 3.5 26.0 1.0 H021 A:EDT1302 3.6 31.9 1.0 H041 A:EDT1302 3.7 25.6 1.0 H042 A:EDT1302 3.8 25.6 1.0 H022 A:EDT1302 3.9 31.9 1.0 O20 A:EDT1302 4.0 16.5 1.0 NH1 A:ARG1120 4.1 21.6 1.0 O17 A:EDT1302 4.2 30.1 1.0 H061 A:EDT1302 4.2 30.8 1.0 HH11 A:ARG1120 4.3 26.0 1.0 O A:HOH1517 4.7 32.9 1.0 HH22 A:ARG1120 4.8 26.2 1.0 HG12 A:ILE1117 4.9 18.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the VWFA2 Subdomain of Type VII Collagen


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the VWFA2 Subdomain of Type VII Collagen within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1303 b:33.5 occ:1.00 H A:GLY1132 2.5 30.7 1.0 HE1 A:HIS1061 2.8 28.9 1.0 HG1 A:THR1063 3.0 23.2 1.0 HE2 A:HIS1061 3.0 27.1 1.0 HA A:SER1131 3.2 37.9 1.0 OE1 A:GLU1168 3.3 54.6 1.0 N A:GLY1132 3.3 25.6 1.0 OE2 A:GLU1168 3.4 59.6 1.0 HB2 A:SER1131 3.4 44.9 1.0 HB2 A:ASP1065 3.4 34.0 1.0 CE1 A:HIS1061 3.4 24.1 1.0 OD2 A:ASP1065 3.5 38.8 1.0 NE2 A:HIS1061 3.5 22.6 1.0 O A:GLY1132 3.6 23.2 1.0 HG21 A:THR1063 3.6 24.6 1.0 CD A:GLU1168 3.7 54.6 1.0 OG1 A:THR1063 3.8 19.4 1.0 CA A:SER1131 3.9 31.5 1.0 C A:GLY1132 4.0 22.6 1.0 HB2 A:ASN1133 4.0 25.2 1.0 CB A:SER1131 4.1 37.4 1.0 CB A:ASP1065 4.1 28.3 1.0 C A:SER1131 4.1 27.6 1.0 HB3 A:ASP1065 4.2 34.0 1.0 CA A:GLY1132 4.2 23.6 1.0 CG A:ASP1065 4.3 35.4 1.0 CG2 A:THR1063 4.4 20.4 1.0 HB3 A:SER1131 4.5 44.9 1.0 HG23 A:THR1063 4.5 24.6 1.0 CB A:THR1063 4.6 19.6 1.0 HA2 A:GLY1132 4.6 28.4 1.0 ND1 A:HIS1061 4.7 23.6 1.0 HB A:THR1063 4.8 23.6 1.0 N A:ASN1133 4.8 20.7 1.0 CD2 A:HIS1061 4.9 21.8 1.0 CB A:ASN1133 4.9 21.0 1.0

J.M.Gebauer, F.Flachsenberg, C.Windler, B.Richer, U.Baumann, K.Seeger. Structural and Biophysical Characterization of the Type VII Collagen VWFA2 Subdomain Leads to Identification of Two Binding Sites. Febs Open Bio 2020.
ISSN: ESSN 2211-5463
PubMed: 32031736
DOI: 10.1002/2211-5463.12807