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Magnesium in PDB 3ucp: Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6

Protein crystallography data

The structure of Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6, PDB code: 3ucp was solved by M.J.Edwards, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.91 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.640, 106.090, 151.650, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.7

Other elements in 3ucp:

The structure of Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6 also contains other interesting chemical elements:

Iron (Fe) 11 atoms
Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6 (pdb code 3ucp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6, PDB code: 3ucp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ucp

Go back to Magnesium Binding Sites List in 3ucp
Magnesium binding site 1 out of 2 in the Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg913

b:10.6
occ:1.00
O A:HIS684 2.2 7.0 1.0
O A:THR670 2.3 7.9 1.0
O A:HIS667 2.3 8.4 1.0
O2D A:HEC908 2.4 8.3 1.0
O1D A:HEC908 2.5 8.8 1.0
CGD A:HEC908 2.8 12.0 1.0
C A:HIS684 3.3 9.1 1.0
C A:HIS667 3.3 7.2 1.0
C A:THR670 3.3 8.7 1.0
N A:THR670 3.6 8.6 1.0
CA A:HIS684 3.7 7.0 1.0
CB A:HIS684 3.7 7.3 1.0
CB A:HIS667 3.8 8.1 1.0
CA A:HIS667 3.9 7.4 1.0
CA A:THR670 3.9 9.2 1.0
CA A:ALA672 4.0 10.1 1.0
ND1 A:HIS684 4.0 8.6 1.0
N A:ALA672 4.1 9.5 1.0
C A:HIS671 4.2 10.4 1.0
CB A:THR670 4.3 8.9 1.0
CBD A:HEC908 4.3 8.7 1.0
CG A:HIS684 4.4 9.0 1.0
CB A:ALA672 4.4 10.8 1.0
N A:ALA668 4.4 8.2 1.0
N A:LEU669 4.5 8.4 1.0
N A:HIS671 4.5 8.3 1.0
N A:SER685 4.5 7.8 1.0
O A:HIS671 4.6 8.1 1.0
C A:SER685 4.6 8.5 1.0
C A:ALA668 4.7 8.4 1.0
C A:LEU669 4.8 9.2 1.0
O A:HOH1004 4.8 3.9 1.0
CG A:HIS667 4.8 6.5 1.0
CA A:HIS671 4.8 9.7 1.0
O A:SER685 4.8 9.4 1.0
N A:ALA686 4.9 7.1 1.0
CA A:ALA668 4.9 8.3 1.0
CA A:SER685 4.9 7.3 1.0

Magnesium binding site 2 out of 2 in 3ucp

Go back to Magnesium Binding Sites List in 3ucp
Magnesium binding site 2 out of 2 in the Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Outer Membrane Endecaheme Cytochrome Unda From Shewanella Sp. Hrcr-6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg914

b:13.5
occ:1.00
O A:LEU554 2.3 10.8 1.0
O A:ASN551 2.3 14.0 1.0
O A:VAL548 2.4 15.4 1.0
O A:HOH1776 2.4 13.1 1.0
O A:HOH1625 2.4 9.9 1.0
O A:HOH1710 2.6 16.4 1.0
C A:ASN551 3.4 12.2 1.0
C A:LEU554 3.5 12.2 1.0
C A:VAL548 3.5 18.1 1.0
N A:ASN551 4.0 13.2 1.0
CG1 A:VAL548 4.1 22.3 1.0
N A:LEU554 4.2 10.6 1.0
CA A:ASN551 4.2 12.6 1.0
O A:HOH1248 4.3 38.7 1.0
N A:ALA552 4.3 11.9 1.0
CA A:LEU554 4.3 11.0 1.0
CA A:GLU549 4.3 21.4 1.0
C A:GLU549 4.3 20.8 1.0
N A:GLU549 4.4 20.6 1.0
CA A:ALA552 4.4 14.3 1.0
CA A:VAL548 4.4 18.1 1.0
N A:THR555 4.5 10.6 1.0
O A:HOH1196 4.5 30.4 1.0
O A:GLU549 4.5 22.2 1.0
CB A:ASN551 4.6 10.6 1.0
CG2 A:THR555 4.6 13.9 1.0
CA A:THR555 4.6 13.4 1.0
C A:ALA552 4.6 14.2 1.0
CB A:LEU554 4.7 8.8 1.0
O A:HOH1534 4.7 7.2 1.0
CB A:VAL548 4.7 23.8 1.0
N A:THR550 4.8 15.9 1.0
O A:HOH2254 4.9 29.9 1.0
O A:ALA552 4.9 14.4 1.0

Reference:

M.J.Edwards, A.Hall, L.Shi, J.K.Fredrickson, J.M.Zachara, J.N.Butt, D.J.Richardson, T.A.Clarke. The Crystal Structure of the Extracellular 11-Heme Cytochrome Unda Reveals A Conserved 10-Heme Motif and Defined Binding Site For Soluble Iron Chelates. Structure V. 20 1275 2012.
ISSN: ISSN 0969-2126
PubMed: 22682743
DOI: 10.1016/J.STR.2012.04.016
Page generated: Mon Dec 14 08:56:23 2020

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