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Magnesium in PDB 3ufk: Crystal Structure of Unda Complexed with Iron Nitrilotriacetate

Protein crystallography data

The structure of Crystal Structure of Unda Complexed with Iron Nitrilotriacetate, PDB code: 3ufk 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) 61.61 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.500, 105.870, 151.520, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20.5

Other elements in 3ufk:

The structure of Crystal Structure of Unda Complexed with Iron Nitrilotriacetate also contains other interesting chemical elements:

Iron (Fe) 15 atoms
Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Unda Complexed with Iron Nitrilotriacetate (pdb code 3ufk). 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 Unda Complexed with Iron Nitrilotriacetate, PDB code: 3ufk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ufk

Go back to Magnesium Binding Sites List in 3ufk
Magnesium binding site 1 out of 2 in the Crystal Structure of Unda Complexed with Iron Nitrilotriacetate


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 Unda Complexed with Iron Nitrilotriacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg913

b:10.2
occ:1.00
O A:HIS684 2.2 8.6 1.0
O A:THR670 2.2 6.2 1.0
O A:HIS667 2.3 5.7 1.0
O2D A:HEC908 2.4 10.2 1.0
O1D A:HEC908 2.5 10.6 1.0
CGD A:HEC908 2.8 15.7 1.0
C A:HIS684 3.2 8.6 1.0
C A:HIS667 3.3 9.1 1.0
C A:THR670 3.3 11.1 1.0
N A:THR670 3.6 10.9 1.0
CA A:HIS684 3.6 6.2 1.0
CB A:HIS684 3.7 6.6 1.0
CB A:HIS667 3.9 7.1 1.0
CA A:HIS667 3.9 9.4 1.0
CA A:THR670 3.9 10.3 1.0
CA A:ALA672 4.0 10.9 1.0
N A:ALA672 4.1 13.3 1.0
ND1 A:HIS684 4.2 7.3 1.0
C A:HIS671 4.2 11.1 1.0
CB A:THR670 4.3 11.3 1.0
CBD A:HEC908 4.3 7.3 1.0
CB A:ALA672 4.4 9.9 1.0
N A:ALA668 4.4 10.3 1.0
N A:HIS671 4.4 8.6 1.0
CG A:HIS684 4.4 8.1 1.0
O A:HIS671 4.4 8.2 1.0
N A:SER685 4.4 8.4 1.0
C A:SER685 4.5 8.9 1.0
N A:LEU669 4.6 10.4 1.0
O A:SER685 4.7 8.0 1.0
C A:ALA668 4.7 11.5 1.0
C A:LEU669 4.8 13.6 1.0
CA A:HIS671 4.8 10.0 1.0
N A:ALA686 4.8 8.6 1.0
CA A:ALA668 4.8 10.5 1.0
CA A:SER685 4.8 10.9 1.0
CG A:HIS667 4.9 10.3 1.0
O A:HOH1004 4.9 10.7 1.0

Magnesium binding site 2 out of 2 in 3ufk

Go back to Magnesium Binding Sites List in 3ufk
Magnesium binding site 2 out of 2 in the Crystal Structure of Unda Complexed with Iron Nitrilotriacetate


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 Unda Complexed with Iron Nitrilotriacetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg914

b:17.3
occ:1.00
O A:LEU554 2.2 15.0 1.0
O A:HOH1390 2.4 16.7 1.0
O A:ASN551 2.4 14.5 1.0
O A:VAL548 2.4 20.3 1.0
O A:HOH1537 2.4 23.5 1.0
O A:HOH1472 2.7 24.0 1.0
C A:LEU554 3.5 14.3 1.0
C A:ASN551 3.5 15.0 1.0
C A:VAL548 3.5 23.7 1.0
CG1 A:VAL548 3.9 25.7 1.0
N A:ASN551 4.1 16.9 1.0
N A:LEU554 4.2 14.2 1.0
CA A:ASN551 4.3 14.4 1.0
CA A:LEU554 4.3 14.1 1.0
CA A:GLU549 4.3 23.7 1.0
N A:GLU549 4.4 24.9 1.0
C A:GLU549 4.4 23.6 1.0
CA A:VAL548 4.4 22.9 1.0
N A:THR555 4.4 14.9 1.0
O A:GLU549 4.4 23.6 1.0
N A:ALA552 4.4 15.8 1.0
CA A:THR555 4.5 15.4 1.0
CG2 A:THR555 4.5 17.1 1.0
CA A:ALA552 4.5 18.3 1.0
O A:HOH1302 4.6 15.5 1.0
CB A:ASN551 4.7 15.1 1.0
CB A:LEU554 4.7 12.7 1.0
C A:ALA552 4.7 18.9 1.0
CB A:VAL548 4.8 25.9 1.0
O A:HOH1956 4.8 41.7 1.0
O A:ALA552 4.9 18.9 1.0
N A:THR550 4.9 20.3 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 08:56:34 2020

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