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Sodium in PDB 5uos: Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12

Protein crystallography data

The structure of Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12, PDB code: 5uos was solved by A.Shanmuganathan, A.Karasik, M.Ruetz, R.Banerjee, B.Krautler, M.Koutmos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.10 / 2.51
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.432, 114.432, 150.631, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 21.4

Other elements in 5uos:

The structure of Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Cobalt (Co) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12 (pdb code 5uos). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12, PDB code: 5uos:

Sodium binding site 1 out of 1 in 5uos

Go back to Sodium Binding Sites List in 5uos
Sodium binding site 1 out of 1 in the Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Cblc (Mmachc) (1-238), A Human B12 Processing Enzyme, Complexed with An Antivitamin B12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:60.6
occ:0.50
O2 A:171304 2.3 87.4 1.0
O1 A:171304 2.9 0.5 1.0
H12 A:171304 3.2 91.6 1.0
S A:171304 3.2 0.6 1.0
H2' A:171304 3.4 85.8 1.0
C1 A:171304 4.0 91.6 1.0
HH22 A:ARG91 4.2 52.1 1.0
C2 A:171304 4.2 0.7 1.0
HH12 A:ARG91 4.3 59.3 1.0
O3 A:171304 4.3 0.3 1.0
C2' A:171304 4.3 85.8 1.0
H11 A:171304 4.4 91.6 1.0
H21 A:171304 4.6 0.7 1.0
NH2 A:ARG91 4.7 52.1 1.0
NH1 A:ARG91 4.8 59.3 1.0
H3' A:171304 4.9 85.1 1.0

Reference:

M.Ruetz, A.Shanmuganathan, C.Gherasim, A.Karasik, R.Salchner, C.Kieninger, K.Wurst, R.Banerjee, M.Koutmos, B.Krautler. Antivitamin B12 Inhibition of the Human B12 -Processing Enzyme Cblc: Crystal Structure of An Inactive Ternary Complex with Glutathione As the Cosubstrate. Angew. Chem. Int. Ed. Engl. V. 56 7387 2017.
ISSN: ESSN 1521-3773
PubMed: 28544088
DOI: 10.1002/ANIE.201701583
Page generated: Tue Dec 15 11:42:49 2020

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