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Manganese in PDB 5ekb: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution)

Enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution)

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution):
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution), PDB code: 5ekb was solved by J.J.Griese, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 2.07
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.041, 97.217, 128.279, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.4

Other elements in 5ekb:

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution) also contains other interesting chemical elements:

Iron (Fe) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution) (pdb code 5ekb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution), PDB code: 5ekb:

Manganese binding site 1 out of 1 in 5ekb

Go back to Manganese Binding Sites List in 5ekb
Manganese binding site 1 out of 1 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:45.9
occ:0.79
 O1 A:PLM403 1.8 61.2 1.0
OE1 A:GLU69 2.1 53.8 1.0
ND1 A:HIS105 2.1 51.0 1.0
O A:HOH502 2.1 59.7 1.0
OE1 A:GLU102 2.1 45.7 1.0
O A:HOH501 2.5 56.4 1.0
C1 A:PLM403 2.6 59.9 1.0
CE1 A:HIS105 3.0 51.8 1.0
O2 A:PLM403 3.0 59.5 1.0
CD A:GLU69 3.0 53.1 1.0
HE1 A:HIS105 3.1 62.2 1.0
CD A:GLU102 3.2 49.2 1.0
OE2 A:GLU69 3.2 65.9 1.0
CG A:HIS105 3.2 53.7 1.0
HB3 A:HIS105 3.4 59.2 1.0
OE2 A:GLU102 3.4 55.6 1.0
HB2 A:HIS105 3.6 59.2 1.0
FE A:FE402 3.6 47.2 0.8
CB A:HIS105 3.6 49.3 1.0
HA A:GLU102 3.8 49.5 1.0
HG21 A:VAL72 3.9 66.5 1.0
OE1 A:GLU202 3.9 53.1 1.0
HG A:LEU198 3.9 51.1 1.0
C2 A:PLM403 4.1 55.7 1.0
HA A:GLU69 4.1 69.5 1.0
NE2 A:HIS105 4.1 53.7 1.0
HE1 A:HIS205 4.2 53.1 1.0
CD2 A:HIS105 4.3 51.5 1.0
H31 A:PLM403 4.3 70.9 1.0
H32 A:PLM403 4.3 70.9 1.0
CG A:GLU69 4.4 52.6 1.0
OH A:TYR175 4.5 51.1 1.0
HH A:TYR175 4.5 61.4 1.0
C3 A:PLM403 4.5 59.1 1.0
H22 A:PLM403 4.6 66.9 1.0
CG2 A:VAL72 4.6 55.5 1.0
HB3 A:GLU69 4.6 61.6 1.0
CG A:GLU102 4.6 44.8 1.0
HG22 A:VAL72 4.7 66.5 1.0
CA A:GLU102 4.7 41.2 1.0
HG23 A:VAL72 4.7 66.5 1.0
HD23 A:LEU198 4.7 58.0 1.0
CD A:GLU202 4.8 55.4 1.0
HG3 A:GLU69 4.8 63.1 1.0
H21 A:PLM403 4.8 66.9 1.0
HB3 A:GLU102 4.8 53.0 1.0
OE2 A:GLU202 4.8 52.5 1.0
CG A:LEU198 4.8 42.6 1.0
CE1 A:HIS205 4.8 44.2 1.0
CB A:GLU69 4.9 51.3 1.0
ND1 A:HIS205 4.9 43.4 1.0
HE2 A:HIS105 4.9 64.4 1.0
CA A:GLU69 4.9 57.9 1.0
HG2 A:GLU69 5.0 63.1 1.0
CB A:GLU102 5.0 44.2 1.0

Reference:

Y.Kutin, V.Srinivas, M.Fritz, R.Kositzki, H.S.Shafaat, J.Birrell, E.Bill, M.Haumann, W.Lubitz, M.Hogbom, J.J.Griese, N.Cox. Divergent Assembly Mechanisms of the Manganese/Iron Cofactors in R2LOX and R2C Proteins. J.Inorg.Biochem. V. 162 164 2016.
ISSN: ISSN 0162-0134
PubMed: 27138102
DOI: 10.1016/J.JINORGBIO.2016.04.019
Page generated: Sun Oct 6 00:07:04 2024

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