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Manganese in PDB 6i94: R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe)

Enzymatic activity of R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe)

All present enzymatic activity of R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe):
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe), PDB code: 6i94 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) 38.79 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.815, 97.200, 126.921, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.1

Manganese Binding Sites:

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe) (pdb code 6i94). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe), PDB code: 6i94:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 6i94

Go back to Manganese Binding Sites List in 6i94
Manganese binding site 1 out of 3 in the R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe)


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 G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:23.4
occ:1.00
 OE2 A:GLU69 2.1 23.8 1.0
OE2 A:GLU102 2.1 22.2 1.0
ND1 A:HIS105 2.2 22.2 1.0
O A:HOH509 2.2 44.2 1.0
OE2 A:GLU202 2.3 27.6 1.0
CE1 A:HIS105 3.0 22.8 1.0
HE1 A:HIS105 3.0 27.4 1.0
CD A:GLU69 3.1 29.2 1.0
CD A:GLU102 3.2 21.9 1.0
CG A:HIS105 3.3 18.7 1.0
OE1 A:GLU69 3.3 30.5 1.0
CD A:GLU202 3.3 31.3 1.0
OE1 A:GLU102 3.6 24.8 1.0
HB2 A:HIS105 3.6 25.5 1.0
HB3 A:HIS105 3.6 25.5 1.0
OE2 A:GLU167 3.6 36.5 1.0
HG21 A:VAL72 3.6 29.9 1.0
MN A:MN403 3.6 24.4 1.0
HA A:GLU102 3.7 26.8 1.0
CB A:HIS105 3.7 21.2 1.0
HG A:LEU198 3.9 41.2 1.0
HG3 A:GLU202 4.0 31.5 1.0
HD21 A:LEU198 4.0 48.9 1.0
HG2 A:GLU202 4.1 31.5 1.0
CG A:GLU202 4.1 26.3 1.0
NE2 A:HIS105 4.2 24.3 1.0
OE1 A:GLU202 4.2 25.8 1.0
HE1 A:HIS205 4.3 28.0 1.0
HA A:GLU69 4.3 29.1 1.0
HG23 A:VAL72 4.3 29.9 1.0
CD2 A:HIS105 4.3 23.6 1.0
CG2 A:VAL72 4.4 24.9 1.0
HD11 A:LEU198 4.4 31.4 1.0
CG A:GLU69 4.4 26.6 1.0
CG A:GLU102 4.5 19.4 1.0
HB3 A:GLU69 4.6 28.8 1.0
CA A:GLU102 4.6 22.4 1.0
CG A:LEU198 4.6 34.3 1.0
OH A:TYR175 4.6 40.9 0.6
HG22 A:VAL72 4.7 29.9 1.0
CD2 A:LEU198 4.7 40.7 1.0
HH A:TYR175 4.7 49.1 0.6
HB3 A:GLU102 4.7 26.0 1.0
HD22 A:LEU68 4.7 33.2 1.0
HD23 A:LEU68 4.8 33.2 1.0
HD23 A:LEU198 4.8 48.9 1.0
HG3 A:GLU69 4.8 31.9 1.0
CD A:GLU167 4.8 31.4 1.0
CE1 A:HIS205 4.8 23.4 1.0
CB A:GLU102 4.9 21.6 1.0
ND1 A:HIS205 4.9 25.1 1.0
HE2 A:HIS105 4.9 29.1 1.0
HD21 A:LEU68 4.9 33.2 1.0
CB A:GLU69 4.9 24.0 1.0

Manganese binding site 2 out of 3 in 6i94

Go back to Manganese Binding Sites List in 6i94
Manganese binding site 2 out of 3 in the R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:93.6
occ:1.00
 NE2 A:HIS130 2.3 33.2 1.0
CD2 A:HIS130 3.2 42.6 1.0
CE1 A:HIS130 3.2 46.0 1.0
HD2 A:HIS130 3.4 51.1 1.0
HE1 A:HIS130 3.4 55.2 1.0
O A:HOH522 4.0 42.9 1.0
OD2 A:ASP129 4.3 58.5 1.0
ND1 A:HIS130 4.3 44.1 1.0
CG A:HIS130 4.4 37.8 1.0
OD1 A:ASP129 4.5 41.2 1.0
O A:HOH584 4.7 43.7 1.0
HA3 A:GLY240 4.7 40.8 1.0
O A:HOH610 4.9 58.0 1.0
CG A:ASP129 4.9 47.0 1.0

Manganese binding site 3 out of 3 in 6i94

Go back to Manganese Binding Sites List in 6i94
Manganese binding site 3 out of 3 in the R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of R2-Like Ligand-Binding Oxidase G68L Mutant with Non-Activated Mn/Mn Cofactor (After Aerobic Reconstitution with Mn and Fe) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:24.4
occ:1.00
 OE2 A:GLU167 2.0 36.5 1.0
OE1 A:GLU102 2.1 24.8 1.0
ND1 A:HIS205 2.1 25.1 1.0
OE1 A:GLU202 2.2 25.8 1.0
OE1 A:GLU167 2.2 25.6 1.0
OE2 A:GLU202 2.3 27.6 1.0
CD A:GLU167 2.4 31.4 1.0
CD A:GLU202 2.5 31.3 1.0
CE1 A:HIS205 3.0 23.4 1.0
CD A:GLU102 3.1 21.9 1.0
HE1 A:HIS205 3.2 28.0 1.0
CG A:HIS205 3.2 21.6 1.0
HB3 A:HIS205 3.3 31.9 1.0
OE2 A:GLU102 3.4 22.2 1.0
HB2 A:HIS205 3.5 31.9 1.0
CB A:HIS205 3.6 26.6 1.0
MN A:MN401 3.6 23.4 1.0
HE2 A:PHE98 3.7 30.3 1.0
CG A:GLU167 3.9 29.1 1.0
HZ A:PHE98 3.9 32.1 1.0
CE2 A:PHE98 3.9 25.3 1.0
CG A:GLU202 4.0 26.3 1.0
HE2 A:TYR162 4.0 33.6 1.0
HA A:GLU202 4.0 30.4 1.0
CZ A:PHE98 4.0 26.7 1.0
HB3 A:GLU167 4.1 36.7 1.0
NE2 A:HIS205 4.2 26.3 1.0
HG2 A:GLU167 4.3 34.9 1.0
HE1 A:HIS105 4.3 27.4 1.0
HG21 A:VAL72 4.3 29.9 1.0
CD2 A:HIS205 4.3 24.9 1.0
O A:HOH516 4.3 35.2 1.0
HG3 A:GLU167 4.3 34.9 1.0
HG2 A:GLU202 4.4 31.5 1.0
CG A:GLU102 4.4 19.4 1.0
O A:HOH509 4.4 44.2 1.0
HG3 A:GLU202 4.4 31.5 1.0
HG2 A:GLU102 4.5 23.2 1.0
CB A:GLU167 4.6 30.6 1.0
HB3 A:GLU202 4.6 33.7 1.0
HG3 A:GLU102 4.7 23.2 1.0
CD2 A:PHE98 4.7 22.4 1.0
CB A:GLU202 4.7 28.1 1.0
CA A:GLU202 4.8 25.3 1.0
CE1 A:PHE98 4.9 27.3 1.0
CE2 A:TYR162 4.9 28.0 1.0
CE1 A:HIS105 4.9 22.8 1.0
HB A:VAL72 4.9 30.6 1.0
HE2 A:HIS205 5.0 31.6 1.0
ND1 A:HIS105 5.0 22.2 1.0

Reference:

Y.Kutin, R.Kositzki, R.M.M.Branca, V.Srinivas, D.Lundin, M.Haumann, M.Hogbom, N.Cox, J.J.Griese. Chemical Flexibility of Heterobimetallic Mn/Fe Cofactors: R2LOX and R2C Proteins. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31591267
DOI: 10.1074/JBC.RA119.010570
Page generated: Sun Oct 6 04:52:56 2024

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