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Manganese in PDB 6rk9: Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X

Enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X

All present enzymatic activity of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X:
1.14.11.16;

Protein crystallography data

The structure of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X, PDB code: 6rk9 was solved by M.A.Mcdonough, I.Pfeffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.00 / 2.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.472, 59.243, 95.665, 103.97, 91.49, 92.70
R / Rfree (%) 21.1 / 23.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X (pdb code 6rk9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X, PDB code: 6rk9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6rk9

Go back to Manganese Binding Sites List in 6rk9
Manganese binding site 1 out of 2 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:49.2
occ:1.00
 O1 A:OGA802 2.1 46.7 1.0
NE2 A:HIS725 2.3 41.6 1.0
O C:HOH301 2.3 35.6 1.0
NE2 A:HIS679 2.4 41.0 1.0
O2' A:OGA802 2.5 46.6 1.0
OD2 C:ASP255 2.6 44.2 0.5
C1 A:OGA802 2.8 46.2 1.0
C2 A:OGA802 3.0 46.6 1.0
CD2 A:HIS725 3.1 41.7 1.0
CD2 A:HIS679 3.3 41.4 1.0
CE1 A:HIS679 3.3 41.5 1.0
CE1 A:HIS725 3.4 42.2 1.0
CG C:ASP255 3.6 43.6 0.5
O C:ASP255 4.0 48.9 1.0
O2 A:OGA802 4.0 45.7 1.0
NH1 A:ARG688 4.2 37.4 1.0
CB C:ASP255 4.3 47.3 0.5
CB C:ASP255 4.3 47.3 0.5
CG A:HIS725 4.3 42.3 1.0
O C:HOH302 4.4 40.1 1.0
ND1 A:HIS679 4.4 41.6 1.0
OD1 C:ASP255 4.4 45.3 0.5
ND1 A:HIS725 4.4 42.5 1.0
CG A:HIS679 4.4 40.7 1.0
N1 A:OGA802 4.5 46.4 1.0
OD2 A:ASP721 4.6 38.6 1.0
CA C:ASP255 4.8 47.9 0.5
CA C:ASP255 4.8 47.9 0.5
C C:ASP255 4.8 48.3 1.0
CB A:ASP721 4.9 35.7 1.0
CG C:ASP255 4.9 45.1 0.5

Manganese binding site 2 out of 2 in 6rk9

Go back to Manganese Binding Sites List in 6rk9
Manganese binding site 2 out of 2 in the Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Aspartyl/Asparaginyl Beta-Hydroxylase (Asph)Oxygenase and Tpr Domains in Complex with Manganese, N-Oxalylglycine and Cyclic Peptide Substrate Mimic of Factor X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:38.0
occ:1.00
 O2 B:OGA802 2.2 39.5 1.0
NE2 B:HIS725 2.2 42.7 1.0
NE2 B:HIS679 2.2 52.3 1.0
O B:HOH957 2.3 37.1 1.0
O B:HOH925 2.4 37.2 1.0
O2' B:OGA802 2.4 37.3 1.0
C1 B:OGA802 2.9 39.8 1.0
C2 B:OGA802 3.0 39.0 1.0
CE1 B:HIS679 3.0 51.1 1.0
CE1 B:HIS725 3.1 39.6 1.0
CD2 B:HIS725 3.2 39.3 1.0
CD2 B:HIS679 3.2 50.9 1.0
O B:HOH1002 4.0 41.3 1.0
O1 B:OGA802 4.1 40.1 1.0
ND1 B:HIS679 4.1 51.1 1.0
O B:HOH986 4.2 46.0 1.0
ND1 B:HIS725 4.2 39.6 1.0
NH1 B:ARG688 4.2 37.7 1.0
CG B:HIS679 4.3 49.9 1.0
CG B:HIS725 4.3 39.0 1.0
OD2 B:ASP721 4.4 33.0 1.0
N1 B:OGA802 4.4 40.3 1.0
CB B:ASP721 5.0 37.3 1.0

Reference:

I.Pfeffer, L.Brewitz, T.Krojer, S.A.Jensen, G.T.Kochan, N.J.Kershaw, K.S.Hewitson, L.A.Mcneill, H.Kramer, M.Munzel, R.J.Hopkinson, U.Oppermann, P.A.Handford, M.A.Mcdonough, C.J.Schofield. Aspartate/Asparagine-Beta-Hydroxylase Crystal Structures Reveal An Unexpected Epidermal Growth Factor-Like Domain Substrate Disulfide Pattern. Nat Commun V. 10 4910 2019.
ISSN: ESSN 2041-1723
PubMed: 31659163
DOI: 10.1038/S41467-019-12711-7
Page generated: Sun Oct 6 07:00:50 2024

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