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Manganese in PDB 1jfz: Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution

Enzymatic activity of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution:
3.1.26.3;

Protein crystallography data

The structure of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution, PDB code: 1jfz was solved by J.Blaszczyk, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.741, 140.549, 49.759, 90.00, 117.42, 90.00
R / Rfree (%) 20.8 / 28.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution (pdb code 1jfz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution, PDB code: 1jfz:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1jfz

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Manganese binding site 1 out of 4 in the Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn761

b:24.6
occ:1.00
 OE2 A:GLU40 2.0 16.7 1.0
O A:HOH1137 2.2 40.8 1.0
OE1 A:GLU110 2.2 17.3 1.0
O A:HOH1056 2.3 25.4 1.0
O A:HOH1004 2.3 5.6 1.0
OD1 A:ASP107 2.4 23.4 1.0
CD A:GLU110 3.0 21.0 1.0
CD A:GLU40 3.0 20.0 1.0
OE2 A:GLU110 3.3 19.0 1.0
CG A:GLU40 3.4 3.8 1.0
CG A:ASP107 3.4 16.7 1.0
O A:HOH1064 3.8 24.8 1.0
O A:HOH1054 4.0 23.7 1.0
CA A:ASP107 4.2 15.6 1.0
OE1 A:GLU40 4.2 18.0 1.0
CB A:ASP107 4.2 14.3 1.0
OD2 A:ASP107 4.2 26.9 1.0
OD2 A:ASP44 4.3 31.5 1.0
CG A:GLU110 4.4 21.7 1.0
O A:HOH1037 4.7 21.1 1.0
N A:ASP107 4.8 14.8 1.0
O A:HOH1427 4.8 41.8 1.0
CB A:GLU40 4.9 4.5 1.0
O A:HOH1213 4.9 38.1 1.0
O A:GLY106 4.9 18.1 1.0
CG A:ASP44 5.0 6.6 1.0
CB A:GLU110 5.0 15.0 1.0

Manganese binding site 2 out of 4 in 1jfz

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Manganese binding site 2 out of 4 in the Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn762

b:46.3
occ:1.00
 OE1 B:GLU310 2.2 34.0 1.0
OD1 B:ASP307 2.3 36.2 1.0
O B:HOH1007 2.4 19.0 1.0
O B:HOH1325 2.6 25.7 1.0
OE1 B:GLU240 2.7 48.6 1.0
O B:HOH1246 3.1 44.1 1.0
CD B:GLU310 3.2 27.0 1.0
CG B:ASP307 3.5 29.1 1.0
OE2 B:GLU310 3.6 38.3 1.0
CD B:GLU240 3.8 33.7 1.0
OD2 B:ASP307 4.2 23.9 1.0
OE2 B:GLU240 4.3 27.1 1.0
O B:HOH1291 4.4 35.7 1.0
CE D:LYS633 4.4 59.5 1.0
O B:HOH1256 4.5 37.3 1.0
CA B:ASP307 4.5 20.9 1.0
CG B:GLU310 4.6 19.9 1.0
CB B:ASP307 4.6 28.3 1.0
O B:HOH1293 4.6 37.5 1.0
OD2 B:ASP244 4.7 29.5 1.0
CB B:GLU310 4.9 20.9 1.0

Manganese binding site 3 out of 4 in 1jfz

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Manganese binding site 3 out of 4 in the Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn763

b:29.4
occ:1.00
 OE2 C:GLU440 1.8 21.9 1.0
O C:HOH1015 2.5 19.9 1.0
OE1 C:GLU510 2.5 16.2 1.0
OD1 C:ASP507 2.5 15.4 1.0
O C:HOH1008 2.6 17.1 1.0
O C:HOH1039 2.7 35.2 1.0
CD C:GLU440 2.9 15.3 1.0
OE2 C:GLU510 3.1 23.4 1.0
CD C:GLU510 3.1 11.8 1.0
CG C:GLU440 3.4 11.6 1.0
CG C:ASP507 3.5 15.6 1.0
O C:HOH1500 3.7 35.9 1.0
O C:HOH1062 3.9 21.9 1.0
OE1 C:GLU440 4.0 13.5 1.0
O C:HOH1274 4.1 25.3 1.0
OD2 C:ASP444 4.1 30.9 1.0
OD2 C:ASP507 4.2 33.0 1.0
CA C:ASP507 4.2 12.4 1.0
CB C:ASP507 4.2 9.9 1.0
O C:HOH1081 4.4 29.2 1.0
O C:HOH1235 4.5 54.5 1.0
CG C:GLU510 4.6 1.7 1.0
O D:HOH1153 4.7 31.0 1.0
CB C:GLU440 4.9 10.8 1.0
N C:ASP507 4.9 20.1 1.0

Manganese binding site 4 out of 4 in 1jfz

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Manganese binding site 4 out of 4 in the Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Mn(II)-Complex of Rnase III Endonuclease Domain From Aquifex Aeolicus at 2.10 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn764

b:31.2
occ:1.00
 OE1 D:GLU710 2.2 9.4 1.0
O D:HOH1124 2.3 35.4 1.0
OE1 D:GLU640 2.4 52.7 1.0
OD1 D:ASP707 2.5 38.6 1.0
OE2 D:GLU640 2.7 50.5 1.0
O D:HOH1308 2.8 42.1 1.0
O D:HOH1311 2.9 40.4 1.0
CD D:GLU640 2.9 47.7 1.0
CD D:GLU710 3.3 21.5 1.0
CG D:ASP707 3.5 31.0 1.0
OE2 D:GLU710 3.8 18.3 1.0
O D:HOH1020 4.0 27.2 1.0
CA D:ASP707 4.1 26.5 1.0
CB D:ASP707 4.2 23.6 1.0
OD2 D:ASP707 4.3 38.5 1.0
CG D:GLU640 4.4 39.1 1.0
O D:HOH1440 4.5 26.1 1.0
CG D:GLU710 4.5 18.3 1.0
N D:ASP707 4.6 33.3 1.0
CB D:GLU710 4.9 21.5 1.0
O D:HOH1042 4.9 23.0 1.0
CB D:ASP644 5.0 19.5 1.0

Reference:

J.Blaszczyk, J.E.Tropea, M.Bubunenko, K.M.Routzahn, D.S.Waugh, D.L.Court, X.Ji. Crystallographic and Modeling Studies of Rnase III Suggest A Mechanism For Double-Stranded Rna Cleavage. Structure V. 9 1225 2001.
ISSN: ISSN 0969-2126
PubMed: 11738048
DOI: 10.1016/S0969-2126(01)00685-2
Page generated: Sat Oct 5 11:10:19 2024

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