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Calcium in PDB 2iuf: The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole

Enzymatic activity of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole

All present enzymatic activity of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole:
1.11.1.6;

Protein crystallography data

The structure of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole, PDB code: 2iuf was solved by G.Murshudov, A.Borovik, A.Grebenko, V.Barynin, A.Vagin, W.Melik-Adamyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 119.52 / 1.71
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.440, 142.440, 132.230, 90.00, 90.00, 120.00
R / Rfree (%) 12.9 / 15.4

Other elements in 2iuf:

The structure of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole (pdb code 2iuf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole, PDB code: 2iuf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2iuf

Go back to Calcium Binding Sites List in 2iuf
Calcium binding site 1 out of 6 in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1696

b:23.9
occ:1.00
 O A:SER653 2.3 14.8 1.0
O A:VAL658 2.3 15.8 1.0
O A:ARG655 2.4 14.2 1.0
O A:HOH2718 2.5 21.2 1.0
O A:HOH2721 2.5 19.4 1.0
C A:VAL658 3.5 14.2 1.0
C A:SER653 3.5 16.3 1.0
C A:ARG655 3.5 14.5 1.0
N A:VAL658 3.8 13.2 1.0
C A:GLU654 4.0 16.6 1.0
CA A:VAL658 4.0 12.2 1.0
O A:GLU654 4.1 18.1 1.0
N A:ARG655 4.1 15.2 1.0
CB A:VAL658 4.2 13.3 1.0
N A:GLN656 4.3 14.1 1.0
CA A:GLN656 4.3 15.2 1.0
N A:GLY657 4.3 14.1 1.0
N A:GLU654 4.3 15.8 1.0
CA A:SER653 4.4 16.6 1.0
CA A:GLU654 4.4 17.2 1.0
CA A:ARG655 4.4 14.8 1.0
C A:GLN656 4.5 14.3 1.0
N A:TYR659 4.6 12.3 1.0
O A:HOH2720 4.8 40.1 1.0
CB A:SER653 4.9 18.6 1.0
C A:GLY657 4.9 14.8 1.0
CA A:TYR659 5.0 13.3 1.0

Calcium binding site 2 out of 6 in 2iuf

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Calcium binding site 2 out of 6 in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1697

b:19.8
occ:1.00
 O A:THR432 2.3 15.1 1.0
O E:HOH2044 2.3 30.1 1.0
O A:HOH2507 2.4 25.4 1.0
O A:HOH2209 2.4 22.5 1.0
O A:HOH2210 2.4 13.4 1.0
O E:HOH2041 2.5 12.2 1.0
O A:HOH2510 2.8 16.0 1.0
C A:THR432 3.5 14.3 1.0
OG E:SER32 4.2 14.7 1.0
O E:GLN35 4.2 15.2 1.0
N A:THR432 4.2 11.9 1.0
O A:HOH2207 4.2 15.9 1.0
O E:HOH2047 4.3 31.4 1.0
O E:SER30 4.3 11.8 1.0
OD2 A:ASP146 4.4 12.2 1.0
N A:LEU433 4.4 12.6 1.0
OG1 A:THR432 4.4 17.5 1.0
CA A:LEU433 4.4 13.0 1.0
CA A:THR432 4.4 13.6 1.0
OD1 E:ASN29 4.5 13.0 1.0
N A:SER434 4.5 12.4 1.0
CG A:PRO342 4.7 13.9 1.0
CB E:SER32 4.8 12.7 1.0
CB E:ASN29 4.8 11.3 1.0
O E:HOH2052 4.9 15.5 1.0
C A:LEU433 4.9 12.6 1.0
O E:HOH2055 4.9 14.9 1.0

Calcium binding site 3 out of 6 in 2iuf

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Calcium binding site 3 out of 6 in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1697

b:32.6
occ:1.00
 O E:VAL658 2.3 21.8 1.0
O E:SER653 2.3 26.3 1.0
O E:HOH2675 2.3 28.5 1.0
O E:HOH2667 2.4 33.0 1.0
O E:HOH2670 2.4 36.7 1.0
O E:ARG655 2.5 20.4 1.0
C E:SER653 3.5 25.1 1.0
C E:VAL658 3.5 19.8 1.0
C E:ARG655 3.6 19.6 1.0
N E:VAL658 3.9 16.6 1.0
C E:GLU654 3.9 23.8 1.0
N E:ARG655 4.0 21.4 1.0
CA E:VAL658 4.1 17.3 1.0
O E:GLU654 4.2 23.7 1.0
CB E:VAL658 4.2 17.7 1.0
CA E:GLU654 4.3 25.4 1.0
N E:GLU654 4.3 24.7 1.0
O E:HOH2266 4.3 48.5 1.0
CA E:SER653 4.3 24.8 1.0
N E:GLN656 4.4 18.2 1.0
CA E:ARG655 4.5 20.6 1.0
CA E:GLN656 4.5 17.8 1.0
O E:HOH2674 4.6 24.7 1.0
N E:GLY657 4.6 17.4 1.0
N E:TYR659 4.6 19.0 1.0
C E:GLN656 4.7 17.9 1.0
O E:HOH2677 4.8 29.7 1.0
CA E:TYR659 4.9 20.5 1.0
CB E:SER653 4.9 25.8 1.0

Calcium binding site 4 out of 6 in 2iuf

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Calcium binding site 4 out of 6 in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1698

b:21.2
occ:1.00
 O E:THR432 2.3 18.5 1.0
O A:HOH2059 2.3 33.2 1.0
O E:HOH2474 2.4 36.2 1.0
O E:HOH2189 2.4 24.1 1.0
O A:HOH2051 2.4 13.0 1.0
O E:HOH2187 2.4 13.4 1.0
O E:HOH2476 2.7 17.0 1.0
C E:THR432 3.5 16.2 1.0
O A:GLN35 4.1 19.4 1.0
OG A:SER32 4.1 16.9 1.0
N E:THR432 4.2 15.3 1.0
O E:HOH2185 4.3 14.7 1.0
O A:HOH2060 4.3 30.8 1.0
O A:SER30 4.3 14.2 1.0
OG1 E:THR432 4.4 20.8 1.0
CA E:LEU433 4.4 14.0 1.0
N E:LEU433 4.4 14.0 1.0
OD2 E:ASP146 4.4 11.7 1.0
CA E:THR432 4.5 15.9 1.0
OD1 A:ASN29 4.5 13.7 1.0
N E:SER434 4.5 14.8 1.0
CG E:PRO342 4.8 15.4 1.0
CB A:SER32 4.8 14.6 1.0
O A:HOH2065 4.9 19.5 1.0
C E:LEU433 4.9 14.8 1.0
CB A:ASN29 4.9 13.1 1.0
O A:HOH2067 4.9 16.4 1.0

Calcium binding site 5 out of 6 in 2iuf

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Calcium binding site 5 out of 6 in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1710

b:35.4
occ:1.00
 O A:HOH2702 2.2 17.0 1.0
O E:HOH2297 2.2 22.5 1.0
O E:HOH2650 2.2 32.3 1.0
O A:HOH2319 2.3 20.0 1.0
O E:HOH2652 2.3 18.0 1.0
O E:HOH2294 2.5 48.3 1.0
OE1 A:GLN245 3.9 13.3 1.0
OE1 E:GLN245 3.9 14.9 1.0
OD2 A:ASP628 4.0 15.0 1.0
O A:HOH2655 4.0 13.8 1.0
OD2 E:ASP628 4.0 15.5 1.0
OD1 A:ASP628 4.1 17.0 1.0
OD1 E:ASP628 4.1 15.8 1.0
ND2 A:ASN624 4.1 16.8 1.0
OD1 A:ASN624 4.1 19.0 1.0
O E:HOH2609 4.1 17.3 1.0
ND2 E:ASN624 4.2 17.4 1.0
OD1 E:ASN624 4.2 19.7 1.0
CG A:ASP628 4.4 14.6 1.0
CG E:ASP628 4.5 15.3 1.0
CG A:ASN624 4.5 17.7 1.0
CG E:ASN624 4.6 18.5 1.0
CD A:GLN245 4.7 14.0 1.0
CD E:GLN245 4.7 14.5 1.0
NH2 A:ARG631 4.7 34.5 1.0
NH2 E:ARG631 4.8 31.9 1.0
O E:HOH2296 4.8 16.8 1.0
O E:HOH2112 4.8 40.1 1.0
O E:HOH2257 4.9 35.1 1.0
NE2 A:GLN245 4.9 14.1 1.0
O A:HOH2320 4.9 17.9 1.0
NE2 E:GLN245 5.0 10.5 1.0

Calcium binding site 6 out of 6 in 2iuf

Go back to Calcium Binding Sites List in 2iuf
Calcium binding site 6 out of 6 in the The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structures of Penicillium Vitale Catalase: Resting State, Oxidised State (Compound I) and Complex with Aminotriazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1711

b:29.4
occ:0.50
 O E:HOH2160 2.0 33.2 1.0
O E:HOH2395 2.1 19.0 1.0
O A:HOH2430 2.1 16.0 0.5
O E:HOH2393 2.2 19.5 0.5
O E:GLY360 4.1 14.7 1.0
O A:GLY360 4.1 13.5 1.0
O E:HOH2394 4.3 25.5 1.0
O A:HOH2429 4.3 32.7 1.0
O E:HOH2392 4.6 27.7 1.0
O A:HOH2431 4.7 36.2 1.0
CA E:GLY360 4.7 11.9 1.0
CA A:GLY360 4.8 11.5 1.0
C E:GLY360 4.8 14.0 1.0
C A:GLY360 4.9 12.5 1.0

Reference:

M.Alfonso-Prieto, A.Borovik, X.Carpena, G.Murshudov, W.Melik-Adamyan, I.Fita, C.Rovira, P.C.Loewen. The Structures and Electronic Configuration of Compound I Intermediates of Helicobacter Pylori and Penicillium Vitale Catalases Determined By X-Ray Crystallography and Qm/Mm Density Functional Theory Calculations. J.Am.Chem.Soc. V. 129 4193 2007.
ISSN: ISSN 0002-7863
PubMed: 17358056
DOI: 10.1021/JA063660Y
Page generated: Sat Dec 12 03:40:37 2020

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