Atomistry » Calcium » PDB 2io4-2j3o » 2iuf
Atomistry »
  Calcium »
    PDB 2io4-2j3o »
      2iuf »

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

Go back to Calcium Binding Sites List in 2iuf
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

Go back to Calcium Binding Sites List in 2iuf
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

Go back to Calcium Binding Sites List in 2iuf
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

Go back to Calcium Binding Sites List in 2iuf
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: Fri Jul 12 13:10:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy