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Analysis of the Cupredoxins - blue copper proteins (CATH:2.60.40.420) dataset

There are 3 entries in this dataset.


Entry Number Enzyme Name EC Code PDB Code CATH Code
M0004
Structure Overview
nitrite reductase (NO-forming) 1.7.2.1 1nia 2.60.40.420
2.60.40.420
M0124
Structure Overview
cytochrome-c oxidase 1.9.3.1 1v54 1.20.210.10
2.60.40.420
4.10.51.10
1.20.210.10
1.10.442.10
2.60.11.10
1.25.40.40
1.20.120.80
4.10.81.10
4.10.91.10
4.10.93.10
1.10.10.140
1.10.287.90
4.10.95.10
4.10.49.10
1.10.287.70
M0278
Structure Overview
plastoquinol-plastocyanin reductase 1.10.99.1 2b3i 2.60.40.420

EC Class Composition

    


CATH Domain Composition

Step Analysis

There are an average of 5.33 number of steps in this dataset. The median number of steps is 3. The maximum number of steps in this dataset is 11 and the minimum is 2. The following graph shows the frequency of MACiE entries in this dataset with a given number of steps.


Amino Acid Residues

There are an average of 6.66 number of catalytic amino acid residues in a MACiE reaction for this dataset. The maximum number of amino acid residues in this dataset is 12 and the minimum is 4. The following barchart shows the frequency of the different catalytic amino acid residues in this dataset.


For the purposes of the following graph, amino acid residues are split into three generaic categories: polar (neutral), polar (charged) and hydrophobic. The neutral residues are: Ser, Thr, Cys, Asn, Gln, Tyr as well as the main chain portions of the amide and carbonyl groups. The charged residues are: Lys, Arg, His, Asp, Glu as well as the main chain portions of the N and C termini. The hydrophobic residues are: Ala, Val, Leu, Ile, Met, Phe, Trp, Pro, Gly. The following pie charts show the distribution of amino acid residue type by dataset (left) to the complete MACiE dataset (right)

    

Key

1.0-0.9 0.9-0.8 0.8-0.7 0.7-0.6 0.6-0.5 0.5-0.4 0.4-0.3 0.3-0.2 0.2-0.1 0.1-0.0 =0

Functional Profiles of the catalytic amino acids in Cupredoxins - blue copper proteins (CATH:2.60.40.420) Entries

Activation Steric Stabilisation Proton Shuttling Hydrogen Shuttling Single Electron Shuttling Electron Pair Shuttling Covalent Catalysis
Arg
(0.33)
---1
0.33
----
Asn--------
Asp
(0.66)
0.5
0.33
--0.5
0.33
----
Cys
(0.66)
--0.5
0.33
--0.5
0.33
--
Gln--------
Glu
(0.33)
---1
0.33
----
His
(1)
0.16
0.16
-0.5
0.5
0.33
0.33
-0.33
0.33
--
Lys
(0.33)
---1
0.33
----
Phe--------
Ser
(0.33)
---1
0.33
----
Thr
(0.33)
---1
0.33
----
Trp
(0.33)
---1
0.33
----
Tyr
(0.33)
---1
0.33
1
0.33
1
0.33
--

The number below the residue name is the normalisation factor, and is calculated as the number of reactions in which that residue type occurs, divided by the total number of reactions in the dataset. The top number (emboldened) is the raw profile of that residue type and is calculated as the total number of unique residues of a given type performing a given function divided by the total number of that residue type in the dataset. The lower number is the normalised profile, which is calculated as the raw profile multiplied by the normalisation factor. Thus, if the residue is only ever seen in the dataset acting as a stabiliser, the raw profile will be 1, however, if that residue is only present in half the reactions, then the normailsation factor will be 0.5 and the normalised profile will also be 0.5.

Catalytic Machinery Similarities

This is calculated as a combination of the complement of catalytic amino acid residues present in each entry and the superimposition of the active site as calculated using IsoCleft.


M0004
1.7.2.1
M0124
1.9.3.1
M0278
1.10.99.1
M0004
1.7.2.1
10.21760.6427
M0124
1.9.3.1
0.217610.1655
M0278
1.10.99.1
0.64270.16551

Cofactors

Number of Metal Cofactors Number of Organic CofactorsCu(II)Dinuclear CuHeme A
M0004
1.7.2.1
2 2
M0124
1.9.3.1
4 112
M0278
1.10.99.1
1 1

Mechanisms

The following graphs show the distribution of mechanism class by dataset (left) to the complete MACiE dataset (right)

    

The following graphs show the distribution of mechanism type by dataset (left) to the complete MACiE dataset (right)

    


Bond Changes

Overall Reaction Overview

N-O
Cleaved
O-H
Formed
O-O
Cleaved
M0004
1.7.2.1
11
M0124
1.9.3.1
41
M0278
1.10.99.1

Overall Reaction (Bond only) Similarities

Key

1.0-0.9 0.9-0.8 0.8-0.7 0.7-0.6 0.6-0.5 0.5-0.4 0.4-0.3 0.3-0.2 0.2-0.1 0.1-0.0 =0

M0004
1.7.2.1
M0124
1.9.3.1
M0278
1.10.99.1
M0004
1.7.2.1
10.26660
M0124
1.9.3.1
0.266610
M0278
1.10.99.1
001

View overall reaction images

Step Centric Overview

MACiE Id Total Number of Overall Bond Changes Total Number of Steps Total Number of Step Bond Changes Average Number of bond changes per step Total Number of Bonds Formed Total Number of Bonds Cleaved Total Number of Bonds Changed Order
M0004
1.7.2.1
2 3 7 2.33 3 4 0
M0124
1.9.3.1
5 11 304 27.63 140 142 22
M0278
1.10.99.1
0 2 0 0 0 0 0

C-O
1 to 2
C-O
2 to 1
Cu-N
Formed
Cu-O
Formed
Cu-O
Cleaved
Fe-O
Cleaved
Fe-O
1 to 2
Fe-O
2 to 1
N-H
Formed
N-H
Cleaved
N-O
Cleaved
O-H
Formed
O-H
Cleaved
O-O
Cleaved
M0004
1.7.2.1
1111111
M0124
1.9.3.1
1010121113131261261
M0278
1.10.99.1

Composite Reaction (Bond only) Similarities

Key

1.0-0.9 0.9-0.8 0.8-0.7 0.7-0.6 0.6-0.5 0.5-0.4 0.4-0.3 0.3-0.2 0.2-0.1 0.1-0.0 =0

This measure of similarity is based off the sum of all the bond changes in all the steps involved in the reaction mechanism.


M0004
1.7.2.1
M0124
1.9.3.1
M0278
1.10.99.1
M0004
1.7.2.1
10.00870
M0124
1.9.3.1
0.008710
M0278
1.10.99.1
001

Reaction Similarities

Key

1.0-0.9 0.9-0.8 0.8-0.7 0.7-0.6 0.6-0.5 0.5-0.4 0.4-0.3 0.3-0.2 0.2-0.1 0.1-0.0 =0

Combined Similarities

This measure of similarity is based off the overall reaction bond change (10%), the sum of all the bond changes in all the steps involved in the reaction mechanism (65%) plus the complement of catalytic residues (25%) to give an estimate of the total similarity between two reactions.


M0004
1.7.2.1
M0124
1.9.3.1
M0278
1.10.99.1
M0004
1.7.2.1
10.08670.1606
M0124
1.9.3.1
0.086710.0413
M0278
1.10.99.1
0.16060.04131
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