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Table 5 Summary of the results of case study 3: Sub-patterns of the Cys2His2 zinc finger

From: GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Gap

Protein

Cath Code (0 = No value)

AVG Distance

G1

G2

G3

PDBs

Classification

Organism

C

A

T

H

ZN-Cys1

ZN-Cys2

ZN-His1

ZN-His2

2

12

2

4

TRANSCRIPTION (1),

HOMO SAPIENS (4)

0(2)

0(2)

0(2)

0(2)

2.25

2.31

2.07

5.49

    

METAL BINDING

 

3(1)

30(1)

40(1)

200(1)

    
    

PROTEIN/DNA (1),

 

3(1)

30(1)

160(1)

60(1)

    
    

TRANSCRIPTION/DNA(1),

         
    

...

         

2

12

3

4

TRANSCRIPTION (139),

HOMO SAPIENS (261),

0(198)

0(198)

0(198)

0(198)

2.33

2.26

2.08

2.07

    

TRANSCRIPTION/DNA (91),

UNDEFINED (50),

2(1)

60(1)

40(1)

10(1)

    
    

GENE REGULATION/DNA (10),

MUS MUSCULUS (40),

3(172)

30(172)

160(172)

60(172)

    
    

UNKNOWN FUNCTION (5),

MUS (10),

3(4)

30(4)

428(4)

10(4)

    
    

...

...

        

2

12

4

97

TRANSCRIPTION (29),

MUS MUSCULUS (6),

0(66)

0(66)

0(66)

0 (66)

2.30

2.24

2.05

2.05

    

TRANSCRIPTION/DNA (22),

HOMO SAPIENS (70),

2(1)

170(1)

270(1)

10(1)

    
    

METAL BINDING PROTEIN (7),

UNDEFINED (11),

3(30)

30(30)

160(30)

60(30)

    
    

...

...

        

2

12

5

15

TRANSCRIPTION (15),

HOMO SAPIENS (9),

0(4)

0(4)

0(4)

0(4)

2.32

2.29

2.37

2.60

    

RNA BINDING

MUS MUSCULUS (1),

1(1)

10(1)

10(1)

790(1)

    
    

PROTEIN RNA (1),

XENOPUS LAEVIS (2),

3(10)

30(10)

160(10)

60(10)

    
    

...

...

        

3

12

4

1

METAL BINDING PROTEIN (1)

HOMO SAPIENS (1)

0(1)

0(1)

0(1)

0(1)

6.00

1.72

1.94

2.32

3

12

5

2

RNA BINDING PROTEIN (69),

XENOPUS LAEVIS (1),

2(1)

30(1)

170(1)

10(1)

5.60

3.15

3.60

4.29

    

METAL BINDING PROTEIN (1)

SYNECHOCOCCUS

3(1)

30(1)

160(1)

60(1)

    
     

ELONGATUS (1)

        

4

12

3

117

TRANSCRIPTION DNA (69),

HOMO SAPIENS (63),

0(42)

0(42)

0(42)

0(42)

2.28

2.30

2.07

2.04

    

TRANSCRIPTION

MUS MUSCULUS (19),

3(75)

30(75)

160(75)

60(75)

    
    

FACTOR/DNA (6),

ESCHERICHIA COLI (2),

        
    

...

...

        

4

12

4

8

METAL BINDING PROTEIN (1),

HOMO SAPIENS (3),

0(4)

0(4)

0(4)

0(4)

2.26

2.26

2.07

2.14

    

PROTEIN BINDING (1),

ARABIDOPSIS

3(4)

30(4)

160(4)

60(4)

    
    

DNA BINDING PROTEIN (2),

THALIANA (1),

        
    

...

...

        

4

12

6

2

TRANSLATION

HOMO SAPIENS (2)

3(2)

30(2)

40(2)

130(2)

2.13

2.13

1.99

6.95

    

REGULATOR (1),

         
    

METAL BINDING PROTEIN (1)

         
   

630

      

2.33

2.26

2.08

2.12

  1. Each row contains information of a sub-pattern, where G1, G2 and G3 indicate the specific sizes for the gaps of the pattern shown in Fig. 7a. For instance, the textual representation of the first sub-pattern is C-X(2)-C-X(12)-H-X(2)-H