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Table 3 Zinc binding site patterns

From: Predicting zinc binding at the proteome level

Binding Site Patterns

N

Type

[CHDE] x(·) [CHDE] x(·) [CHDE] x(·) [CHDE]

232

 

[CH] x(·) [CH] x(·) [CH] x(·) [CH]

196

 

[CHDE] x(0–7) [CHDE] x(·) [CHDE] x(0–7) [CHDE]

161

 

[CHDE] x(0–7) [CHDE] x(> 7) [CHDE] x(0–7) [CHDE]

141

SLS

[CHDE] x(·) [CHDE] x(·) [CHDE]

122

 

[C] x(·) [C] x(·) [C] x(·) [C]

85

 

[CHDE] x(·) [CHDE]

62

 

[CHDE] x(0–7) [CHDE] x(> 7) [CHDE]

55

SL

[CH] x(·) [CH] x(·) [CH]

37

 

[CHDE] x(> 7) [CHDE] x(0–7) [CHDE]

24

LS

[CH] x(·) [CH]

21

 

[CHDE] x(0–7) [CHDE] x(> 7) [CHDE] x(> 7) [CHDE]

17

SLL

[CHDE] x(> 7) [CHDE] x(0–7) [CHDE] x(0–7) [CHDE]

16

LSS

[DE] x(·) [DE]

15

 

[DE] x(·) [DE] x(·) [DE]

10

 

[CHDE] x(> 7) [CHDE] x(> 7) [CHDE] x(0–7) [CHDE]

10

LLS

[CHDE] x(0–7) [CHDE] x(0–7) [CHDE] x(> 7) [CHDE]

8

SSL

[DE] x(·) [DE] x(·) [DE] x(·) [DE]

1

 
  1. Binding site patterns ordered by number of matches, N, in the 464 sites. Note that more than one pattern can match at a given site, thus the total number of matches is greater than the total number of sites. Square brackets denote alternative binding residues, x(·) denotes a sequence of residues of an arbitrary length, x(n - m) denotes a sequence of between n and m residues, x(> n) denotes a sequence of more than n residues. The type column highlights some common binding site patterns: S stands for "short" and refers to x(0–7), L stands for "long" and refers to x(> 7).
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BMC Bioinformatics

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