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Zinc in PDB 5j0e: Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)

Protein crystallography data

The structure of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32), PDB code: 5j0e was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.62 / 2.81
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 46.906, 46.906, 99.044, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) (pdb code 5j0e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32), PDB code: 5j0e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5j0e

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Zinc binding site 1 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:42.2
occ:1.00
N7 A:DG12 2.3 45.6 1.0
C5 A:DG12 3.2 41.3 1.0
O6 A:DG12 3.2 49.4 1.0
C8 A:DG12 3.3 39.4 1.0
C6 A:DG12 3.6 44.0 1.0
OP2 A:DG12 4.3 32.1 1.0
C4 A:DG12 4.4 34.9 1.0
N9 A:DG12 4.5 33.9 1.0
N1 A:DG12 5.0 40.7 1.0

Zinc binding site 2 out of 9 in 5j0e

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Zinc binding site 2 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:39.1
occ:1.00
O A:HOH205 1.8 8.0 1.0
O A:HOH203 2.2 38.3 1.0
OP1 A:DG12 2.2 28.6 1.0
P A:DG12 3.6 33.3 1.0
OP2 A:DG12 4.3 32.1 1.0
O3' A:DC11 4.3 27.9 1.0
O A:HOH208 4.6 2.0 1.0
O5' A:DG12 4.7 27.0 1.0
C5' A:DG12 5.0 26.8 1.0

Zinc binding site 3 out of 9 in 5j0e

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Zinc binding site 3 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn101

b:31.2
occ:1.00
O B:HOH201 1.8 2.0 1.0
N7 B:DG24 2.1 13.3 1.0
O B:HOH204 2.2 2.0 1.0
C5 B:DG24 3.1 14.4 1.0
C8 B:DG24 3.1 13.8 1.0
O6 B:DG24 3.2 14.2 1.0
C6 B:DG24 3.5 14.9 1.0
OP2 B:DG24 3.9 25.3 1.0
C4 B:DG24 4.2 14.4 1.0
N9 B:DG24 4.3 16.2 1.0
N1 B:DG24 4.8 15.8 1.0

Zinc binding site 4 out of 9 in 5j0e

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Zinc binding site 4 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:48.1
occ:1.00
N7 C:DG12 2.5 55.8 1.0
C5 C:DG12 3.4 55.5 1.0
C8 C:DG12 3.5 52.1 1.0
O6 C:DG12 3.5 57.1 1.0
C6 C:DG12 3.8 58.8 1.0
OP2 C:DG12 4.6 50.8 1.0
N9 C:DG12 4.7 49.5 1.0
C4 C:DG12 4.7 50.1 1.0

Zinc binding site 5 out of 9 in 5j0e

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Zinc binding site 5 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn102

b:37.2
occ:1.00
OP1 C:DG12 2.1 49.4 1.0
P C:DG12 3.5 52.4 1.0
OP2 C:DG12 4.2 50.8 1.0
O3' C:DC11 4.4 45.3 1.0
O5' C:DG12 4.5 49.2 1.0

Zinc binding site 6 out of 9 in 5j0e

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Zinc binding site 6 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:43.6
occ:1.00
O D:HOH204 2.0 4.9 1.0
N7 D:DG24 2.3 29.0 1.0
O D:HOH203 2.4 5.9 1.0
O6 D:DG24 3.1 30.8 1.0
C5 D:DG24 3.2 28.2 1.0
C8 D:DG24 3.4 28.2 1.0
C6 D:DG24 3.5 29.3 1.0
OP2 D:DG24 3.7 52.2 1.0
C4 D:DG24 4.5 26.6 1.0
N9 D:DG24 4.6 28.6 1.0
N1 D:DG24 4.9 30.5 1.0

Zinc binding site 7 out of 9 in 5j0e

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Zinc binding site 7 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:35.0
occ:1.00
O E:HOH204 2.0 10.7 1.0
N7 E:DG12 2.1 22.6 1.0
O E:HOH206 2.2 26.4 1.0
O E:HOH201 2.3 3.3 1.0
C8 E:DG12 2.9 24.2 1.0
C5 E:DG12 3.3 21.4 1.0
OP2 E:DG12 3.7 47.8 1.0
O6 E:DG12 3.9 19.6 1.0
C6 E:DG12 4.0 21.9 1.0
N9 E:DG12 4.2 25.2 1.0
C4 E:DG12 4.4 21.5 1.0
O5' E:DG12 4.7 39.4 1.0
P E:DG12 4.8 48.4 1.0

Zinc binding site 8 out of 9 in 5j0e

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Zinc binding site 8 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn101

b:50.4
occ:1.00
N7 F:DG24 2.4 37.4 1.0
C5 F:DG24 3.4 34.2 1.0
C8 F:DG24 3.4 35.5 1.0
O6 F:DG24 3.4 38.9 1.0
C6 F:DG24 3.8 37.5 1.0
OP2 F:DG24 4.4 46.7 1.0
N9 F:DG24 4.6 35.2 1.0
C4 F:DG24 4.6 31.2 1.0

Zinc binding site 9 out of 9 in 5j0e

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Zinc binding site 9 out of 9 in the Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structures of Pribnow Box Consensus Promoter Sequence (P32) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn102

b:43.1
occ:1.00
O F:HOH209 1.9 2.0 1.0
OP1 F:DG24 2.2 32.3 1.0
P F:DG24 3.6 40.9 1.0
O F:HOH215 4.3 8.5 1.0
OP2 F:DG24 4.4 46.7 1.0
O3' F:DC23 4.4 38.1 1.0
O5' F:DG24 4.8 36.5 1.0

Reference:

P.K.Mandal, G.W.Collie, S.C.Srivastava, B.Kauffmann, I.Huc. Structure Elucidation of the Pribnow Box Consensus Promoter Sequence By Racemic Dna Crystallography. Nucleic Acids Res. V. 44 5936 2016.
ISSN: ESSN 1362-4962
PubMed: 27137886
DOI: 10.1093/NAR/GKW367
Page generated: Wed Dec 16 06:24:14 2020

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