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Zinc in PDB 3ez5: Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).

Enzymatic activity of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).

All present enzymatic activity of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).:
2.7.7.7;

Protein crystallography data

The structure of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form)., PDB code: 3ez5 was solved by J.J.Warren, E.Y.Wu, A.A.Golosov, M.Karplus, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.83 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.551, 108.572, 149.756, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form). (pdb code 3ez5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form)., PDB code: 3ez5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3ez5

Go back to Zinc Binding Sites List in 3ez5
Zinc binding site 1 out of 5 in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:29.5
occ:0.30
 O2G A:DAD201 1.9 42.2 1.0
O2B A:DAD201 1.9 41.6 1.0
OD2 A:ASP830 2.0 40.6 1.0
O A:TYR654 2.0 40.1 1.0
O2A A:DAD201 2.2 39.0 1.0
OD1 A:ASP653 2.7 50.1 1.0
CG A:ASP830 3.1 36.8 1.0
C A:TYR654 3.2 40.1 1.0
PB A:DAD201 3.2 40.0 1.0
PG A:DAD201 3.3 43.3 1.0
CG A:ASP653 3.4 44.3 1.0
PA A:DAD201 3.5 38.3 1.0
OD2 A:ASP653 3.6 48.6 1.0
O3B A:DAD201 3.6 39.5 1.0
OD1 A:ASP830 3.6 36.9 1.0
ZN A:ZN5 3.7 32.1 0.2
O3A A:DAD201 3.8 38.1 1.0
N A:TYR654 4.1 39.5 1.0
N A:SER655 4.1 40.1 1.0
CA A:TYR654 4.1 39.9 1.0
C5' A:DAD201 4.2 38.1 1.0
CA A:SER655 4.2 40.6 1.0
N A:GLN656 4.2 41.1 1.0
O3G A:DAD201 4.3 44.0 1.0
CB A:ASP830 4.4 33.2 1.0
O5' A:DAD201 4.4 39.4 1.0
C A:SER655 4.5 40.8 1.0
O1G A:DAD201 4.5 39.5 1.0
CB A:TYR654 4.5 39.7 1.0
C A:ASP653 4.6 40.2 1.0
O1B A:DAD201 4.6 40.5 1.0
CG2 A:ILE657 4.7 40.8 1.0
CB A:ASP653 4.7 41.6 1.0
N A:ILE657 4.7 41.5 1.0
O A:ASP830 4.7 33.3 1.0
O1A A:DAD201 4.7 38.4 1.0

Zinc binding site 2 out of 5 in 3ez5

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Zinc binding site 2 out of 5 in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5

b:32.1
occ:0.20
 OE2 A:GLU831 2.1 42.7 1.0
OD1 A:ASP830 2.2 36.9 1.0
OD2 A:ASP653 2.6 48.6 1.0
O2A A:DAD201 2.8 39.0 1.0
OD1 A:ASP653 2.9 50.1 1.0
CG A:ASP653 3.0 44.3 1.0
CG A:ASP830 3.2 36.8 1.0
CD A:GLU831 3.2 40.0 1.0
OD2 A:ASP830 3.4 40.6 1.0
CG A:GLU831 3.7 36.4 1.0
ZN A:ZN4 3.7 29.5 0.3
C3' B:DG29 4.0 27.1 1.0
CB A:GLU831 4.1 33.3 1.0
PA A:DAD201 4.2 38.3 1.0
OE1 A:GLU831 4.3 38.4 1.0
CB A:ASP653 4.3 41.6 1.0
C5' B:DG29 4.3 28.1 1.0
C4' B:DG29 4.4 28.0 1.0
O A:ASP830 4.4 33.3 1.0
C A:ASP830 4.5 32.9 1.0
O2G A:DAD201 4.5 42.2 1.0
CB A:ASP830 4.5 33.2 1.0
O1A A:DAD201 4.6 38.4 1.0
O5' A:DAD201 4.6 39.4 1.0
N A:GLU831 4.7 32.2 1.0
O A:VAL828 4.7 30.2 1.0
OP1 B:DG29 4.8 31.9 1.0
C5' A:DAD201 4.8 38.1 1.0
O5' B:DG29 4.9 29.2 1.0
CA A:ASP830 4.9 32.5 1.0
CA A:GLU831 5.0 32.9 1.0

Zinc binding site 3 out of 5 in 3ez5

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Zinc binding site 3 out of 5 in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:29.6
occ:0.50
 O2G D:DAD202 1.9 31.0 1.0
OD2 D:ASP830 2.1 28.6 1.0
O2B D:DAD202 2.1 28.0 1.0
O2A D:DAD202 2.1 28.9 1.0
O D:TYR654 2.1 24.0 1.0
OD2 D:ASP653 2.4 29.9 0.5
PB D:DAD202 3.2 25.7 1.0
CG D:ASP830 3.2 23.7 1.0
C D:TYR654 3.4 24.2 1.0
PG D:DAD202 3.4 30.4 1.0
PA D:DAD202 3.5 24.7 1.0
CG D:ASP653 3.6 28.2 0.5
O3B D:DAD202 3.7 27.3 1.0
ZN D:ZN2 3.7 29.1 0.2
OD1 D:ASP830 3.8 28.0 1.0
O3A D:DAD202 3.8 26.7 1.0
OD1 D:ASP653 4.2 31.9 0.5
N D:GLN656 4.2 24.3 1.0
C5' D:DAD202 4.2 23.2 1.0
N D:SER655 4.3 23.3 1.0
N D:TYR654 4.3 24.4 1.0
CA D:TYR654 4.3 23.6 1.0
CA D:SER655 4.3 24.6 1.0
O D:HOH1027 4.4 41.0 1.0
CB D:ASP830 4.4 21.4 1.0
O5' D:DAD202 4.4 26.0 1.0
O3G D:DAD202 4.5 32.3 1.0
C D:SER655 4.5 23.8 1.0
O1G D:DAD202 4.5 25.7 1.0
O1B D:DAD202 4.6 27.4 1.0
N D:ILE657 4.7 21.3 1.0
CB D:TYR654 4.7 23.9 1.0
CB D:ASP653 4.7 27.0 0.5
CG2 D:ILE657 4.7 24.3 1.0
O1A D:DAD202 4.7 25.2 1.0
CB D:ASP653 4.7 27.7 0.5
O D:ASP830 4.8 21.1 1.0
C D:ASP653 4.9 27.1 1.0

Zinc binding site 4 out of 5 in 3ez5

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Zinc binding site 4 out of 5 in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:29.1
occ:0.20
 O D:HOH1027 2.0 41.0 1.0
O D:HOH968 2.0 46.2 1.0
OD1 D:ASP830 2.2 28.0 1.0
OD1 D:ASP653 2.3 31.9 0.5
O2A D:DAD202 2.8 28.9 1.0
OD2 D:ASP653 2.9 29.9 0.5
CG D:ASP653 2.9 28.2 0.5
CG D:ASP830 3.1 23.7 1.0
OD2 D:ASP830 3.3 28.6 1.0
ZN D:ZN1 3.7 29.6 0.5
C3' E:DG29 3.8 21.3 1.0
PA D:DAD202 4.1 24.7 1.0
C5' E:DG29 4.1 20.7 1.0
CB D:GLU831 4.2 23.6 1.0
C4' E:DG29 4.2 19.0 1.0
OE1 D:GLU831 4.3 37.6 1.0
CB D:ASP653 4.4 27.7 0.5
CB D:ASP653 4.4 27.0 0.5
O5' D:DAD202 4.5 26.0 1.0
CB D:ASP830 4.5 21.4 1.0
O1A D:DAD202 4.5 25.2 1.0
O D:VAL828 4.6 21.9 1.0
C D:ASP830 4.6 22.0 1.0
O D:ASP830 4.6 21.1 1.0
O2G D:DAD202 4.6 31.0 1.0
O5' E:DG29 4.6 22.5 1.0
C5' D:DAD202 4.8 23.2 1.0
CD D:GLU831 4.8 38.0 1.0
N D:GLU831 4.8 21.0 1.0
OP1 E:DG29 4.9 26.3 1.0
N D:ASP830 4.9 20.8 1.0
CA D:ASP830 4.9 21.2 1.0

Zinc binding site 5 out of 5 in 3ez5

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Zinc binding site 5 out of 5 in the Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cocrystal Structure of Bacillus Fragment Dna Polymerase I with Duplex Dna , Dctp, and Zinc (Closed Form). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn3

b:46.4
occ:0.25
 NE2 D:HIS867 2.1 43.2 1.0
OD2 D:ASP865 2.4 45.7 1.0
OD1 D:ASP865 2.7 44.1 1.0
CE1 D:HIS867 2.8 41.6 1.0
CG D:ASP865 2.9 39.1 1.0
CD2 D:HIS867 3.3 38.7 1.0
ND1 D:HIS867 4.1 41.7 1.0
CG D:HIS867 4.3 37.2 1.0
CB D:ASP865 4.4 34.8 1.0
OXT D:LYS876 4.5 47.9 1.0

Reference:

A.A.Golosov, J.J.Warren, L.S.Beese, M.Karplus. The Mechanism of the Translocation Step in Dna Replication By Dna Polymerase I: A Computer Simulation Analysis. Structure V. 18 83 2010.
ISSN: ISSN 0969-2126
PubMed: 20152155
DOI: 10.1016/J.STR.2009.10.014
Page generated: Wed Dec 16 04:17:19 2020

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