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Zinc in PDB 2kzm: Klenow Fragment with Normal Substrate and Zinc and Manganese

Enzymatic activity of Klenow Fragment with Normal Substrate and Zinc and Manganese

All present enzymatic activity of Klenow Fragment with Normal Substrate and Zinc and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Klenow Fragment with Normal Substrate and Zinc and Manganese, PDB code: 2kzm was solved by C.A.Brautigam, S.Sun, J.A.Piccirilli, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 102.600, 102.600, 86.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.3

Other elements in 2kzm:

The structure of Klenow Fragment with Normal Substrate and Zinc and Manganese also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Klenow Fragment with Normal Substrate and Zinc and Manganese (pdb code 2kzm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Klenow Fragment with Normal Substrate and Zinc and Manganese, PDB code: 2kzm:

Zinc binding site 1 out of 1 in 2kzm

Go back to Zinc Binding Sites List in 2kzm
Zinc binding site 1 out of 1 in the Klenow Fragment with Normal Substrate and Zinc and Manganese


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Klenow Fragment with Normal Substrate and Zinc and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:23.8
occ:1.00
OD2 A:ASP501 1.9 23.1 1.0
OD2 A:ASP355 2.0 27.4 1.0
OP1 B:DC1008 2.0 35.9 1.0
OE2 A:GLU357 2.2 31.5 1.0
CG A:ASP501 3.0 24.8 1.0
CG A:ASP355 3.0 29.8 1.0
CD A:GLU357 3.2 30.7 1.0
P B:DC1008 3.3 25.3 1.0
OE1 A:GLU357 3.5 38.4 1.0
OD1 A:ASP355 3.5 40.5 1.0
CB A:ASP501 3.5 22.4 1.0
MN B:MN2 3.7 69.8 1.0
CE1 A:TYR497 3.8 19.9 1.0
OP2 B:DC1008 3.9 24.4 1.0
O5' B:DC1008 4.1 21.0 1.0
OD1 A:ASP501 4.1 25.6 1.0
O A:THR356 4.2 22.2 1.0
CB A:ASP355 4.3 25.4 1.0
CD1 A:TYR497 4.4 16.9 1.0
O3' B:DG1007 4.4 26.2 1.0
C5' B:DC1008 4.4 21.6 1.0
CG A:GLU357 4.5 30.1 1.0
CA A:ALA498 4.5 14.9 1.0
O A:ALA498 4.7 20.9 1.0
CZ A:TYR497 4.7 22.0 1.0
OH A:TYR497 4.8 18.8 1.0
O A:TYR497 4.9 17.6 1.0

Reference:

C.A.Brautigam, S.Sun, J.A.Piccirilli, T.A.Steitz. Structures of Normal Single-Stranded Dna and Deoxyribo-3'-S-Phosphorothiolates Bound to the 3'-5' Exonucleolytic Active Site of Dna Polymerase I From Escherichia Coli. Biochemistry V. 38 696 1999.
ISSN: ISSN 0006-2960
PubMed: 9888810
DOI: 10.1021/BI981537G
Page generated: Wed Dec 16 03:35:39 2020

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