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Manganese in PDB 2kfn: Klenow Fragment with Bridging-Sulfur Substrate and Manganese

Enzymatic activity of Klenow Fragment with Bridging-Sulfur Substrate and Manganese

All present enzymatic activity of Klenow Fragment with Bridging-Sulfur Substrate and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Klenow Fragment with Bridging-Sulfur Substrate and Manganese, PDB code: 2kfn 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 / 2.03
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 102.900, 102.900, 86.400, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25

Other elements in 2kfn:

The structure of Klenow Fragment with Bridging-Sulfur Substrate and Manganese also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 3 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 1 in 2kfn

Go back to Manganese Binding Sites List in 2kfn
Manganese binding site 1 out of 1 in the Klenow Fragment with Bridging-Sulfur Substrate and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Klenow Fragment with Bridging-Sulfur Substrate and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn2

b:65.8
occ:1.00
O A:HOH4 2.2 34.8 1.0
OD1 A:ASP355 2.4 43.9 1.0
S B:US11006 2.6 58.1 1.0
OP1 B:DG1007 2.9 51.7 1.0
CG A:ASP355 3.4 30.6 1.0
P B:DG1007 3.4 47.0 1.0
OD2 A:ASP355 3.7 31.1 1.0
C4' B:US11006 3.8 61.7 1.0
ZN A:ZN1 3.9 31.9 1.0
C3' B:US11006 3.9 60.2 1.0
OD1 A:ASP424 3.9 23.6 1.0
O A:GLN419 4.1 22.0 1.0
O A:HOH18 4.1 25.4 1.0
O A:THR356 4.1 18.8 1.0
OD2 A:ASP424 4.2 27.3 1.0
C5' B:US11006 4.3 60.4 1.0
O5' B:DG1007 4.4 52.6 1.0
C5' B:DG1007 4.4 44.4 1.0
O A:HOH165 4.4 39.7 1.0
CG A:ASP424 4.5 23.0 1.0
OP2 B:DG1007 4.5 49.3 1.0
CB A:ASP355 4.6 21.8 1.0
C2' B:US11006 4.6 60.5 1.0
N A:THR356 4.7 22.3 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: Tue Dec 15 04:03:29 2020

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