Atomistry » Zinc » PDB 3wym-3zqr » 3zfk
Atomistry »
  Zinc »
    PDB 3wym-3zqr »
      3zfk »

Zinc in PDB 3zfk: N-Terminal Truncated Nuclease Domain of Colicin E7

Protein crystallography data

The structure of N-Terminal Truncated Nuclease Domain of Colicin E7, PDB code: 3zfk was solved by E.Toth, A.Czene, B.Gyurcsik, H.Otten, J.-C.N.Poulsen, S.Larsen, H.E.M.Christensen, K.Nagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.099 / 1.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 55.400, 55.400, 73.200, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 23.43

Other elements in 3zfk:

The structure of N-Terminal Truncated Nuclease Domain of Colicin E7 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the N-Terminal Truncated Nuclease Domain of Colicin E7 (pdb code 3zfk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the N-Terminal Truncated Nuclease Domain of Colicin E7, PDB code: 3zfk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3zfk

Go back to Zinc Binding Sites List in 3zfk
Zinc binding site 1 out of 2 in the N-Terminal Truncated Nuclease Domain of Colicin E7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N-Terminal Truncated Nuclease Domain of Colicin E7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:40.5
occ:1.00
HE2 A:HIS569 1.4 25.6 1.0
HE2 A:HIS573 1.5 39.4 1.0
ND1 A:HIS544 2.0 27.5 1.0
NE2 A:HIS569 2.2 21.4 1.0
O4 A:SO41136 2.2 19.7 1.0
NE2 A:HIS573 2.3 32.8 1.0
CE1 A:HIS544 2.8 29.6 1.0
HD2 A:HIS569 2.9 27.7 1.0
O3 A:SO41136 2.9 26.2 1.0
CD2 A:HIS569 2.9 23.1 1.0
HE1 A:HIS544 2.9 35.5 1.0
HA A:HIS544 3.0 24.3 1.0
S A:SO41136 3.0 26.1 1.0
CG A:HIS544 3.1 19.0 1.0
CD2 A:HIS573 3.1 37.1 1.0
HD2 A:HIS573 3.2 44.6 1.0
CE1 A:HIS569 3.3 22.4 1.0
CE1 A:HIS573 3.3 40.4 1.0
H A:HIS545 3.4 17.8 1.0
HB2 A:HIS544 3.4 26.9 1.0
CB A:HIS544 3.6 22.4 1.0
HE1 A:HIS573 3.6 48.5 1.0
HE1 A:HIS569 3.7 26.9 1.0
CA A:HIS544 3.7 20.2 1.0
O A:HOH2072 4.0 33.0 1.0
NE2 A:HIS544 4.0 25.0 1.0
N A:HIS545 4.0 14.8 1.0
O2 A:SO41136 4.0 33.2 1.0
O1 A:SO41136 4.0 38.3 1.0
CG A:HIS569 4.1 22.8 1.0
CD2 A:HIS544 4.1 22.4 1.0
ND1 A:HIS569 4.3 23.3 1.0
CG A:HIS573 4.3 38.2 1.0
C A:HIS544 4.4 14.4 1.0
ND1 A:HIS573 4.4 38.0 1.0
HB3 A:HIS544 4.5 26.9 1.0
O A:LEU543 4.6 20.0 1.0
O A:HIS545 4.7 20.4 1.0
HE2 A:HIS544 4.8 30.0 1.0
N A:HIS544 4.9 19.9 1.0
HB A:ILE572 5.0 52.5 1.0

Zinc binding site 2 out of 2 in 3zfk

Go back to Zinc Binding Sites List in 3zfk
Zinc binding site 2 out of 2 in the N-Terminal Truncated Nuclease Domain of Colicin E7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N-Terminal Truncated Nuclease Domain of Colicin E7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:24.6
occ:1.00
ND1 B:HIS544 1.7 17.6 1.0
NE2 B:HIS569 2.1 20.6 1.0
NE2 B:HIS573 2.1 29.2 1.0
O1 B:SO41134 2.1 23.6 1.0
CE1 B:HIS544 2.5 33.8 1.0
HE1 B:HIS544 2.7 40.6 1.0
O3 B:SO41134 2.8 35.1 1.0
CG B:HIS544 2.8 20.9 1.0
CD2 B:HIS569 2.9 24.9 1.0
CD2 B:HIS573 2.9 34.3 1.0
HD2 B:HIS573 2.9 41.1 1.0
HD2 B:HIS569 3.0 29.9 1.0
S B:SO41134 3.0 27.6 1.0
HA B:HIS544 3.1 23.6 1.0
CE1 B:HIS569 3.2 18.0 1.0
CE1 B:HIS573 3.2 41.2 1.0
HB2 B:HIS544 3.3 27.5 1.0
CB B:HIS544 3.4 22.9 1.0
HE1 B:HIS569 3.5 21.6 1.0
H B:HIS545 3.5 19.0 1.0
HE1 B:HIS573 3.5 49.5 1.0
NE2 B:HIS544 3.7 20.8 1.0
CA B:HIS544 3.7 19.6 1.0
CD2 B:HIS544 3.9 25.3 1.0
O B:HOH2065 3.9 31.4 1.0
O4 B:SO41134 4.0 31.6 1.0
O2 B:SO41134 4.0 38.2 1.0
N B:HIS545 4.1 15.9 1.0
CG B:HIS569 4.1 21.1 1.0
CG B:HIS573 4.1 41.1 1.0
ND1 B:HIS569 4.2 21.6 1.0
ND1 B:HIS573 4.2 37.0 1.0
HB3 B:HIS544 4.4 27.5 1.0
C B:HIS544 4.4 14.4 1.0
HE2 B:HIS544 4.4 25.0 1.0
O B:LEU543 4.7 16.7 1.0
O B:HIS545 4.7 19.1 1.0
HD2 B:HIS544 4.7 30.4 1.0
HB B:ILE572 4.9 51.8 1.0
N B:HIS544 4.9 18.7 1.0
HD1 B:HIS569 5.0 26.0 1.0

Reference:

A.Czene, E.Toth, E.Nemeth, H.Otten, J.-C.N.Poulsen, H.E.M.Christensen, L.Rulisek, K.Nagata, S.Larsen, B.Gyurcsik. Tracing the Reason of Inactivity of A Mutant Colicin E7 Metallonuclease: A Hint to An Alternative Catalytic Mechanism? To Be Published.
Page generated: Wed Dec 16 04:59:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy