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Zinc in PDB 3m7k: Crystal Structure of Paci-Dna Enzyme Product Complex

Protein crystallography data

The structure of Crystal Structure of Paci-Dna Enzyme Product Complex, PDB code: 3m7k was solved by B.W.Shen, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.26 / 1.92
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 37.089, 114.927, 114.322, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.1

Other elements in 3m7k:

The structure of Crystal Structure of Paci-Dna Enzyme Product Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Platinum (Pt) 1 atom
Sodium (Na) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Paci-Dna Enzyme Product Complex (pdb code 3m7k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Paci-Dna Enzyme Product Complex, PDB code: 3m7k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3m7k

Go back to Zinc Binding Sites List in 3m7k
Zinc binding site 1 out of 2 in the Crystal Structure of Paci-Dna Enzyme Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn143

b:23.8
occ:1.00
SG A:CYS66 2.3 36.2 1.0
SG A:CYS109 2.3 28.0 1.0
SG A:CYS112 2.3 31.1 1.0
SG A:CYS63 2.4 32.3 1.0
CB A:CYS112 3.2 25.4 1.0
CB A:CYS63 3.2 35.4 1.0
CB A:CYS66 3.3 37.2 1.0
CB A:CYS109 3.5 26.4 1.0
N A:CYS66 3.8 37.5 1.0
N A:CYS109 4.0 27.1 1.0
N A:CYS112 4.1 24.0 1.0
CA A:CYS66 4.1 37.6 1.0
CA A:CYS112 4.3 25.2 1.0
CG2 A:ILE68 4.3 36.4 1.0
CA A:CYS109 4.3 26.0 1.0
O A:CYS109 4.7 25.1 1.0
CA A:CYS63 4.7 35.8 1.0
NE1 A:TRP136 4.8 37.8 1.0
C A:CYS109 4.8 25.3 1.0
CB A:TYR65 4.8 37.4 1.0
C A:CYS66 4.9 38.2 1.0
C A:TYR65 4.9 37.9 1.0
N A:GLY67 5.0 38.3 1.0

Zinc binding site 2 out of 2 in 3m7k

Go back to Zinc Binding Sites List in 3m7k
Zinc binding site 2 out of 2 in the Crystal Structure of Paci-Dna Enzyme Product Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Paci-Dna Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn144

b:37.8
occ:1.00
SG A:CYS4 2.3 53.9 1.0
SG A:CYS27 2.3 42.0 1.0
SG A:CYS24 2.3 42.9 1.0
SG A:CYS7 2.5 51.5 1.0
CB A:CYS4 3.1 56.2 1.0
CB A:CYS7 3.3 51.9 1.0
CB A:CYS27 3.3 39.6 1.0
CB A:CYS24 3.4 43.6 1.0
N A:CYS7 3.6 53.6 1.0
N A:CYS24 3.9 47.0 1.0
CA A:CYS7 4.0 52.3 1.0
N A:CYS27 4.1 38.2 1.0
CA A:CYS24 4.2 44.0 1.0
NH2 A:ARG9 4.2 44.5 1.0
CA A:CYS27 4.3 39.3 1.0
CB A:ARG6 4.5 56.2 1.0
CA A:CYS4 4.6 56.5 1.0
C A:ARG6 4.6 55.0 1.0
NE A:ARG9 4.7 46.0 1.0
CD1 A:LEU11 4.7 52.0 1.0
C A:CYS24 4.8 42.2 1.0
O A:CYS24 4.8 40.9 1.0
CA A:ARG6 4.9 55.9 1.0
N A:ARG6 4.9 55.8 1.0
C A:CYS4 5.0 56.3 1.0
CZ A:ARG9 5.0 44.2 1.0
CG A:ARG6 5.0 59.6 1.0

Reference:

B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, B.L.Stoddard. Unusual Target Site Disruption By the Rare-Cutting Hnh Restriction Endonuclease Paci. Structure V. 18 734 2010.
ISSN: ISSN 0969-2126
PubMed: 20541511
DOI: 10.1016/J.STR.2010.03.009
Page generated: Wed Dec 16 04:34:30 2020

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