Atomistry » Calcium » PDB 1px7-1qcp » 1q39
Atomistry »
  Calcium »
    PDB 1px7-1qcp »
      1q39 »

Calcium in PDB 1q39: Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution.

Protein crystallography data

The structure of Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution., PDB code: 1q39 was solved by G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.Kycia, A.P.Grollman, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.02 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.721, 79.578, 169.653, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 29.9

Other elements in 1q39:

The structure of Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution. also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution. (pdb code 1q39). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution., PDB code: 1q39:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 1q39

Go back to Calcium Binding Sites List in 1q39
Calcium binding site 1 out of 3 in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:56.8
occ:1.00
NE2 A:HIS184 2.5 72.2 1.0
O A:HIS262 2.8 60.2 1.0
CE1 A:HIS184 3.0 72.7 1.0
C A:HIS262 3.3 61.1 1.0
CD2 A:HIS184 3.7 71.2 1.0
CD2 A:HIS262 3.9 65.0 1.0
ND1 A:HIS184 4.3 73.0 1.0
CG A:HIS262 4.4 64.2 1.0
NE2 A:HIS262 4.5 65.4 1.0
CA A:HIS262 4.6 62.4 1.0
CG A:HIS184 4.7 70.8 1.0
CD2 A:LEU180 4.7 55.5 1.0
CB A:HIS262 4.8 61.5 1.0

Calcium binding site 2 out of 3 in 1q39

Go back to Calcium Binding Sites List in 1q39
Calcium binding site 2 out of 3 in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:30.6
occ:1.00
NE2 A:HIS220 2.1 61.7 1.0
CD2 A:HIS220 2.9 63.4 1.0
CE1 A:HIS220 3.1 62.3 1.0
CG A:HIS220 4.1 63.8 1.0
ND1 A:HIS220 4.2 63.7 1.0
CB A:HIS221 4.7 52.0 1.0

Calcium binding site 3 out of 3 in 1q39

Go back to Calcium Binding Sites List in 1q39
Calcium binding site 3 out of 3 in the Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Dna Repair Enzyme Endonuclease-VIII (Nei) From E. Coli: the Wt Enzyme at 2.8 Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:87.4
occ:1.00
O A:GLU173 3.0 46.2 1.0
CE3 A:TRP176 3.0 37.9 1.0
OE1 A:GLU173 3.3 65.7 1.0
CG A:LYS228 3.6 66.8 1.0
CZ3 A:TRP176 3.6 38.8 1.0
C A:GLU173 3.7 44.7 1.0
CA A:GLU173 3.8 45.2 1.0
CB A:GLU173 3.8 55.0 1.0
NZ A:LYS228 4.0 70.9 1.0
CB A:GLN177 4.0 68.8 1.0
CD2 A:TRP176 4.1 39.6 1.0
CB A:LYS228 4.2 63.5 1.0
CD A:GLU173 4.2 63.9 1.0
N A:GLN177 4.3 70.4 1.0
CB A:TRP176 4.5 42.1 1.0
CA A:GLN177 4.5 73.1 1.0
CG A:GLU173 4.6 60.7 1.0
CG A:TRP176 4.7 40.3 1.0
C A:TRP176 4.8 65.4 1.0
N A:ILE174 4.8 43.6 1.0
CD A:LYS228 4.8 68.0 1.0
CE A:LYS228 4.9 70.2 1.0
CH2 A:TRP176 4.9 38.5 1.0

Reference:

G.Golan, D.O.Zharkov, H.Feinberg, A.S.Fernandes, E.I.Zaika, J.H.Kycia, A.P.Grollman, G.Shoham. Structure of the Uncomplexed Dna Repair Enzyme Endonuclease VIII Indicates Significant Interdomain Flexibility. Nucleic Acids Res. V. 33 5006 2005.
ISSN: ISSN 0305-1048
PubMed: 16145054
DOI: 10.1093/NAR/GKI796
Page generated: Sat Dec 12 03:15:04 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy