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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: Thu Jul 11 13:58:08 2024

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