Atomistry » Sodium » PDB 1c8v-1de7 » 1cz0
Atomistry »
  Sodium »
    PDB 1c8v-1de7 »
      1cz0 »

Sodium in PDB 1cz0: Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion

Protein crystallography data

The structure of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion, PDB code: 1cz0 was solved by E.A.Galburt, B.Chevalier, M.S.Jurica, K.E.Flick, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.866, 113.866, 89.040, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 21.6

Other elements in 1cz0:

The structure of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion (pdb code 1cz0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion, PDB code: 1cz0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1cz0

Go back to Sodium Binding Sites List in 1cz0
Sodium binding site 1 out of 2 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:9.8
occ:1.00
O B:HOH725 2.3 19.2 1.0
OD1 B:ASN319 2.3 15.5 1.0
O B:HOH724 2.4 20.1 1.0
O B:HOH723 2.5 12.9 1.0
OP1 C:DG414 2.6 18.6 1.0
O3' C:DA413 2.6 21.9 1.0
P C:DG414 3.1 19.1 1.0
CG B:ASN319 3.4 16.6 1.0
O B:ASN319 3.7 16.1 1.0
C3' C:DA413 3.8 20.9 1.0
N B:HIS298 3.9 14.3 1.0
O5' C:DG414 4.0 18.4 1.0
OG B:SER297 4.0 19.7 1.0
ND2 B:ASN319 4.0 14.3 1.0
C4' C:DA413 4.2 20.1 1.0
C B:ASN319 4.2 15.9 1.0
O B:HIS298 4.3 14.6 1.0
OP2 C:DG414 4.4 18.0 1.0
C2' C:DA413 4.4 19.4 1.0
O C:HOH369 4.5 32.6 1.0
CA B:SER297 4.6 17.4 1.0
CB B:HIS298 4.6 14.9 1.0
CB B:ASN319 4.6 14.9 1.0
CA B:HIS298 4.7 13.4 1.0
CA B:ASN319 4.7 14.4 1.0
C B:SER297 4.7 17.4 1.0
OD1 B:ASN323 4.7 14.5 1.0
ND1 B:HIS301 4.7 12.7 1.0
CE1 B:HIS301 4.8 12.0 1.0
CB B:SER297 4.8 16.4 1.0
N B:LYS320 4.8 16.4 1.0
C5' C:DA413 4.8 17.9 1.0
C B:HIS298 4.9 15.6 1.0

Sodium binding site 2 out of 2 in 1cz0

Go back to Sodium Binding Sites List in 1cz0
Sodium binding site 2 out of 2 in the Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Intron Encoded Homing Endonuclease I-Ppoi/Dna Complex Lacking Catalytic Metal Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na605

b:12.5
occ:1.00
O A:HOH737 2.2 17.4 1.0
O A:HOH738 2.3 22.2 1.0
OD1 A:ASN119 2.4 13.5 1.0
OP1 D:DG514 2.6 18.5 1.0
O3' D:DA513 2.7 19.8 1.0
O A:HOH740 2.8 31.5 1.0
P D:DG514 3.2 17.1 1.0
CG A:ASN119 3.5 11.3 1.0
O A:ASN119 3.6 14.3 1.0
N A:HIS98 3.9 12.4 1.0
C3' D:DA513 4.0 19.3 1.0
O5' D:DG514 4.0 18.0 1.0
OG A:SER97 4.0 13.1 1.0
ND2 A:ASN119 4.1 13.4 1.0
C A:ASN119 4.1 14.1 1.0
O A:HIS98 4.2 17.1 1.0
C4' D:DA513 4.3 18.5 1.0
OP2 D:DG514 4.4 17.7 1.0
CA A:SER97 4.5 12.1 1.0
OD1 A:ASN123 4.5 17.7 1.0
CB A:HIS98 4.6 13.8 1.0
C A:SER97 4.6 12.8 1.0
C2' D:DA513 4.6 17.7 1.0
CA A:HIS98 4.6 14.5 1.0
CB A:ASN119 4.7 9.1 1.0
CA A:ASN119 4.7 10.7 1.0
C A:HIS98 4.8 17.6 1.0
ND1 A:HIS101 4.8 14.4 1.0
N A:LYS120 4.8 13.4 1.0
CB A:SER97 4.9 10.4 1.0
C5' D:DA513 4.9 19.3 1.0
CE1 A:HIS101 5.0 15.6 1.0

Reference:

E.A.Galburt, B.Chevalier, W.Tang, M.S.Jurica, K.E.Flick, R.J.Monnat Jr., B.L.Stoddard. A Novel Endonuclease Mechanism Directly Visualized For I-Ppoi. Nat.Struct.Biol. V. 6 1096 1999.
ISSN: ISSN 1072-8368
PubMed: 10581547
DOI: 10.1038/70027
Page generated: Tue Dec 15 05:22:48 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