Sodium in PDB 8vnh: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S

Protein crystallography data

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S, PDB code: 8vnh was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 1.76
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.06, 114.06, 88.02, 90, 90, 120
R / Rfree (%) 18.1 / 20.6

Other elements in 8vnh:

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S (pdb code 8vnh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S, PDB code: 8vnh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8vnh

Go back to Sodium Binding Sites List in 8vnh
Sodium binding site 1 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:14.3
occ:0.80
MN C:MN501 0.1 14.3 0.2
O B:HOH613 2.2 22.5 1.0
OD1 B:ASN319 2.2 14.9 1.0
OP3 C:DG414 2.3 17.0 0.2
O3' C:DA413 2.3 15.8 0.8
O3' C:DA413 2.3 15.8 0.2
OP1 C:DG414 2.4 17.8 0.8
O B:HOH525 2.4 17.8 1.0
O B:HOH522 2.5 18.9 1.0
P C:DG414 2.9 17.6 0.8
CG B:ASN319 3.4 17.3 1.0
P C:DG414 3.5 17.6 0.2
C3' C:DA413 3.6 15.5 0.8
C3' C:DA413 3.7 15.6 0.2
O5' C:DG414 3.8 17.0 0.8
OP1 C:DG414 3.9 17.2 0.2
N B:HIS298 3.9 15.9 1.0
O B:ASN319 3.9 17.6 1.0
ND2 B:ASN319 3.9 16.2 1.0
C4' C:DA413 4.0 17.0 0.8
O5' C:DG414 4.0 17.4 0.2
C4' C:DA413 4.1 17.0 0.2
OP2 C:DG414 4.1 17.5 0.8
O C:HOH642 4.2 27.9 1.0
OG B:SER297 4.2 18.3 1.0
C2' C:DA413 4.3 15.9 0.8
O B:HIS298 4.3 15.3 1.0
C B:ASN319 4.3 17.2 1.0
C2' C:DA413 4.4 16.1 0.2
CA B:SER297 4.5 15.9 1.0
OD1 B:ASN323 4.6 14.2 1.0
CB B:ASN319 4.6 15.3 1.0
C5' C:DA413 4.6 16.3 0.8
CB B:HIS298 4.7 16.1 1.0
C B:SER297 4.7 18.2 1.0
CA B:HIS298 4.7 16.2 1.0
C5' C:DA413 4.7 16.4 0.2
CA B:ASN319 4.7 14.7 1.0
ND1 B:HIS301 4.8 17.1 1.0
OP2 C:DG414 4.8 22.8 0.2
CB B:SER297 4.9 14.8 1.0
C B:HIS298 4.9 14.6 1.0

Sodium binding site 2 out of 2 in 8vnh

Go back to Sodium Binding Sites List in 8vnh
Sodium binding site 2 out of 2 in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 80S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:14.8
occ:0.80
MN D:MN601 0.1 15.0 0.2
OD1 A:ASN119 2.2 13.9 1.0
O3' D:DA513 2.3 15.8 0.8
O A:HOH727 2.3 15.8 1.0
O3' D:DA513 2.3 15.7 0.2
O A:HOH806 2.4 18.9 1.0
OP3 D:DG514 2.4 15.2 0.2
O A:HOH708 2.4 20.4 1.0
OP1 D:DG514 2.5 15.3 0.8
P D:DG514 2.9 14.9 0.8
CG A:ASN119 3.3 15.3 1.0
C3' D:DA513 3.5 16.4 0.8
C3' D:DA513 3.6 16.2 0.2
P D:DG514 3.7 14.6 0.2
O A:ASN119 3.7 15.6 1.0
O5' D:DG514 3.8 14.1 0.8
C4' D:DA513 3.9 17.8 0.8
ND2 A:ASN119 3.9 17.5 1.0
C4' D:DA513 4.0 17.6 0.2
N A:HIS98 4.0 13.7 1.0
O5' D:DG514 4.0 15.1 0.2
OP2 D:DG514 4.1 17.0 0.2
C2' D:DA513 4.2 15.2 0.8
OG A:SER97 4.2 15.2 1.0
OP2 D:DG514 4.2 16.1 0.8
C A:ASN119 4.2 15.4 1.0
C2' D:DA513 4.3 15.4 0.2
O A:HIS98 4.3 17.1 1.0
CA A:SER97 4.5 14.8 1.0
OD1 A:ASN123 4.5 14.2 1.0
CB A:ASN119 4.5 10.4 1.0
O D:HOH740 4.6 34.4 1.0
C5' D:DA513 4.6 17.3 0.8
CA A:ASN119 4.7 13.4 1.0
C5' D:DA513 4.7 17.4 0.2
C A:SER97 4.7 12.6 1.0
CA A:HIS98 4.8 15.9 1.0
CB A:HIS98 4.8 16.8 1.0
ND1 A:HIS101 4.8 18.2 1.0
CB A:SER97 4.9 12.2 1.0
N A:LYS120 4.9 13.1 1.0
OP1 D:DG514 4.9 19.7 0.2

Reference:

C.Chang, Y.Gao. Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.
Page generated: Wed Oct 9 14:09:11 2024

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