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Manganese in PDB 8vnj: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S

Protein crystallography data

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S, PDB code: 8vnj 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) 47.86 / 1.61
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 (%) 18.5 / 19.6

Other elements in 8vnj:

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S (pdb code 8vnj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S, PDB code: 8vnj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8vnj

Go back to Manganese Binding Sites List in 8vnj
Manganese 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 120S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:16.7
occ:0.25
NA C:NA502 0.0 16.8 0.8
OD1 B:ASN319 2.2 18.2 1.0
O3' C:DA413 2.3 17.0 0.8
O B:HOH533 2.3 17.6 1.0
O B:HOH541 2.3 22.8 1.0
O B:HOH596 2.3 22.2 1.0
O3' C:DA413 2.4 17.0 0.2
OP3 C:DG414 2.4 17.0 0.2
OP1 C:DG414 2.5 17.1 0.8
P C:DG414 2.9 15.2 0.8
CG B:ASN319 3.4 17.2 1.0
C3' C:DA413 3.6 18.6 0.8
C3' C:DA413 3.6 18.5 0.2
P C:DG414 3.6 15.7 0.2
O B:ASN319 3.8 15.8 1.0
O5' C:DG414 3.8 17.1 0.8
C4' C:DA413 3.9 18.0 0.8
C4' C:DA413 4.0 17.9 0.2
ND2 B:ASN319 4.0 16.9 1.0
N B:HIS298 4.0 15.8 1.0
OP1 C:DG414 4.1 19.2 0.2
O5' C:DG414 4.1 18.1 0.2
OP2 C:DG414 4.1 18.7 0.8
O C:HOH639 4.2 27.5 1.0
OG B:SER297 4.2 19.0 1.0
C B:ASN319 4.2 17.4 1.0
C2' C:DA413 4.2 16.4 0.8
C2' C:DA413 4.3 16.5 0.2
O B:HIS298 4.3 17.3 1.0
OD1 B:ASN323 4.5 15.4 1.0
CB B:ASN319 4.6 16.1 1.0
C5' C:DA413 4.6 15.4 0.8
CA B:SER297 4.6 16.5 1.0
C5' C:DA413 4.6 15.6 0.2
CA B:ASN319 4.7 17.1 1.0
CB B:HIS298 4.7 16.3 1.0
ND1 B:HIS301 4.7 18.4 1.0
C B:SER297 4.8 17.2 1.0
CA B:HIS298 4.8 16.9 1.0
CE1 B:HIS301 4.9 21.4 1.0
N B:LYS320 4.9 14.6 1.0
OP2 C:DG414 4.9 24.9 0.2
C B:HIS298 4.9 16.6 1.0
CB B:SER297 4.9 19.1 1.0

Manganese binding site 2 out of 2 in 8vnj

Go back to Manganese Binding Sites List in 8vnj
Manganese 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 120S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 120S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:16.4
occ:0.25
NA D:NA602 0.0 16.4 0.8
OD1 A:ASN119 2.2 16.6 1.0
O3' D:DA513 2.3 17.0 0.8
O A:HOH709 2.3 16.3 1.0
O3' D:DA513 2.3 17.0 0.2
O A:HOH803 2.3 20.0 1.0
O A:HOH733 2.4 20.1 1.0
OP3 D:DG514 2.5 16.0 0.2
OP1 D:DG514 2.5 16.1 0.8
P D:DG514 2.9 15.4 0.8
CG A:ASN119 3.4 15.1 1.0
C3' D:DA513 3.5 19.8 0.8
C3' D:DA513 3.5 19.6 0.2
P D:DG514 3.7 15.6 0.2
O A:ASN119 3.8 15.4 1.0
C4' D:DA513 3.8 19.0 0.8
O5' D:DG514 3.9 15.4 0.8
C4' D:DA513 3.9 19.0 0.2
N A:HIS98 4.0 15.5 1.0
ND2 A:ASN119 4.0 16.3 1.0
O5' D:DG514 4.1 16.6 0.2
OP2 D:DG514 4.1 18.5 0.8
C2' D:DA513 4.2 16.8 0.8
OP2 D:DG514 4.2 18.7 0.2
C2' D:DA513 4.2 16.9 0.2
C A:ASN119 4.2 16.7 1.0
OG A:SER97 4.3 17.9 1.0
O A:HIS98 4.3 17.5 1.0
O D:HOH727 4.4 30.7 1.0
OD1 A:ASN123 4.4 17.6 1.0
C5' D:DA513 4.5 18.4 0.8
C5' D:DA513 4.6 18.4 0.2
CA A:SER97 4.6 13.2 1.0
CB A:ASN119 4.6 13.2 1.0
CA A:ASN119 4.7 16.2 1.0
CB A:HIS98 4.7 16.9 1.0
ND1 A:HIS101 4.7 19.8 1.0
C A:SER97 4.7 14.3 1.0
CA A:HIS98 4.8 17.3 1.0
N A:LYS120 4.9 14.9 1.0
CE1 A:HIS101 4.9 19.1 1.0
CB A:SER97 5.0 14.8 1.0
O A:HOH769 5.0 23.3 1.0
C A:HIS98 5.0 16.4 1.0
OP1 D:DG514 5.0 21.5 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: Sun Aug 17 01:59:22 2025

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