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Manganese in PDB 8vnm: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 320S

Protein crystallography data

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 320S, PDB code: 8vnm 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) 37.33 / 1.59
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 (%) 17.4 / 19

Other elements in 8vnm:

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 320S also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Sodium (Na) 2 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 320S (pdb code 8vnm). 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 320S, PDB code: 8vnm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8vnm

Go back to Manganese Binding Sites List in 8vnm
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 320S


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 320S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:15.6
occ:0.80
NA C:NA502 0.0 15.5 0.2
OP1 C:DG414 2.1 16.1 0.2
OD1 B:ASN319 2.1 16.4 1.0
O B:HOH600 2.2 18.3 1.0
O3' C:DA413 2.2 16.9 0.8
OP3 C:DG414 2.2 15.7 0.8
O B:HOH564 2.2 18.8 1.0
O3' C:DA413 2.3 16.6 0.2
O B:HOH519 2.3 15.7 1.0
P C:DG414 2.7 15.8 0.2
CG B:ASN319 3.2 16.1 1.0
P C:DG414 3.4 15.6 0.8
C3' C:DA413 3.5 15.5 0.8
C3' C:DA413 3.5 15.7 0.2
O5' C:DG414 3.6 16.1 0.2
OP1 C:DG414 3.6 15.5 0.8
ND2 B:ASN319 3.8 15.6 1.0
O5' C:DG414 3.9 15.2 0.8
O B:ASN319 3.9 15.4 1.0
OP2 C:DG414 4.0 16.8 0.2
C4' C:DA413 4.0 16.6 0.2
O C:HOH634 4.0 22.7 1.0
C4' C:DA413 4.0 16.7 0.8
N B:HIS298 4.1 14.8 1.0
C2' C:DA413 4.1 15.9 0.2
C2' C:DA413 4.2 16.0 0.8
C B:ASN319 4.2 15.4 1.0
OG B:SER297 4.3 16.8 1.0
O B:HIS298 4.3 16.0 1.0
CB B:ASN319 4.5 16.1 1.0
OD1 B:ASN323 4.5 16.0 1.0
ND1 B:HIS301 4.6 18.2 1.0
OP2 C:DG414 4.6 18.3 0.8
CA B:ASN319 4.6 15.1 1.0
CA B:SER297 4.7 16.0 1.0
C5' C:DA413 4.7 16.5 0.2
C5' C:DA413 4.7 16.4 0.8
C B:SER297 4.8 15.9 1.0
CB B:HIS298 4.8 14.4 1.0
CE1 B:HIS301 4.9 20.9 1.0
CA B:HIS298 4.9 14.0 1.0
N B:LYS320 4.9 13.0 1.0
C5' C:DG414 4.9 17.1 0.2
O B:HOH501 5.0 18.1 0.1
CB B:SER297 5.0 14.8 1.0

Manganese binding site 2 out of 2 in 8vnm

Go back to Manganese Binding Sites List in 8vnm
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 320S


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 320S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:14.3
occ:0.80
NA D:NA602 0.0 14.4 0.2
OD1 A:ASN119 2.1 14.0 1.0
OP1 D:DG514 2.1 15.7 0.2
O3' D:DA513 2.2 17.7 0.8
O A:HOH713 2.2 14.3 1.0
O A:HOH796 2.2 17.4 1.0
O A:HOH748 2.2 19.2 1.0
OP3 D:DG514 2.2 15.5 0.8
O3' D:DA513 2.3 17.3 0.2
P D:DG514 2.7 17.6 0.2
CG A:ASN119 3.2 13.7 1.0
P D:DG514 3.4 14.0 0.8
C3' D:DA513 3.5 16.9 0.8
C3' D:DA513 3.5 16.8 0.2
O5' D:DG514 3.6 15.6 0.2
OP2 D:DG514 3.7 15.1 0.8
ND2 A:ASN119 3.8 15.4 1.0
O A:ASN119 3.8 15.1 1.0
O5' D:DG514 3.9 12.1 0.8
OP2 D:DG514 4.0 17.4 0.2
C4' D:DA513 4.0 17.2 0.2
C4' D:DA513 4.0 17.3 0.8
C2' D:DA513 4.1 15.7 0.2
C2' D:DA513 4.1 15.6 0.8
O D:HOH732 4.1 22.3 1.0
N A:HIS98 4.1 14.6 1.0
C A:ASN119 4.2 15.2 1.0
OG A:SER97 4.2 17.3 1.0
O A:HIS98 4.4 18.5 1.0
CB A:ASN119 4.5 13.1 1.0
OD1 A:ASN123 4.5 16.6 1.0
ND1 A:HIS101 4.6 20.2 1.0
OP1 D:DG514 4.6 16.6 0.8
CA A:ASN119 4.6 14.9 1.0
CA A:SER97 4.6 13.5 1.0
C5' D:DA513 4.7 16.0 0.2
C5' D:DA513 4.8 15.8 0.8
C A:SER97 4.8 13.1 1.0
N A:LYS120 4.9 13.3 1.0
CE1 A:HIS101 4.9 20.0 1.0
CB A:HIS98 4.9 15.0 1.0
CA A:HIS98 4.9 15.6 1.0
C5' D:DG514 5.0 15.9 0.2
CB A:SER97 5.0 15.3 1.0
O A:HOH701 5.0 16.9 0.1

Reference:

C.Chang, Y.Gao. Homing Endonuclease I-Ppoi-Dna Complex:Reaction with 500 Um MG2+ For 160S To Be Published.
Page generated: Sun Oct 6 14:08:02 2024

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