Atomistry » Manganese » PDB 8v7f-8wzt » 8vnk
Atomistry »
  Manganese »
    PDB 8v7f-8wzt »
      8vnk »

Manganese in PDB 8vnk: Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S

Protein crystallography data

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S, PDB code: 8vnk 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) 43.07 / 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 (%) 18.2 / 19.4

Other elements in 8vnk:

The structure of Homing Endonuclease I-Ppoi-Dna Complex:Reaction at PH6.0 (K+ Mes) with 500 Um MN2+ For 160S 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 160S (pdb code 8vnk). 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 160S, PDB code: 8vnk:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 8vnk

Go back to Manganese Binding Sites List in 8vnk
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 160S


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 160S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:15.8
occ:0.40
NA C:NA502 0.1 16.0 0.6
OD1 B:ASN319 2.2 18.4 1.0
O B:HOH595 2.2 21.5 1.0
OP3 C:DG414 2.3 16.6 0.4
O B:HOH520 2.3 16.8 1.0
OP1 C:DG414 2.3 17.4 0.6
O B:HOH541 2.3 23.1 1.0
O3' C:DA413 2.4 17.3 0.8
O3' C:DA413 2.5 17.2 0.2
P C:DG414 2.8 17.5 0.6
CG B:ASN319 3.3 16.8 1.0
P C:DG414 3.5 15.4 0.4
C3' C:DA413 3.7 17.9 0.2
C3' C:DA413 3.7 18.0 0.8
O5' C:DG414 3.7 17.3 0.6
O B:ASN319 3.8 16.8 1.0
OP1 C:DG414 3.9 18.1 0.4
ND2 B:ASN319 3.9 16.8 1.0
O5' C:DG414 4.0 17.3 0.4
C4' C:DA413 4.0 19.6 0.8
N B:HIS298 4.0 16.7 1.0
C4' C:DA413 4.1 19.5 0.2
OP2 C:DG414 4.1 19.9 0.6
O C:HOH641 4.1 26.9 1.0
C B:ASN319 4.2 18.0 1.0
OG B:SER297 4.2 18.4 1.0
C2' C:DA413 4.3 17.8 0.8
C2' C:DA413 4.3 18.0 0.2
O B:HIS298 4.3 17.4 1.0
CB B:ASN319 4.5 15.8 1.0
OD1 B:ASN323 4.6 16.1 1.0
ND1 B:HIS301 4.6 19.8 1.0
CA B:SER297 4.6 16.2 1.0
CA B:ASN319 4.6 16.3 1.0
C5' C:DA413 4.7 17.6 0.8
CB B:HIS298 4.8 15.9 1.0
OP2 C:DG414 4.8 21.8 0.4
C5' C:DA413 4.8 17.8 0.2
C B:SER297 4.8 16.6 1.0
CA B:HIS298 4.8 16.5 1.0
CE1 B:HIS301 4.8 19.3 1.0
N B:LYS320 4.9 15.2 1.0
CB B:SER297 4.9 17.2 1.0
C B:HIS298 5.0 15.8 1.0

Manganese binding site 2 out of 2 in 8vnk

Go back to Manganese Binding Sites List in 8vnk
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 160S


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 160S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:15.5
occ:0.45
NA D:NA602 0.1 15.6 0.6
OD1 A:ASN119 2.2 16.5 1.0
OP3 D:DG514 2.3 15.9 0.5
O A:HOH716 2.3 14.9 1.0
O3' D:DA513 2.3 17.2 0.8
OP1 D:DG514 2.3 15.8 0.6
O A:HOH803 2.3 19.3 1.0
O3' D:DA513 2.3 17.4 0.2
O A:HOH736 2.3 21.2 1.0
P D:DG514 2.8 17.8 0.6
CG A:ASN119 3.3 14.0 1.0
P D:DG514 3.5 14.1 0.5
C3' D:DA513 3.5 19.6 0.8
C3' D:DA513 3.6 19.1 0.2
O5' D:DG514 3.7 14.5 0.6
O A:ASN119 3.8 16.1 1.0
C4' D:DA513 3.9 20.2 0.8
ND2 A:ASN119 3.9 15.8 1.0
OP2 D:DG514 3.9 18.4 0.5
O5' D:DG514 4.0 15.6 0.5
OP2 D:DG514 4.0 18.4 0.6
C4' D:DA513 4.0 19.9 0.2
N A:HIS98 4.1 15.0 1.0
C2' D:DA513 4.1 17.1 0.8
O D:HOH741 4.2 28.4 1.0
C2' D:DA513 4.2 17.2 0.2
C A:ASN119 4.2 16.4 1.0
OG A:SER97 4.3 17.2 1.0
O A:HIS98 4.4 17.7 1.0
OD1 A:ASN123 4.5 17.0 1.0
CB A:ASN119 4.5 14.4 1.0
CA A:SER97 4.6 14.9 1.0
C5' D:DA513 4.6 18.3 0.8
CA A:ASN119 4.7 16.4 1.0
C5' D:DA513 4.7 18.4 0.2
ND1 A:HIS101 4.7 20.4 1.0
C A:SER97 4.8 13.9 1.0
OP1 D:DG514 4.8 20.7 0.5
CB A:HIS98 4.8 15.3 1.0
CA A:HIS98 4.9 16.4 1.0
N A:LYS120 4.9 15.7 1.0
CE1 A:HIS101 4.9 20.4 1.0
CB A:SER97 5.0 14.3 1.0

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 14:07:41 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy