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Manganese in PDB 5bud: Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+

Protein crystallography data

The structure of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+, PDB code: 5bud was solved by V.Y.Wang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.47 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 97.854, 114.638, 84.458, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ (pdb code 5bud). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+, PDB code: 5bud:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5bud

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Manganese binding site 1 out of 6 in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.2
occ:1.00
 OD2 A:ASP225 2.1 19.6 1.0
OE1 A:GLU244 2.1 20.3 1.0
O A:HOH581 2.2 20.1 1.0
O A:LEU245 2.2 18.5 1.0
OP1 D:U2 2.4 28.4 1.0
OP2 D:U2 2.5 34.2 1.0
P D:U2 2.9 40.5 1.0
CG A:ASP225 3.1 21.0 1.0
CD A:GLU244 3.1 20.7 1.0
C A:LEU245 3.3 18.2 1.0
OD1 A:ASP225 3.4 18.8 1.0
MN A:MN402 3.5 44.3 1.0
N A:LEU245 3.6 18.3 1.0
OE2 A:GLU244 3.8 18.7 1.0
CA A:LEU245 3.9 18.6 1.0
O5' D:U2 4.0 27.7 1.0
OP3 D:U2 4.1 33.8 1.0
C5' D:U2 4.1 26.6 1.0
OE2 A:GLU174 4.1 25.0 1.0
CG A:GLU244 4.1 18.1 1.0
NZ A:LYS246 4.2 21.9 1.0
CB A:LEU245 4.2 18.6 1.0
O A:HOH801 4.4 20.5 1.0
O A:HOH599 4.4 28.9 1.0
CD A:LYS246 4.4 21.2 1.0
N A:LYS246 4.4 18.3 1.0
CB A:ASP225 4.5 21.0 1.0
CE A:LYS246 4.6 20.7 1.0
C A:GLU244 4.6 19.2 1.0
CA A:LYS246 4.8 19.8 1.0
O A:HOH628 4.9 35.4 1.0
CA A:GLU244 4.9 19.7 1.0
CG A:LYS246 5.0 20.7 1.0

Manganese binding site 2 out of 6 in 5bud

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Manganese binding site 2 out of 6 in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:44.3
occ:1.00
 OP2 D:U2 2.1 34.2 1.0
OD1 A:ASP225 2.2 18.8 1.0
OE1 A:GLU223 2.3 44.6 1.0
O A:HOH599 2.6 28.9 1.0
O A:HOH628 2.7 35.4 1.0
CG A:ASP225 3.1 21.0 1.0
CD A:GLU223 3.3 42.7 1.0
OD2 A:ASP225 3.5 19.6 1.0
MN A:MN401 3.5 22.2 1.0
P D:U2 3.6 40.5 1.0
O A:HOH563 3.6 43.2 1.0
OE2 A:GLU223 3.6 46.2 1.0
OE2 A:GLU174 4.0 25.0 1.0
OE1 A:GLU244 4.2 20.3 1.0
OE2 A:GLU244 4.2 18.7 1.0
OP3 D:U2 4.2 33.8 1.0
C5' D:U2 4.3 26.6 1.0
O5' D:U2 4.3 27.7 1.0
O A:HOH581 4.3 20.1 1.0
CB A:ASP225 4.5 21.0 1.0
O A:HOH748 4.5 64.6 1.0
OP1 D:U2 4.5 28.4 1.0
CD A:GLU244 4.6 20.7 1.0
O A:GLU223 4.6 25.3 1.0
CA A:ASP225 4.6 21.2 1.0
N A:ASP225 4.7 21.8 1.0
CG A:GLU223 4.7 38.0 1.0
NH2 A:ARG103 4.8 45.2 1.0
MN A:MN403 4.8 54.4 1.0
CB A:GLU223 4.9 31.6 1.0
CD A:GLU174 4.9 27.4 1.0
C A:GLU223 4.9 25.5 1.0

Manganese binding site 3 out of 6 in 5bud

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Manganese binding site 3 out of 6 in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:54.4
occ:1.00
 OE1 A:GLU174 2.2 32.2 1.0
O A:HOH737 2.3 49.6 1.0
O A:HOH898 2.4 43.6 1.0
O A:HOH563 2.4 43.2 1.0
O A:HOH524 2.4 44.8 1.0
O A:HOH628 2.6 35.4 1.0
CD A:GLU174 3.1 27.4 1.0
OE2 A:GLU174 3.3 25.0 1.0
OE2 A:GLU223 3.4 46.2 1.0
O A:HOH529 3.6 42.2 1.0
O A:HOH767 3.7 39.7 1.0
O A:HOH831 4.2 34.6 1.0
O A:GLU203 4.2 25.2 1.0
O A:HOH595 4.5 21.0 1.0
O A:HOH939 4.5 53.3 1.0
CG A:GLU174 4.5 25.8 1.0
CD1 A:TYR171 4.5 22.9 1.0
OD1 A:ASP225 4.5 18.8 1.0
CD A:GLU223 4.5 42.7 1.0
O A:HOH947 4.7 42.1 1.0
CE1 A:TYR171 4.7 23.7 1.0
CB A:GLU174 4.8 23.7 1.0
MN A:MN402 4.8 44.3 1.0
OE1 A:GLU223 5.0 44.6 1.0

Manganese binding site 4 out of 6 in 5bud

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Manganese binding site 4 out of 6 in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:18.6
occ:1.00
 O B:HOH582 2.1 19.5 1.0
OD2 B:ASP225 2.2 15.2 1.0
OE1 B:GLU244 2.2 17.4 1.0
O B:LEU245 2.2 14.9 1.0
OP1 E:U2 2.3 25.2 1.0
OP2 E:U2 2.4 32.3 1.0
P E:U2 2.7 41.6 1.0
CG B:ASP225 3.1 15.8 1.0
CD B:GLU244 3.2 18.6 1.0
C B:LEU245 3.3 15.3 1.0
OD1 B:ASP225 3.4 14.2 1.0
MN B:MN402 3.5 47.4 1.0
N B:LEU245 3.7 16.2 1.0
OE2 B:GLU244 3.8 18.9 1.0
OP3 E:U2 3.9 32.7 1.0
O5' E:U2 3.9 26.3 1.0
CA B:LEU245 4.0 16.0 1.0
C5' E:U2 4.1 25.7 1.0
NZ B:LYS246 4.2 18.7 1.0
OE2 B:GLU174 4.2 22.3 1.0
CG B:GLU244 4.2 17.5 1.0
CB B:LEU245 4.3 16.6 1.0
CD B:LYS246 4.3 18.6 1.0
O B:HOH556 4.3 24.3 1.0
N B:LYS246 4.4 16.0 1.0
O B:HOH789 4.5 13.9 1.0
CB B:ASP225 4.5 16.8 1.0
CE B:LYS246 4.6 17.8 1.0
C B:GLU244 4.7 16.9 1.0
CA B:LYS246 4.8 16.7 1.0
O B:HOH610 4.9 31.9 1.0
CG B:LYS246 5.0 17.4 1.0

Manganese binding site 5 out of 6 in 5bud

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Manganese binding site 5 out of 6 in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:47.4
occ:1.00
 OP2 E:U2 2.0 32.3 1.0
OD1 B:ASP225 2.2 14.2 1.0
O B:HOH860 2.6 52.1 1.0
O B:HOH556 2.6 24.3 1.0
O B:HOH610 2.7 31.9 1.0
CG B:ASP225 3.2 15.8 1.0
CG B:GLU223 3.3 40.1 1.0
OD2 B:ASP225 3.5 15.2 1.0
MN B:MN401 3.5 18.6 1.0
P E:U2 3.5 41.6 1.0
CD B:GLU223 3.5 43.5 1.0
O B:HOH625 3.5 36.4 1.0
OE2 B:GLU223 3.8 50.9 1.0
OE1 B:GLU223 4.0 48.2 1.0
OE2 B:GLU174 4.1 22.3 1.0
OE1 B:GLU244 4.2 17.4 1.0
OP3 E:U2 4.2 32.7 1.0
C5' E:U2 4.2 25.7 1.0
O5' E:U2 4.2 26.3 1.0
O B:HOH582 4.3 19.5 1.0
OE2 B:GLU244 4.3 18.9 1.0
OP1 E:U2 4.5 25.2 1.0
CB B:ASP225 4.5 16.8 1.0
CB B:GLU223 4.6 32.3 1.0
CA B:ASP225 4.7 17.8 1.0
N B:ASP225 4.7 18.4 1.0
CD B:GLU244 4.7 18.6 1.0
O B:GLU223 4.8 24.6 1.0
MN B:MN403 4.9 46.2 1.0
CD B:GLU174 4.9 24.3 1.0

Manganese binding site 6 out of 6 in 5bud

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Manganese binding site 6 out of 6 in the Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Candida Albicans RAI1 in Complex with PU5-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:46.2
occ:1.00
 O B:HOH863 2.2 42.1 1.0
OE1 B:GLU174 2.2 26.5 1.0
O B:HOH546 2.3 34.6 1.0
O B:HOH625 2.4 36.4 1.0
O B:HOH946 2.5 39.5 1.0
O B:HOH610 2.6 31.9 1.0
CD B:GLU174 3.2 24.3 1.0
OE2 B:GLU174 3.4 22.3 1.0
OE2 B:GLU223 3.5 50.9 1.0
O B:HOH619 3.7 37.9 1.0
O B:HOH683 3.9 38.2 1.0
O B:HOH897 4.1 32.0 1.0
O B:GLU203 4.2 21.8 1.0
CD1 B:TYR171 4.4 20.1 1.0
O B:HOH976 4.5 51.2 1.0
CD B:GLU223 4.5 43.5 1.0
O B:HOH568 4.5 21.6 1.0
CG B:GLU174 4.5 20.1 1.0
OD1 B:ASP225 4.6 14.2 1.0
O B:HOH647 4.6 38.0 1.0
CE1 B:TYR171 4.7 22.1 1.0
O B:HOH973 4.8 34.6 1.0
MN B:MN402 4.9 47.4 1.0
CB B:GLU174 4.9 19.3 1.0
OE1 B:GLU223 5.0 48.2 1.0
O B:HOH895 5.0 41.0 1.0

Reference:

V.Y.Wang, X.Jiao, M.Kiledjian, L.Tong. Structural and Biochemical Studies of the Distinct Activity Profiles of RAI1 Enzymes. Nucleic Acids Res. V. 43 6596 2015.
ISSN: ESSN 1362-4962
PubMed: 26101253
DOI: 10.1093/NAR/GKV620
Page generated: Sat Oct 5 23:39:11 2024

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