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Manganese in PDB 5bte: Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+

Protein crystallography data

The structure of Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+, PDB code: 5bte 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) 42.41 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.655, 79.742, 160.143, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ (pdb code 5bte). 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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+, PDB code: 5bte:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5bte

Go back to Manganese Binding Sites List in 5bte
Manganese binding site 1 out of 6 in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:8.3
occ:1.00
 OE2 B:GLU235 2.0 12.2 1.0
OD2 B:ASP217 2.1 9.6 1.0
O B:LEU236 2.1 12.4 1.0
OP3 D:U2 2.2 13.1 1.0
O B:HOH535 2.2 6.0 1.0
OP1 D:U2 2.3 12.9 1.0
P D:U2 2.8 14.4 1.0
CD B:GLU235 3.1 13.2 1.0
CG B:ASP217 3.1 10.3 1.0
C B:LEU236 3.1 13.6 1.0
N B:LEU236 3.4 13.1 1.0
OD1 B:ASP217 3.5 10.2 1.0
O D:HOH102 3.6 14.3 1.0
CA B:LEU236 3.7 13.1 1.0
OE1 B:GLU235 3.7 12.6 1.0
MN B:MN402 3.8 11.0 1.0
O5' D:U2 3.9 14.2 1.0
CB B:LEU236 4.0 13.2 1.0
OP2 D:U2 4.0 13.9 1.0
C5' D:U2 4.0 15.0 1.0
CG B:GLU235 4.1 13.8 1.0
OE2 B:GLU166 4.1 15.5 1.0
N B:LYS237 4.3 14.9 1.0
O B:HOH550 4.3 15.3 1.0
NZ B:LYS237 4.3 21.2 1.0
O B:HOH530 4.3 8.2 1.0
C B:GLU235 4.4 13.4 1.0
CB B:ASP217 4.4 10.9 1.0
CE B:LYS237 4.5 21.6 1.0
CD B:LYS237 4.5 21.3 1.0
CA B:LYS237 4.7 16.4 1.0
CA B:GLU235 4.8 13.6 1.0
O B:HOH572 4.9 12.2 1.0

Manganese binding site 2 out of 6 in 5bte

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Manganese binding site 2 out of 6 in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:11.0
occ:1.00
 OE1 B:GLU215 2.1 15.8 1.0
OD1 B:ASP217 2.1 10.2 1.0
OP3 D:U2 2.1 13.1 1.0
O B:HOH552 2.1 12.5 1.0
O B:HOH530 2.2 8.2 1.0
O B:HOH572 2.4 12.2 1.0
CD B:GLU215 3.0 14.8 1.0
CG B:ASP217 3.2 10.3 1.0
OE2 B:GLU215 3.2 15.6 1.0
P D:U2 3.4 14.4 1.0
OD2 B:ASP217 3.6 9.6 1.0
MN B:MN401 3.8 8.3 1.0
OP2 D:U2 3.8 13.9 1.0
OE2 B:GLU166 3.9 15.5 1.0
O5' D:U2 3.9 14.2 1.0
OE2 B:GLU235 4.2 12.2 1.0
O B:HOH543 4.2 12.8 1.0
CG B:GLU215 4.3 13.8 1.0
OE1 B:GLU235 4.3 12.6 1.0
C5' D:U2 4.3 15.0 1.0
O B:GLU215 4.4 10.7 1.0
CB B:ASP217 4.5 10.9 1.0
O B:HOH637 4.5 18.0 1.0
OP1 D:U2 4.6 12.9 1.0
O B:HOH535 4.6 6.0 1.0
N B:ASP217 4.6 10.8 1.0
CB B:GLU215 4.6 13.0 1.0
CD B:GLU235 4.7 13.2 1.0
CA B:ASP217 4.7 11.1 1.0
C B:GLU215 4.7 11.4 1.0
NE2 B:GLN261 4.9 21.3 1.0
C B:VAL216 4.9 11.8 1.0
CD B:GLU166 4.9 15.5 1.0
N B:VAL216 5.0 11.2 1.0

Manganese binding site 3 out of 6 in 5bte

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Manganese binding site 3 out of 6 in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:42.4
occ:1.00
 O B:HOH531 2.2 27.3 1.0
O B:HOH623 2.2 22.6 1.0
O B:HOH541 2.2 29.8 1.0
O B:HOH543 2.4 12.8 1.0
O B:HOH538 2.4 14.2 1.0
O B:HOH515 2.5 11.7 1.0
O B:HOH551 3.5 16.1 1.0
O B:HOH617 3.8 16.6 1.0
OE2 B:GLU215 3.8 15.6 1.0
O B:PRO195 3.8 15.6 1.0
O B:ASN42 4.0 12.2 1.0
O B:VAL216 4.2 11.9 1.0
O B:ASP217 4.4 11.3 1.0
O B:HOH590 4.4 30.7 1.0
OG B:SER44 4.4 11.2 1.0
OE1 B:GLU166 4.5 17.8 1.0
CA B:GLN196 4.5 13.4 1.0
N B:TYR197 4.6 13.6 1.0
C B:PRO195 4.8 13.8 1.0
CA B:ASP217 4.9 11.1 1.0
C B:ASP217 5.0 11.8 1.0
CD B:GLU215 5.0 14.8 1.0
C B:GLN196 5.0 13.2 1.0

Manganese binding site 4 out of 6 in 5bte

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Manganese binding site 4 out of 6 in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:10.5
occ:1.00
 OE2 A:GLU235 2.1 12.3 1.0
OD2 A:ASP217 2.1 9.4 1.0
O A:LEU236 2.1 13.3 1.0
OP3 C:U2 2.1 13.2 1.0
O A:HOH540 2.2 6.5 1.0
OP1 C:U2 2.5 13.4 1.0
P C:U2 2.8 14.1 1.0
CD A:GLU235 3.1 12.9 1.0
CG A:ASP217 3.1 9.2 1.0
C A:LEU236 3.2 14.1 1.0
OD1 A:ASP217 3.4 8.3 1.0
N A:LEU236 3.5 13.7 1.0
OE1 A:GLU235 3.7 12.8 1.0
MN C:MN402 3.7 11.4 1.0
CA A:LEU236 3.7 13.8 1.0
O C:HOH508 3.8 9.0 1.0
OP2 C:U2 3.9 13.6 1.0
O5' C:U2 3.9 14.7 1.0
C5' C:U2 4.0 15.3 1.0
CB A:LEU236 4.0 14.5 1.0
CG A:GLU235 4.1 13.2 1.0
OE2 A:GLU166 4.1 12.9 1.0
O A:HOH527 4.2 6.6 1.0
NZ A:LYS237 4.2 16.7 1.0
CD A:LYS237 4.2 16.5 1.0
O A:HOH609 4.2 11.1 1.0
N A:LYS237 4.3 14.3 1.0
C A:GLU235 4.4 13.6 1.0
CB A:ASP217 4.4 9.5 1.0
O A:HOH536 4.7 13.8 1.0
CA A:GLU235 4.7 13.9 1.0
CE A:LYS237 4.8 16.7 1.0
CA A:LYS237 4.8 14.4 1.0

Manganese binding site 5 out of 6 in 5bte

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Manganese binding site 5 out of 6 in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:11.4
occ:1.00
 O A:HOH527 2.1 6.6 1.0
OP3 C:U2 2.1 13.2 1.0
OD1 A:ASP217 2.1 8.3 1.0
OE1 A:GLU215 2.2 16.2 1.0
O A:HOH598 2.2 18.2 1.0
O A:HOH536 2.2 13.8 1.0
CD A:GLU215 3.1 15.3 1.0
CG A:ASP217 3.2 9.2 1.0
P C:U2 3.3 14.1 1.0
OE2 A:GLU215 3.4 16.4 1.0
O A:HOH646 3.6 25.8 1.0
OD2 A:ASP217 3.7 9.4 1.0
OP2 C:U2 3.7 13.6 1.0
MN C:MN401 3.7 10.5 1.0
O5' C:U2 3.8 14.7 1.0
OE2 A:GLU166 3.9 12.9 1.0
O A:HOH539 4.2 16.3 1.0
OE2 A:GLU235 4.2 12.3 1.0
OE1 A:GLU235 4.3 12.8 1.0
C5' C:U2 4.4 15.3 1.0
CG A:GLU215 4.4 13.9 1.0
O A:HOH540 4.4 6.5 1.0
OP1 C:U2 4.5 13.4 1.0
O A:HOH607 4.5 23.5 1.0
CB A:ASP217 4.5 9.5 1.0
O A:GLU215 4.5 11.6 1.0
O A:HOH535 4.6 40.8 1.0
N A:ASP217 4.7 10.2 1.0
CB A:GLU215 4.7 13.2 1.0
CD A:GLU235 4.7 12.9 1.0
CA A:ASP217 4.7 9.9 1.0
C A:GLU215 4.7 11.8 1.0
C A:VAL216 4.9 11.0 1.0
CD A:GLU166 5.0 13.8 1.0
N A:VAL216 5.0 11.2 1.0

Manganese binding site 6 out of 6 in 5bte

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Manganese binding site 6 out of 6 in the Crystal Structure of Ashbya Gossypii RAI1 in Complex with Pu(S)6-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 Ashbya Gossypii RAI1 in Complex with Pu(S)6-MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:43.9
occ:1.00
 O A:HOH604 2.2 18.0 1.0
O A:HOH565 2.3 22.9 1.0
O A:HOH504 2.3 35.1 1.0
O A:HOH539 2.3 16.3 1.0
O A:HOH522 2.4 19.0 1.0
O A:HOH545 2.4 15.3 1.0
O A:HOH582 3.5 13.1 1.0
O A:HOH590 3.7 21.8 1.0
OE2 A:GLU215 3.7 16.4 1.0
O A:PRO195 3.9 16.0 1.0
O A:ASN42 4.2 12.0 1.0
O A:HOH647 4.2 27.0 1.0
O A:VAL216 4.3 10.8 1.0
OE1 A:GLU166 4.3 14.9 1.0
O A:ASP217 4.4 10.8 1.0
O A:HOH535 4.5 40.8 1.0
OG A:SER44 4.5 10.8 1.0
CA A:GLN196 4.5 14.8 1.0
O A:HOH597 4.6 20.4 1.0
N A:TYR197 4.6 14.8 1.0
C A:PRO195 4.8 14.3 1.0
CD A:GLU215 4.9 15.3 1.0
CA A:ASP217 5.0 9.9 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 23:39:04 2024

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