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Manganese in PDB 4gim: Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate

Protein crystallography data

The structure of Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate, PDB code: 4gim was solved by S.Huang, N.Mahanta, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.33 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.657, 76.511, 199.162, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate (pdb code 4gim). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate, PDB code: 4gim:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4gim

Go back to Manganese Binding Sites List in 4gim
Manganese binding site 1 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate


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 Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.8
occ:1.00
 O C:HOH502 2.2 13.8 1.0
OD1 A:ASP145 2.2 16.5 1.0
O A:HOH503 2.2 17.8 1.0
O A:HOH516 2.2 12.5 1.0
O C:HOH505 2.3 15.7 1.0
O A:HOH502 2.3 15.5 1.0
CG A:ASP145 3.2 16.6 1.0
OD2 A:ASP145 3.5 15.7 1.0
OE2 C:GLU179 3.9 19.4 1.0
OE1 C:GLU179 4.0 17.0 1.0
NE2 A:HIS137 4.1 15.8 1.0
O A:HOH511 4.1 13.4 1.0
O C:HOH509 4.1 14.0 1.0
OP1 A:PSU400 4.1 13.0 1.0
O A:GLY266 4.2 20.0 1.0
CD C:GLU179 4.2 21.7 1.0
O A:HOH571 4.2 16.2 1.0
OE1 C:GLU176 4.3 18.0 1.0
OP2 A:PSU400 4.3 16.9 1.0
CD2 A:HIS137 4.3 14.8 1.0
C A:GLY266 4.3 20.4 1.0
CA A:GLY266 4.5 19.9 1.0
CB A:ASP145 4.5 16.5 1.0
N A:ILE146 4.6 12.2 1.0
O A:ILE146 4.7 15.5 1.0
CA A:ASP145 4.7 14.5 1.0
C A:ASP145 4.8 16.6 1.0
C A:ILE146 4.8 14.3 1.0
P A:PSU400 4.8 14.4 1.0
CE1 A:HIS137 4.9 20.3 1.0
O C:HOH506 4.9 17.8 1.0
N A:SER147 4.9 11.8 1.0
N A:LYS267 5.0 17.8 1.0
CA A:SER147 5.0 12.9 1.0

Manganese binding site 2 out of 3 in 4gim

Go back to Manganese Binding Sites List in 4gim
Manganese binding site 2 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate


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 Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:14.7
occ:1.00
 OD1 B:ASP145 2.1 13.2 1.0
O B:HOH503 2.2 12.8 1.0
O A:HOH504 2.2 14.2 1.0
O B:HOH513 2.2 15.4 1.0
O B:HOH506 2.3 15.0 1.0
O B:HOH501 2.3 14.0 1.0
CG B:ASP145 3.1 14.2 1.0
OD2 B:ASP145 3.5 17.3 1.0
OE2 A:GLU179 3.9 14.4 1.0
OP3 B:PSU400 4.0 15.7 1.0
OE1 A:GLU179 4.0 12.5 1.0
NE2 B:HIS137 4.1 13.1 1.0
O A:HOH513 4.1 11.7 1.0
CD A:GLU179 4.2 13.5 1.0
O B:GLY266 4.2 16.9 1.0
O B:HOH516 4.2 13.8 1.0
OE1 A:GLU176 4.2 15.7 1.0
O B:HOH510 4.3 12.6 1.0
CD2 B:HIS137 4.3 14.7 1.0
C B:GLY266 4.3 14.6 1.0
OP1 B:PSU400 4.4 16.1 1.0
CB B:ASP145 4.5 12.4 1.0
CA B:GLY266 4.5 14.4 1.0
N B:ILE146 4.6 13.7 1.0
CA B:ASP145 4.7 15.4 1.0
C B:ASP145 4.7 18.2 1.0
P B:PSU400 4.8 13.0 1.0
O B:ILE146 4.8 13.0 1.0
C B:ILE146 4.8 15.0 1.0
CE1 B:HIS137 4.8 15.7 1.0
O B:HOH520 4.9 16.6 1.0
N B:LYS267 4.9 14.9 1.0
N B:SER147 4.9 14.8 1.0
CA B:SER147 5.0 12.3 1.0

Manganese binding site 3 out of 3 in 4gim

Go back to Manganese Binding Sites List in 4gim
Manganese binding site 3 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate


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 Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:17.4
occ:1.00
 OD1 C:ASP145 2.2 17.9 1.0
O B:HOH502 2.2 16.2 1.0
O C:HOH511 2.2 18.8 1.0
O B:HOH526 2.2 17.1 1.0
O C:HOH528 2.3 20.8 1.0
O C:HOH507 2.3 16.2 1.0
CG C:ASP145 3.2 17.0 1.0
OD2 C:ASP145 3.5 20.2 1.0
OE2 B:GLU179 3.8 23.0 1.0
OE1 B:GLU179 4.0 17.8 1.0
OP1 C:PSU400 4.0 19.3 1.0
NE2 C:HIS137 4.1 17.9 1.0
O B:HOH527 4.1 16.3 1.0
CD B:GLU179 4.1 20.0 1.0
O C:HOH537 4.1 18.3 1.0
O C:GLY266 4.2 17.8 1.0
O C:HOH538 4.2 15.7 1.0
OE1 B:GLU176 4.2 20.3 1.0
C C:GLY266 4.3 16.4 1.0
CD2 C:HIS137 4.3 18.4 1.0
OP2 C:PSU400 4.4 19.6 1.0
CA C:GLY266 4.5 18.6 1.0
CB C:ASP145 4.5 16.6 1.0
N C:ILE146 4.5 13.6 1.0
O C:ILE146 4.7 14.5 1.0
P C:PSU400 4.7 19.3 1.0
C C:ASP145 4.7 18.0 1.0
CA C:ASP145 4.7 17.0 1.0
C C:ILE146 4.8 14.5 1.0
O C:HOH540 4.8 17.2 1.0
N C:LYS267 4.9 20.9 1.0
CE1 C:HIS137 4.9 18.0 1.0
N C:SER147 4.9 16.6 1.0
CA C:SER147 4.9 17.5 1.0

Reference:

S.Huang, N.Mahanta, T.P.Begley, S.E.Ealick. Pseudouridine Monophosphate Glycosidase: A New Glycosidase Mechanism. Biochemistry V. 51 9245 2012.
ISSN: ISSN 0006-2960
PubMed: 23066817
DOI: 10.1021/BI3006829
Page generated: Sat Oct 5 19:31:46 2024

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