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Bromine in PDB 4p5a: Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump

Enzymatic activity of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump

All present enzymatic activity of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump:
2.1.1.148;

Protein crystallography data

The structure of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump, PDB code: 4p5a was solved by Y.Li, W.Chen, J.Li, Z.Xia, Z.Deng, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.897, 94.160, 91.948, 90.00, 98.30, 90.00
R / Rfree (%) 15.4 / 19.3

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump (pdb code 4p5a). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump, PDB code: 4p5a:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 4p5a

Go back to Bromine Binding Sites List in 4p5a
Bromine binding site 1 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:17.4
occ:1.00
 BR A:5BU302 0.0 17.4 1.0
C5 A:5BU302 1.9 11.3 1.0
C6 A:5BU302 2.8 12.0 1.0
C4 A:5BU302 2.9 15.0 1.0
O4 A:5BU302 3.1 16.8 1.0
OH B:TYR124 3.3 32.7 1.0
N5 B:FAD302 3.3 14.5 1.0
OG A:SER96 3.3 15.2 1.0
C5X B:FAD302 3.6 16.9 1.0
C6 B:FAD302 3.6 16.5 1.0
CD A:ARG98 3.6 12.2 1.0
OP2 A:5BU302 3.6 15.2 1.0
NH1 A:ARG98 3.8 13.6 1.0
CZ B:TYR124 3.9 31.2 1.0
C4X B:FAD302 4.0 12.5 1.0
CB A:ARG98 4.0 14.0 1.0
CB A:SER96 4.1 11.7 1.0
N1 A:5BU302 4.1 9.8 1.0
CG A:ARG98 4.1 13.5 1.0
N3 A:5BU302 4.2 12.2 1.0
O4 B:FAD302 4.3 13.2 1.0
CE1 B:TYR124 4.4 34.9 1.0
C4 B:FAD302 4.4 12.1 1.0
C9A B:FAD302 4.5 12.0 1.0
NE A:ARG98 4.5 12.9 1.0
C7 B:FAD302 4.5 19.2 1.0
C2 A:5BU302 4.6 11.3 1.0
CZ A:ARG98 4.6 15.2 1.0
CE2 B:TYR124 4.6 36.5 1.0
C10 B:FAD302 4.8 13.8 1.0
P A:5BU302 4.9 13.4 1.0

Bromine binding site 2 out of 4 in 4p5a

Go back to Bromine Binding Sites List in 4p5a
Bromine binding site 2 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br301

b:17.6
occ:1.00
 BR B:5BU301 0.0 17.6 1.0
C5 B:5BU301 1.9 14.0 1.0
C6 B:5BU301 2.8 11.9 1.0
C4 B:5BU301 2.8 17.4 1.0
O4 B:5BU301 3.1 17.5 1.0
OH A:TYR124 3.2 28.3 1.0
N5 A:FAD301 3.3 14.5 1.0
OG B:SER96 3.4 16.7 1.0
C5X A:FAD301 3.6 16.0 1.0
C6 A:FAD301 3.6 16.4 1.0
CD B:ARG98 3.6 11.1 1.0
OP3 B:5BU301 3.7 14.8 1.0
CZ A:TYR124 3.7 27.1 1.0
O A:HOH578 3.8 34.0 1.0
NH1 B:ARG98 3.9 9.8 1.0
CB B:ARG98 4.0 13.3 1.0
C4X A:FAD301 4.0 13.8 1.0
CB B:SER96 4.1 15.2 1.0
N3 B:5BU301 4.1 10.9 1.0
CE1 A:TYR124 4.1 28.2 1.0
N1 B:5BU301 4.1 9.1 1.0
CG B:ARG98 4.2 10.5 1.0
O4 A:FAD301 4.2 13.8 1.0
C4 A:FAD301 4.4 13.7 1.0
CE2 A:TYR124 4.5 29.9 1.0
C7 A:FAD301 4.5 14.0 1.0
C9A A:FAD301 4.5 15.2 1.0
NE B:ARG98 4.5 14.5 1.0
C2 B:5BU301 4.6 13.1 1.0
CZ B:ARG98 4.6 12.9 1.0
C10 A:FAD301 4.9 10.6 1.0
P B:5BU301 4.9 13.6 1.0
O5' B:5BU301 5.0 12.6 1.0

Bromine binding site 3 out of 4 in 4p5a

Go back to Bromine Binding Sites List in 4p5a
Bromine binding site 3 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br302

b:15.1
occ:1.00
 BR C:5BU302 0.0 15.1 1.0
C5 C:5BU302 1.9 10.4 1.0
C6 C:5BU302 2.8 11.9 1.0
C4 C:5BU302 2.9 12.6 1.0
O4 C:5BU302 3.1 15.0 1.0
OH D:TYR124 3.2 29.6 1.0
OG C:SER96 3.3 14.0 1.0
N5 D:FAD302 3.3 14.4 1.0
C6 D:FAD302 3.5 14.9 1.0
C5X D:FAD302 3.5 15.4 1.0
OP1 C:5BU302 3.7 17.2 1.0
CD C:ARG98 3.7 12.4 1.0
CZ D:TYR124 3.8 30.0 1.0
NH1 C:ARG98 3.9 10.1 1.0
C4X D:FAD302 4.0 10.9 1.0
CB C:SER96 4.0 11.8 1.0
CB C:ARG98 4.1 13.7 1.0
N1 C:5BU302 4.1 9.6 1.0
N3 C:5BU302 4.1 9.9 1.0
CG C:ARG98 4.2 12.8 1.0
CE1 D:TYR124 4.2 26.8 1.0
O4 D:FAD302 4.2 11.9 1.0
C4 D:FAD302 4.4 13.0 1.0
C7 D:FAD302 4.5 16.5 1.0
C9A D:FAD302 4.5 10.2 1.0
NE C:ARG98 4.6 12.2 1.0
CE2 D:TYR124 4.6 29.3 1.0
CZ C:ARG98 4.6 15.5 1.0
C2 C:5BU302 4.6 10.9 1.0
C10 D:FAD302 4.8 9.2 1.0
P C:5BU302 4.9 12.5 1.0

Bromine binding site 4 out of 4 in 4p5a

Go back to Bromine Binding Sites List in 4p5a
Bromine binding site 4 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br301

b:17.1
occ:1.00
 BR D:5BU301 0.0 17.1 1.0
C5 D:5BU301 2.0 10.0 1.0
C6 D:5BU301 2.8 14.9 1.0
C4 D:5BU301 2.9 13.2 1.0
O4 D:5BU301 3.0 15.1 1.0
OH C:TYR124 3.3 28.4 1.0
N5 C:FAD301 3.3 12.9 1.0
OG D:SER96 3.4 14.8 1.0
C5X C:FAD301 3.5 13.0 1.0
C6 C:FAD301 3.5 13.8 1.0
CD D:ARG98 3.7 11.3 1.0
OP1 D:5BU301 3.7 17.6 1.0
NH1 D:ARG98 3.8 11.9 1.0
CZ C:TYR124 4.0 28.6 1.0
CB D:ARG98 4.0 12.5 1.0
CB D:SER96 4.1 16.5 1.0
C4X C:FAD301 4.1 13.5 1.0
N1 D:5BU301 4.1 11.1 1.0
N3 D:5BU301 4.1 7.2 1.0
CG D:ARG98 4.2 11.9 1.0
O4 C:FAD301 4.2 14.1 1.0
CE1 C:TYR124 4.4 25.4 1.0
C7 C:FAD301 4.4 12.3 1.0
C4 C:FAD301 4.5 13.6 1.0
NE D:ARG98 4.6 15.2 1.0
C9A C:FAD301 4.6 10.9 1.0
C2 D:5BU301 4.6 11.7 1.0
CZ D:ARG98 4.6 16.6 1.0
P D:5BU301 4.9 13.8 1.0
CE2 C:TYR124 5.0 25.7 1.0
C10 C:FAD301 5.0 9.1 1.0

Reference:

Y.Li, W.Chen, J.Li, Z.Xia, Z.Deng, J.Zhou. Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi with 5-Br Ump To Be Published.
Page generated: Mon Jul 7 07:14:04 2025

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