Atomistry » Bromine » PDB 4mye-4p5b » 4p5a
Atomistry »
  Bromine »
    PDB 4mye-4p5b »
      4p5a »

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

Last articles

Br in 8E6T
Br in 8F82
Br in 8EZ2
Br in 8EO2
Br in 8DXK
Br in 8EYF
Br in 8EYD
Br in 8EJP
Br in 8DX2
Br in 8E9E
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy