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Bromine in PDB 4p5b: Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Dump

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

All present enzymatic activity of Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Dump:
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 Dump, PDB code: 4p5b 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 / 2.27
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.788, 59.502, 118.981, 90.00, 120.31, 90.00
R / Rfree (%) 16.4 / 21.6

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 Dump (pdb code 4p5b). 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 Dump, PDB code: 4p5b:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 4p5b

Go back to Bromine Binding Sites List in 4p5b
Bromine binding site 1 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Dump


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 Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br302

b:30.6
occ:1.00
 BR A:BRU302 0.0 30.6 1.0
C5 A:BRU302 1.9 23.9 1.0
C4 A:BRU302 2.8 22.5 1.0
C6 A:BRU302 2.8 16.9 1.0
O4 A:BRU302 3.1 17.9 1.0
OG A:SER96 3.4 20.6 1.0
N5 B:FAD302 3.5 45.7 1.0
CE1 A:TYR99 3.5 41.7 1.0
OP1 A:BRU302 3.6 20.9 1.0
CD A:ARG98 3.7 15.5 1.0
C6 B:FAD302 3.7 46.4 1.0
C5X B:FAD302 3.8 46.8 1.0
CD1 A:TYR99 3.9 37.2 1.0
O4 B:FAD302 4.0 56.9 1.0
NH1 A:ARG98 4.0 13.1 1.0
C4X B:FAD302 4.0 47.2 1.0
CB A:ARG98 4.0 19.8 1.0
N3 A:BRU302 4.1 23.1 1.0
CB A:SER96 4.1 19.4 1.0
N1 A:BRU302 4.1 21.2 1.0
CG A:ARG98 4.2 16.9 1.0
C4 B:FAD302 4.3 50.6 1.0
C2 A:BRU302 4.6 22.0 1.0
NE A:ARG98 4.6 12.6 1.0
C7 B:FAD302 4.7 46.7 1.0
CZ A:ARG98 4.7 13.1 1.0
C9A B:FAD302 4.7 46.0 1.0
CZ A:TYR99 4.8 47.0 1.0
P A:BRU302 4.8 20.2 1.0
CG B:PRO121 4.9 57.5 1.0
C10 B:FAD302 4.9 42.4 1.0

Bromine binding site 2 out of 4 in 4p5b

Go back to Bromine Binding Sites List in 4p5b
Bromine binding site 2 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Dump


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 Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br301

b:29.7
occ:1.00
 BR B:BRU301 0.0 29.7 1.0
C5 B:BRU301 1.9 22.2 1.0
C4 B:BRU301 2.8 17.4 1.0
C6 B:BRU301 2.9 17.2 1.0
O4 B:BRU301 3.0 15.1 1.0
CE2 B:TYR99 3.1 50.4 1.0
OG B:SER96 3.3 21.6 1.0
N5 A:FAD301 3.3 34.5 1.0
CD2 B:TYR99 3.5 47.2 1.0
C6 A:FAD301 3.6 35.5 1.0
OP3 B:BRU301 3.6 16.3 1.0
C5X A:FAD301 3.7 34.7 1.0
CD B:ARG98 3.7 12.7 1.0
O4 A:FAD301 3.8 39.4 1.0
NH1 B:ARG98 3.9 14.1 1.0
C4X A:FAD301 3.9 35.5 1.0
CB B:SER96 3.9 21.3 1.0
N3 B:BRU301 4.1 17.5 1.0
N1 B:BRU301 4.1 21.4 1.0
C4 A:FAD301 4.2 36.3 1.0
CZ B:TYR99 4.2 53.7 1.0
CB B:ARG98 4.2 19.2 1.0
CG B:ARG98 4.3 16.9 1.0
OH B:TYR99 4.5 59.9 1.0
C2 B:BRU301 4.6 17.8 1.0
NE B:ARG98 4.6 14.3 1.0
C7 A:FAD301 4.6 33.6 1.0
CZ B:ARG98 4.7 16.9 1.0
C9A A:FAD301 4.8 32.0 1.0
CG B:TYR99 4.8 39.5 1.0
C10 A:FAD301 4.9 34.1 1.0
P B:BRU301 4.9 19.1 1.0

Bromine binding site 3 out of 4 in 4p5b

Go back to Bromine Binding Sites List in 4p5b
Bromine binding site 3 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Dump


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 Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br302

b:40.0
occ:1.00
 BR C:BRU302 0.0 40.0 1.0
C5 C:BRU302 1.9 31.2 1.0
C6 C:BRU302 2.8 27.1 1.0
C4 C:BRU302 2.9 25.9 1.0
O4 C:BRU302 3.0 23.9 1.0
OG C:SER96 3.4 27.2 1.0
N5 D:FAD302 3.4 50.4 1.0
CE1 C:TYR99 3.5 48.5 1.0
OP3 C:BRU302 3.8 25.9 1.0
CD1 C:TYR99 3.8 44.2 1.0
CD C:ARG98 3.8 24.4 1.0
C5X D:FAD302 3.8 50.3 1.0
NH1 C:ARG98 3.8 24.4 1.0
C6 D:FAD302 3.9 50.5 1.0
C4X D:FAD302 4.0 52.2 1.0
O4 D:FAD302 4.1 56.0 1.0
CB C:ARG98 4.1 29.9 1.0
CB C:SER96 4.1 26.6 1.0
N1 C:BRU302 4.1 25.0 1.0
N3 C:BRU302 4.2 23.4 1.0
C4 D:FAD302 4.3 54.6 1.0
CG C:ARG98 4.4 26.9 1.0
C2 C:BRU302 4.6 21.6 1.0
NE C:ARG98 4.6 28.7 1.0
CZ C:TYR99 4.7 51.2 1.0
CZ C:ARG98 4.7 31.0 1.0
C9A D:FAD302 4.8 49.0 1.0
C7 D:FAD302 4.8 50.3 1.0
C10 D:FAD302 4.9 50.7 1.0

Bromine binding site 4 out of 4 in 4p5b

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Bromine binding site 4 out of 4 in the Crystal Structure of A Ump/Dump Methylase Polb From Streptomyces Cacaoi Bound with 5-Br Dump


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 Dump within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br301

b:36.0
occ:1.00
 BR D:BRU301 0.0 36.0 1.0
C5 D:BRU301 1.9 27.2 1.0
C6 D:BRU301 2.8 25.4 1.0
C4 D:BRU301 2.8 24.0 1.0
O4 D:BRU301 3.0 19.1 1.0
CE1 D:TYR99 3.4 51.4 1.0
OG D:SER96 3.5 35.5 1.0
N5 C:FAD301 3.6 48.3 1.0
OP3 D:BRU301 3.6 18.3 1.0
CD1 D:TYR99 3.7 45.5 1.0
NH1 D:ARG98 3.8 25.8 1.0
C6 C:FAD301 3.8 51.2 1.0
C5X C:FAD301 3.9 50.0 1.0
CD D:ARG98 3.9 24.4 1.0
CB D:ARG98 4.0 25.3 1.0
CB D:SER96 4.0 23.0 1.0
N1 D:BRU301 4.1 21.9 1.0
N3 D:BRU301 4.1 22.5 1.0
C4X C:FAD301 4.2 49.2 1.0
CG D:ARG98 4.2 27.1 1.0
O4 C:FAD301 4.4 52.9 1.0
CZ D:TYR99 4.4 53.2 1.0
C4 C:FAD301 4.5 50.0 1.0
C2 D:BRU301 4.6 22.7 1.0
CZ D:ARG98 4.6 29.6 1.0
NE D:ARG98 4.7 26.4 1.0
C7 C:FAD301 4.7 51.8 1.0
C9A C:FAD301 4.8 49.5 1.0
OH D:TYR99 4.8 57.3 1.0
CG D:TYR99 4.9 39.6 1.0
P D:BRU301 4.9 23.5 1.0

Reference:

Y.Li, W.Chen, J.Li, Z.Xia, Z.Deng, J.Zhou. Crystal Structure of A Ump/Dump Methylase Polb Form Streptomyces Cacaoi Bound with 5-Br Dump To Be Published.
Page generated: Wed Jul 10 22:14:02 2024

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