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Bromine in PDB 3zwy: Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose

Enzymatic activity of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose

All present enzymatic activity of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose:
3.2.2.5;

Protein crystallography data

The structure of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose, PDB code: 3zwy was solved by M.Kotaka, R.Graeff, L.H.Zhang, H.C.Lee, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.286, 77.013, 140.338, 87.50, 89.27, 88.99
R / Rfree (%) 21.472 / 28.313

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose (pdb code 3zwy). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose, PDB code: 3zwy:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 3zwy

Go back to Bromine Binding Sites List in 3zwy
Bromine binding site 1 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


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 Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1682

b:0.1
occ:1.00
BR1 A:AV11682 0.0 0.1 1.0
C8A A:AV11682 1.9 0.8 1.0
N7A A:AV11682 2.8 0.7 1.0
N9A A:AV11682 2.9 0.7 1.0
C1' A:AV11682 3.4 0.4 1.0
C5A A:AV11682 4.0 0.6 1.0
C4A A:AV11682 4.0 0.5 1.0
CB A:TYR81 4.2 45.0 1.0
O4' A:AV11682 4.2 0.9 1.0
CG A:TYR81 4.3 42.2 1.0
CD1 A:TYR81 4.5 43.3 1.0
C2' A:AV11682 4.6 0.8 1.0
O2' A:AV11682 4.7 0.4 1.0
CD2 A:TYR81 4.9 41.9 1.0

Bromine binding site 2 out of 8 in 3zwy

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Bromine binding site 2 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


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 Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1682

b:0.5
occ:1.00
BR1 B:AV11682 0.0 0.5 1.0
C8A B:AV11682 1.9 1.0 1.0
N7A B:AV11682 2.9 0.0 1.0
N9A B:AV11682 3.0 0.6 1.0
O B:HOH2031 3.5 47.5 1.0
O4' B:AV11682 3.5 0.6 1.0
C1' B:AV11682 3.7 0.0 1.0
CB B:TYR81 3.7 40.7 1.0
C5A B:AV11682 4.0 0.1 1.0
C4A B:AV11682 4.1 1.0 1.0
CG B:TYR81 4.4 41.5 1.0
C2' B:AV11682 4.9 0.2 1.0
CA B:TYR81 4.9 42.9 1.0
CD1 B:TYR81 5.0 43.3 1.0
N B:TYR81 5.0 44.0 1.0

Bromine binding site 3 out of 8 in 3zwy

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Bromine binding site 3 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


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 Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br1682

b:0.1
occ:1.00
BR1 C:AV11682 0.0 0.1 1.0
C8A C:AV11682 1.9 0.8 1.0
N7A C:AV11682 2.9 0.2 1.0
N9A C:AV11682 3.0 0.6 1.0
O4' C:AV11682 3.5 0.7 1.0
C1' C:AV11682 3.6 0.7 1.0
O C:HOH2030 3.7 37.2 1.0
CB C:TYR81 3.8 40.5 1.0
C5A C:AV11682 4.0 0.2 1.0
C4A C:AV11682 4.1 0.8 1.0
CG C:TYR81 4.6 42.2 1.0
C4' C:AV11682 4.9 0.4 1.0
N C:TYR81 5.0 43.6 1.0
CA C:TYR81 5.0 41.8 1.0

Bromine binding site 4 out of 8 in 3zwy

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Bromine binding site 4 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


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 Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br303

b:0.3
occ:1.00
BR1 D:CV1303 0.0 0.3 1.0
C8 D:CV1303 1.9 0.1 1.0
N7 D:CV1303 2.8 0.7 1.0
N9 D:CV1303 2.9 0.3 1.0
O D:HOH2052 3.2 55.7 1.0
OD1 D:ASN107 3.4 40.0 1.0
C1' D:CV1303 3.5 0.3 1.0
N D:SER108 3.8 41.6 1.0
C5 D:CV1303 4.0 0.1 1.0
C4 D:CV1303 4.0 0.1 1.0
CE2 D:TRP140 4.2 39.9 1.0
NE1 D:TRP140 4.2 41.2 1.0
CZ2 D:TRP140 4.2 39.0 1.0
O4' D:CV1303 4.2 0.4 1.0
CA D:SER108 4.3 42.7 1.0
CG D:ASN107 4.5 40.8 1.0
C2' D:CV1303 4.7 0.3 1.0
CA D:ASN107 4.8 40.7 1.0
C D:ASN107 4.8 41.8 1.0
CH2 D:TRP140 4.9 39.7 1.0
CD1 D:TRP140 4.9 42.9 1.0
CD2 D:TRP140 4.9 41.8 1.0
O2' D:CV1303 5.0 0.9 1.0

Bromine binding site 5 out of 8 in 3zwy

Go back to Bromine Binding Sites List in 3zwy
Bromine binding site 5 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br1682

b:0.7
occ:1.00
BR1 E:AV11682 0.0 0.7 1.0
C8A E:AV11682 1.9 1.0 1.0
O4' E:AV11682 2.7 0.9 1.0
N9A E:AV11682 2.9 0.5 1.0
N7A E:AV11682 3.0 1.0 1.0
C1' E:AV11682 3.3 0.7 1.0
O E:HOH2050 4.0 62.4 1.0
C4' E:AV11682 4.1 98.0 1.0
C4A E:AV11682 4.1 0.1 1.0
C5A E:AV11682 4.1 0.2 1.0
C2' E:AV11682 4.5 0.8 1.0
C5' E:AV11682 4.6 90.2 1.0
C3' E:AV11682 4.7 99.8 1.0
O E:HOH2023 4.9 46.0 1.0

Bromine binding site 6 out of 8 in 3zwy

Go back to Bromine Binding Sites List in 3zwy
Bromine binding site 6 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br1682

b:0.2
occ:1.00
BR1 F:AV11682 0.0 0.2 1.0
C8A F:AV11682 1.9 0.6 1.0
N7A F:AV11682 2.8 0.1 1.0
N9A F:AV11682 3.0 0.5 1.0
O4' F:AV11682 3.2 0.0 1.0
O F:HOH2034 3.4 64.0 1.0
C1' F:AV11682 3.6 0.8 1.0
C5A F:AV11682 4.0 0.1 1.0
C4A F:AV11682 4.0 0.0 1.0
C4' F:AV11682 4.5 0.8 1.0
C5' F:AV11682 4.7 0.1 1.0

Bromine binding site 7 out of 8 in 3zwy

Go back to Bromine Binding Sites List in 3zwy
Bromine binding site 7 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br1682

b:0.0
occ:1.00
BR1 G:AV11682 0.0 0.0 1.0
C8A G:AV11682 1.9 0.8 1.0
N7A G:AV11682 2.9 99.5 1.0
N9A G:AV11682 2.9 96.2 1.0
C1' G:AV11682 3.3 91.7 1.0
C5A G:AV11682 4.0 96.8 1.0
C4A G:AV11682 4.0 96.1 1.0
O3' G:AV11682 4.2 88.2 1.0
O2' G:AV11682 4.3 92.3 1.0
C2' G:AV11682 4.3 90.3 1.0
O G:HOH2018 4.4 53.9 1.0
O4' G:AV11682 4.4 86.8 1.0
CB G:TYR81 4.4 47.1 1.0
C3' G:AV11682 4.8 87.8 1.0

Bromine binding site 8 out of 8 in 3zwy

Go back to Bromine Binding Sites List in 3zwy
Bromine binding site 8 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with 8- Bromo-Adp-Ribose and Cyclic 8-Bromo-Cyclic-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br1682

b:0.4
occ:1.00
BR1 H:AV11682 0.0 0.4 1.0
C8A H:AV11682 1.9 0.2 1.0
N7A H:AV11682 2.8 0.0 1.0
O H:HOH2021 2.9 64.1 1.0
N9A H:AV11682 3.0 0.2 1.0
O4' H:AV11682 3.5 0.5 1.0
C1' H:AV11682 3.7 1.0 1.0
C5A H:AV11682 3.9 0.1 1.0
C4A H:AV11682 4.0 0.9 1.0
CB H:TYR81 4.9 51.3 1.0
C4' H:AV11682 5.0 0.1 1.0

Reference:

M.Kotaka, R.Graeff, Z.Chen, L.H.Zhang, H.C.Lee, Q.Hao. Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase. To Be Published.
Page generated: Sat Dec 12 02:17:07 2020

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