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Bromine in PDB 2ewf: Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I

Protein crystallography data

The structure of Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I, PDB code: 2ewf was solved by G.S.Kachalova, H.D.Bartunik, R.I.Artyukh, E.A.Rogulin, T.A.Perevyazova, L.A.Zheleznaya, N.I.Matvienko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.553, 92.562, 76.349, 90.00, 111.88, 90.00
R / Rfree (%) 20 / 23.6

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I (pdb code 2ewf). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 13 binding sites of Bromine where determined in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I, PDB code: 2ewf:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 13 in 2ewf

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Bromine binding site 1 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br605

b:44.5
occ:1.00
 ND2 A:ASN190 3.0 52.5 1.0
CE A:LYS191 3.2 53.1 1.0
CD A:LYS191 3.2 54.4 1.0
O A:HOH2017 3.4 38.1 1.0
CB A:ASN190 3.9 37.0 1.0
CG A:ASN190 4.0 50.4 1.0
N A:LYS191 4.4 36.0 1.0
CG A:LYS191 4.4 53.4 1.0
NZ A:LYS191 4.6 58.0 1.0
C A:ASN190 4.9 42.3 1.0
CA A:LYS191 4.9 44.1 1.0
CA A:ASN190 5.0 35.4 1.0
CB A:LYS191 5.0 42.2 1.0

Bromine binding site 2 out of 13 in 2ewf

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Bromine binding site 2 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br606

b:36.8
occ:1.00
 O A:HOH2445 2.5 48.3 1.0
O A:HOH2204 3.4 41.7 1.0
N A:GLN55 3.4 34.5 1.0
NE2 A:GLN55 3.4 25.2 1.0
O A:HOH2270 3.5 45.1 1.0
CG A:GLN55 3.6 36.9 1.0
CD A:PRO54 3.6 37.5 1.0
CB A:GLN55 3.8 40.4 1.0
CG A:PRO21 3.8 27.6 1.0
CB A:PRO21 3.9 24.4 1.0
CD A:GLN55 4.0 35.6 1.0
N A:PRO54 4.0 38.0 1.0
CB A:PRO54 4.1 35.7 1.0
CB A:LEU53 4.1 38.4 1.0
O A:HOH2639 4.2 80.3 1.0
CA A:GLN55 4.2 33.6 1.0
CG A:PRO54 4.2 40.5 1.0
C A:PRO54 4.4 38.0 1.0
CA A:PRO54 4.4 34.2 1.0
CD2 A:LEU53 4.5 28.3 1.0
CD1 A:LEU53 4.5 28.7 1.0
C A:LEU53 4.5 38.8 1.0
O A:HOH2276 4.6 39.7 1.0
CG A:LEU53 4.6 26.8 1.0
O A:HOH2517 4.8 59.6 1.0
CA A:LEU53 4.8 32.9 1.0

Bromine binding site 3 out of 13 in 2ewf

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Bromine binding site 3 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br607

b:40.8
occ:1.00
 O A:HOH2448 2.8 46.0 1.0
O A:HOH2190 3.1 46.5 1.0
OG1 A:THR78 3.2 32.0 1.0
O A:HOH2112 3.3 42.2 1.0
CA A:PRO75 3.6 25.2 1.0
N A:PRO75 3.7 25.7 1.0
CB A:SER10 3.9 36.8 1.0
CB A:THR78 3.9 29.7 1.0
C A:ALA74 3.9 18.4 1.0
O A:ALA74 4.0 20.9 1.0
CE1 A:TYR8 4.0 59.1 1.0
CB A:PRO75 4.1 25.3 1.0
CD A:PRO75 4.1 28.9 1.0
CB A:ALA74 4.3 45.2 1.0
CG2 A:THR78 4.4 27.6 1.0
CG A:PRO75 4.5 26.2 1.0
OG A:SER10 4.6 32.6 1.0
CA A:SER10 4.6 27.3 1.0
O A:HOH2244 4.7 42.4 1.0
CD1 A:TYR8 4.7 46.9 1.0
N A:SER10 4.7 22.9 1.0
CA A:ALA74 4.8 23.9 1.0
OH A:TYR79 4.9 37.4 1.0
CZ A:TYR8 4.9 63.4 1.0
OH A:TYR8 4.9 62.4 1.0
O A:HOH2155 4.9 32.3 1.0
C A:PRO75 5.0 22.9 1.0

Bromine binding site 4 out of 13 in 2ewf

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Bromine binding site 4 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br608

b:55.3
occ:1.00
 N A:LYS413 3.3 25.9 1.0
O A:HOH2519 3.4 46.8 1.0
O A:HOH2652 3.4 53.2 0.5
CG A:LYS413 3.8 25.2 1.0
CB A:LYS413 3.8 24.7 1.0
CE A:LYS406 3.8 35.5 1.0
CG A:GLU402 3.8 42.8 1.0
O A:HOH2035 3.9 31.9 1.0
CA A:ASN412 3.9 26.1 1.0
C A:ASN412 4.0 30.7 1.0
CA A:LYS413 4.1 26.7 1.0
CG A:LYS406 4.1 33.8 1.0
CB A:ASN412 4.1 26.7 1.0
CA A:GLU402 4.2 25.8 1.0
CB A:GLU402 4.4 29.9 1.0
O A:GLU402 4.5 31.6 1.0
CD A:LYS406 4.6 37.4 1.0
CD A:LYS413 4.7 36.9 1.0
NZ A:LYS406 4.8 53.3 1.0
CG2 A:ILE405 4.8 27.5 1.0
CD A:GLU402 4.8 53.8 1.0
C A:GLU402 4.8 25.0 1.0
CB A:ILE405 4.9 20.8 1.0
OE2 A:GLU402 4.9 58.1 1.0
O A:HOH2164 4.9 43.0 1.0

Bromine binding site 5 out of 13 in 2ewf

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Bromine binding site 5 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br609

b:51.4
occ:1.00
 O A:HOH2102 3.0 27.1 1.0
O A:HOH2067 3.3 45.3 1.0
NH1 A:ARG243 3.4 24.6 1.0
N A:HIS449 3.5 16.0 1.0
NH2 A:ARG243 3.6 31.7 1.0
OG1 A:THR415 3.7 24.2 1.0
ND2 A:ASN412 3.7 34.2 1.0
CB A:HIS449 3.8 23.4 1.0
CZ A:ARG243 4.0 28.6 1.0
CA A:THR448 4.1 22.1 1.0
CG2 A:THR448 4.2 27.5 1.0
CA A:HIS449 4.3 22.3 1.0
C A:THR448 4.3 22.3 1.0
O A:HOH2404 4.5 50.2 1.0
CB A:THR448 4.7 26.6 1.0
CG A:ASN412 4.7 33.2 1.0
O A:HOH2225 4.8 42.8 1.0
O A:VAL447 4.8 25.8 1.0
O A:HOH2110 4.8 42.3 1.0
O A:HOH2290 4.8 38.9 1.0
OG1 A:THR448 4.9 27.3 1.0
OD1 A:ASN412 5.0 41.4 1.0

Bromine binding site 6 out of 13 in 2ewf

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Bromine binding site 6 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br610

b:47.4
occ:1.00
 N A:VAL84 3.2 22.1 1.0
O A:HOH2459 3.3 43.5 1.0
O A:HOH2551 3.5 42.3 0.5
NE2 A:GLN122 3.6 52.5 1.0
O A:HOH2128 3.7 35.2 1.0
CE A:LYS77 3.7 36.8 1.0
CE2 A:PHE121 3.8 31.0 1.0
NZ A:LYS77 3.8 44.0 1.0
CA A:PHE83 3.8 24.5 1.0
CB A:PHE83 3.9 20.4 1.0
C A:PHE83 3.9 30.5 1.0
CB A:VAL84 4.1 26.5 1.0
CD A:LYS77 4.1 26.6 1.0
CA A:VAL84 4.2 21.7 1.0
CD2 A:PHE121 4.2 26.1 1.0
O A:VAL84 4.2 23.1 1.0
CG2 A:VAL84 4.2 25.3 1.0
CG2 A:VAL284 4.4 25.6 1.0
CG A:LYS77 4.5 19.9 1.0
C A:VAL84 4.7 25.3 1.0
CD A:GLN122 4.7 54.9 1.0
CZ A:PHE121 4.9 27.6 1.0

Bromine binding site 7 out of 13 in 2ewf

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Bromine binding site 7 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br611

b:39.2
occ:0.80
 O A:HOH2081 3.2 30.7 1.0
O A:HOH2498 3.4 61.3 1.0
NZ A:LYS413 3.5 30.7 1.0
O A:HOH2055 3.5 37.6 1.0
CD1 A:ILE401 3.6 27.4 1.0
CE A:LYS413 3.8 34.6 1.0
CB A:THR472 4.0 28.4 1.0
CD A:LYS413 4.1 36.9 1.0
CG A:LYS398 4.2 34.1 1.0
CA A:LYS398 4.2 28.6 1.0
O A:HOH2047 4.2 32.7 1.0
CB A:LYS398 4.2 32.3 1.0
OG1 A:THR472 4.2 28.4 1.0
O A:THR472 4.3 34.0 1.0
CE A:LYS474 4.5 51.4 1.0
CG2 A:THR472 4.8 22.6 1.0
CD A:LYS398 4.8 46.6 1.0
CG1 A:ILE401 4.8 25.7 1.0
N A:LYS398 4.9 26.4 1.0
NZ A:LYS474 4.9 41.9 1.0
O A:HOH2661 4.9 32.6 0.5
O A:HOH2486 4.9 56.0 1.0
CB A:ILE401 5.0 23.9 1.0
CG2 A:ILE401 5.0 22.1 1.0

Bromine binding site 8 out of 13 in 2ewf

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Bromine binding site 8 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


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 the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br612

b:57.3
occ:1.00
 O A:HOH2063 3.0 36.3 1.0
O A:HOH2302 3.1 50.9 1.0
O A:HOH2438 3.2 43.0 1.0
NE1 A:TRP34 3.3 27.0 1.0
O A:HOH2106 3.6 79.9 1.0
CA A:ARG70 3.9 48.2 1.0
CB A:VAL73 3.9 32.0 1.0
CG1 A:VAL73 4.0 27.3 1.0
CD1 A:TRP34 4.1 27.6 1.0
CG2 A:VAL73 4.3 30.2 1.0
CG2 A:THR69 4.3 71.2 1.0
CB A:ARG70 4.3 57.1 1.0
CE2 A:TRP34 4.3 25.4 1.0
NZ A:LYS77 4.5 44.0 1.0
N A:ARG70 4.5 45.9 1.0
CE A:LYS77 4.6 36.8 1.0
CZ2 A:TRP34 4.7 25.2 1.0
OE1 A:GLN43 4.7 63.4 1.0
CG A:ARG70 4.8 59.8 1.0
O A:THR69 4.8 46.0 1.0
NE2 A:GLN43 4.8 49.9 1.0
CD A:GLN43 4.9 56.0 1.0
O A:ARG70 4.9 34.4 1.0
C A:ARG70 4.9 36.2 1.0
C A:THR69 4.9 55.2 1.0

Bromine binding site 9 out of 13 in 2ewf

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Bromine binding site 9 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br613

b:69.0
occ:1.00
 CG A:ASN331 3.2 47.4 1.0
N A:ASN331 3.2 32.4 1.0
O A:HOH2105 3.2 33.2 1.0
OD1 A:ASN331 3.3 34.2 1.0
CD A:PRO330 3.4 41.4 1.0
CB A:ASN331 3.6 39.1 1.0
N A:PRO330 3.6 43.7 1.0
ND2 A:ASN331 3.6 30.7 1.0
CA A:PHE329 3.7 33.4 1.0
C A:PHE329 3.7 36.0 1.0
CG A:PRO330 4.0 40.8 1.0
CA A:ASN331 4.0 39.3 1.0
C A:PRO330 4.2 34.4 1.0
CB A:PHE329 4.2 29.4 1.0
CA A:PRO330 4.4 41.5 1.0
CA A:ASN430 4.4 26.4 1.0
O A:PHE329 4.5 38.0 1.0
CD1 A:PHE329 4.5 37.0 1.0
O A:HOH2509 4.5 74.8 1.0
O A:HIS328 4.6 38.7 1.0
O A:HOH2471 4.7 41.7 1.0
N A:ASN430 4.7 25.6 1.0
ND2 A:ASN430 4.7 27.0 1.0
CB A:PRO330 4.8 40.1 1.0
CG A:PHE329 4.9 29.9 1.0
N A:PHE329 4.9 32.3 1.0

Bromine binding site 10 out of 13 in 2ewf

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Bromine binding site 10 out of 13 in the Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of the Site-Specific Dna Nickase N.BSPD6I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br614

b:54.5
occ:1.00
 O A:HOH2044 2.7 36.0 1.0
O A:HOH2343 2.9 23.3 0.5
O A:HOH2051 2.9 25.9 1.0
O A:ILE440 3.3 28.3 1.0
CA A:TYR247 3.6 21.4 1.0
CG1 A:VAL439 3.7 26.3 1.0
CA A:ASP441 3.8 22.4 1.0
O A:ARG246 3.8 22.1 1.0
N A:TYR247 3.8 20.5 1.0
C A:ARG246 3.9 20.2 1.0
C A:ILE440 4.0 24.6 1.0
CG2 A:VAL447 4.0 19.2 1.0
CD1 A:TYR247 4.1 18.1 1.0
CB A:ASP441 4.1 23.4 1.0
N A:ASP441 4.2 20.4 1.0
O A:HOH2363 4.3 48.8 1.0
CB A:TYR247 4.3 20.1 1.0
CB A:ARG246 4.5 16.0 1.0
C A:TYR247 4.7 25.0 1.0
CG A:TYR247 4.7 14.8 1.0
CB A:VAL447 4.8 20.9 1.0
NZ A:LYS106 4.8 44.1 1.0
O A:HOH2001 4.9 18.4 1.0
CA A:ARG246 4.9 19.4 1.0
CE A:LYS106 4.9 28.6 1.0
O A:TYR247 4.9 18.2 1.0
C A:ASP441 4.9 22.6 1.0

Reference:

G.S.Kachalova, E.A.Rogulin, A.K.Yunusova, R.I.Artyukh, T.A.Perevyazova, N.I.Matvienko, L.A.Zheleznaya, H.D.Bartunik. Structural Analysis of the Heterodimeric Type Iis Restriction Endonuclease R.BSPD6I Acting As A Complex Between A Monomeric Site-Specific Nickase and A Catalytic Subunit. J.Mol.Biol. V. 384 489 2008.
ISSN: ISSN 0022-2836
PubMed: 18835275
DOI: 10.1016/J.JMB.2008.09.033
Page generated: Wed Jul 10 17:56:27 2024

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