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Chlorine in PDB 2oge: X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form

Protein crystallography data

The structure of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form, PDB code: 2oge was solved by H.M.Holden, E.S.Burgie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.50 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.798, 143.820, 81.132, 90.00, 106.95, 90.00
R / Rfree (%) n/a / n/a

Other elements in 2oge:

The structure of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form (pdb code 2oge). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form, PDB code: 2oge:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2oge

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Chlorine binding site 1 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1297

b:30.2
occ:1.00
 O A:HOH1482 3.0 36.8 1.0
O B:HOH1450 3.1 41.9 1.0
N A:TYR39 3.1 14.8 1.0
O A:HOH1483 3.2 41.2 1.0
N A:LEU40 3.5 21.1 1.0
CA A:TYR39 3.9 15.1 1.0
CD A:ARG38 4.0 45.9 1.0
CD1 B:LEU15 4.0 17.1 1.0
C A:ARG38 4.1 25.3 1.0
C A:TYR39 4.1 27.7 1.0
CA A:ARG38 4.1 21.3 1.0
CB A:TYR39 4.2 13.5 1.0
CB A:LEU40 4.3 11.8 1.0
O A:LEU40 4.3 22.2 1.0
CA A:LEU40 4.4 13.7 1.0
CD1 A:TYR39 4.4 19.9 1.0
NH1 A:ARG38 4.4 0.0 1.0
O A:GLY37 4.5 15.6 1.0
CG B:PRO191 4.6 23.1 1.0
CB B:PRO191 4.7 14.6 1.0
CG A:TYR39 4.7 16.8 1.0
C A:LEU40 4.8 22.0 1.0
CG A:ARG38 4.9 51.3 1.0
OH B:TYR190 4.9 26.2 1.0
CG A:LEU40 5.0 21.5 1.0

Chlorine binding site 2 out of 8 in 2oge

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Chlorine binding site 2 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1298

b:22.1
occ:1.00
 O B:HOH1313 3.1 14.0 1.0
NE2 A:HIS229 3.1 15.2 1.0
O B:HOH1311 3.2 19.5 1.0
O1 A:EDO1304 3.4 56.1 1.0
CA A:TYR227 3.7 19.3 1.0
CD2 A:HIS229 3.7 15.1 1.0
CD2 B:TYR318 3.8 13.3 1.0
O A:HOH1548 3.8 23.2 1.0
CE1 B:TYR93 3.9 13.6 1.0
C1 A:EDO1304 4.0 36.3 1.0
CD1 B:TYR93 4.0 18.8 1.0
C A:TYR227 4.2 27.5 1.0
CD2 A:TYR227 4.3 46.4 1.0
CE1 A:HIS229 4.3 14.2 1.0
O A:TYR227 4.3 21.5 1.0
N A:TYR227 4.4 20.4 1.0
CB B:TYR318 4.4 20.1 1.0
CG B:TYR318 4.4 16.2 1.0
CE2 B:TYR318 4.5 13.0 1.0
O B:HOH1312 4.5 14.6 1.0
CB A:TYR227 4.6 18.7 1.0
CG2 B:ILE94 4.9 10.9 1.0
O2 A:EDO1304 4.9 26.2 1.0
CG A:TYR227 4.9 40.0 1.0
N A:SER228 5.0 20.5 1.0

Chlorine binding site 3 out of 8 in 2oge

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Chlorine binding site 3 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1300

b:27.3
occ:1.00
 N B:TYR39 3.1 13.3 1.0
O A:HOH1543 3.2 37.5 1.0
O B:HOH1447 3.2 42.9 1.0
N B:LEU40 3.5 18.9 1.0
O B:HOH1469 3.8 35.8 1.0
CA B:TYR39 3.9 15.7 1.0
C B:ARG38 4.1 20.7 1.0
C B:TYR39 4.1 22.6 1.0
CA B:ARG38 4.2 14.8 1.0
NE B:ARG38 4.2 78.6 1.0
CD1 A:LEU15 4.2 15.3 1.0
CB B:TYR39 4.3 13.6 1.0
O B:LEU40 4.3 13.1 1.0
CB B:LEU40 4.5 15.5 1.0
CA B:LEU40 4.5 18.1 1.0
CD B:ARG38 4.5 32.9 1.0
CD1 B:TYR39 4.6 19.9 1.0
CG A:PRO191 4.6 14.9 1.0
CB A:PRO191 4.6 19.1 1.0
CG B:ARG38 4.7 25.6 1.0
O B:GLY37 4.7 23.1 1.0
CG B:TYR39 4.8 22.6 1.0
CG B:LEU40 4.8 25.8 1.0
C B:LEU40 4.9 23.8 1.0
OH A:TYR190 4.9 38.0 1.0

Chlorine binding site 4 out of 8 in 2oge

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Chlorine binding site 4 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1301

b:38.8
occ:1.00
 O A:HOH1435 3.0 21.2 1.0
O A:HOH1437 3.2 19.2 1.0
O2 B:EDO1304 3.2 64.5 1.0
O B:HOH1451 3.5 31.0 1.0
NE2 B:HIS229 3.5 13.3 1.0
CD2 A:TYR318 3.5 19.0 1.0
CA B:TYR227 3.9 20.4 1.0
O B:HOH1317 4.0 29.4 1.0
CD2 B:HIS229 4.1 16.6 1.0
CE1 A:TYR93 4.1 18.8 1.0
CB A:TYR318 4.2 15.6 1.0
CG A:TYR318 4.2 21.8 1.0
CD2 B:TYR227 4.3 18.4 1.0
CD1 A:TYR93 4.3 11.6 1.0
O B:TYR227 4.3 28.5 1.0
C B:TYR227 4.3 25.1 1.0
CE2 A:TYR318 4.3 13.8 1.0
C2 B:EDO1304 4.5 58.9 1.0
N B:TYR227 4.6 16.7 1.0
CE1 B:HIS229 4.6 15.4 1.0
O A:HOH1436 4.7 18.4 1.0
CB B:TYR227 4.8 24.8 1.0
CD A:PRO319 4.8 12.7 1.0

Chlorine binding site 5 out of 8 in 2oge

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Chlorine binding site 5 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1302

b:23.2
occ:1.00
 O C:HOH1343 3.0 27.9 1.0
N C:TYR39 3.2 17.2 1.0
O C:HOH1489 3.5 35.1 1.0
N C:LEU40 3.6 17.5 1.0
CA C:TYR39 3.9 16.5 1.0
CD1 D:LEU15 4.0 24.4 1.0
CB C:TYR39 4.0 16.0 1.0
CA C:ARG38 4.2 15.8 1.0
C C:ARG38 4.2 24.6 1.0
C C:TYR39 4.2 15.9 1.0
CD1 C:TYR39 4.3 17.4 1.0
O C:LEU40 4.3 16.9 1.0
CG C:ARG38 4.5 25.7 1.0
CG C:TYR39 4.5 23.1 1.0
CA C:LEU40 4.5 18.3 1.0
CG D:PRO191 4.5 15.3 1.0
CB C:LEU40 4.5 13.7 1.0
O C:GLY37 4.5 23.8 1.0
CB D:PRO191 4.7 12.2 1.0
NE C:ARG38 4.7 54.1 1.0
CB C:ARG38 4.9 19.9 1.0
C C:LEU40 4.9 20.5 1.0

Chlorine binding site 6 out of 8 in 2oge

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Chlorine binding site 6 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1303

b:30.1
occ:1.00
 NE2 C:HIS229 3.0 15.9 1.0
O2 C:EDO1309 3.0 51.3 1.0
O C:HOH1533 3.1 16.7 1.0
O D:HOH1327 3.1 12.6 1.0
CA C:TYR227 3.6 37.0 1.0
CD2 D:TYR318 3.6 13.0 1.0
CD2 C:HIS229 3.6 21.8 1.0
O C:TYR227 3.9 29.4 1.0
C C:TYR227 4.0 34.2 1.0
O C:HOH1534 4.0 49.2 1.0
CE1 D:TYR93 4.0 15.9 1.0
CB D:TYR318 4.1 17.8 1.0
C2 C:EDO1309 4.1 61.9 1.0
CG D:TYR318 4.1 19.8 1.0
CE1 C:HIS229 4.2 13.5 1.0
CD1 D:TYR93 4.2 15.4 1.0
O D:HOH1328 4.2 20.1 1.0
N C:TYR227 4.4 28.6 1.0
CB C:TYR227 4.4 46.5 1.0
CE2 D:TYR318 4.5 8.7 1.0
O D:HOH1385 4.7 19.9 1.0
CD2 C:TYR227 4.7 61.4 1.0
C1 C:EDO1309 4.9 34.5 1.0
CD D:PRO319 4.9 28.0 1.0
CG C:HIS229 4.9 14.8 1.0
N C:SER228 4.9 19.4 1.0

Chlorine binding site 7 out of 8 in 2oge

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Chlorine binding site 7 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1305

b:27.9
occ:1.00
 N D:TYR39 3.1 19.6 1.0
O C:HOH1325 3.1 40.6 1.0
O D:HOH1469 3.2 28.4 1.0
N D:LEU40 3.4 14.8 1.0
CA D:TYR39 3.8 15.6 1.0
O D:HOH1496 3.8 42.0 1.0
CD1 C:LEU15 3.8 16.0 1.0
NE D:ARG38 3.9 45.8 1.0
CB D:TYR39 4.0 13.6 1.0
C D:ARG38 4.1 20.6 1.0
C D:TYR39 4.1 16.1 1.0
CA D:ARG38 4.1 21.0 1.0
O C:HOH1579 4.2 52.5 1.0
CD1 D:TYR39 4.2 22.2 1.0
O D:LEU40 4.4 20.5 1.0
CA D:LEU40 4.4 14.9 1.0
CG D:TYR39 4.5 15.8 1.0
CG C:PRO191 4.5 19.0 1.0
CD D:ARG38 4.5 63.6 1.0
CB D:LEU40 4.5 15.9 1.0
CZ D:ARG38 4.5 87.6 1.0
NH2 D:ARG38 4.6 75.2 1.0
CB C:PRO191 4.6 19.6 1.0
O D:GLY37 4.6 19.0 1.0
CB D:ARG38 4.8 29.3 1.0
C D:LEU40 4.9 25.0 1.0
CG D:LEU40 5.0 21.8 1.0

Chlorine binding site 8 out of 8 in 2oge

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Chlorine binding site 8 out of 8 in the X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure of S. Venezuelae Desv in Its Internal Aldimine Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1306

b:23.4
occ:1.00
 O C:HOH1374 3.1 12.5 1.0
NE2 D:HIS229 3.2 15.3 1.0
O C:HOH1372 3.3 13.2 1.0
CD2 C:TYR318 3.7 21.6 1.0
O D:HOH1428 3.7 28.1 1.0
CA D:TYR227 3.7 6.8 1.0
CD2 D:HIS229 3.9 14.8 1.0
O D:HOH1323 4.1 23.8 1.0
CB C:TYR318 4.1 17.0 1.0
CD2 D:TYR227 4.2 16.4 1.0
C D:TYR227 4.2 17.7 1.0
CG C:TYR318 4.2 22.5 1.0
CE1 C:TYR93 4.2 16.1 1.0
O D:TYR227 4.3 15.4 1.0
CE1 D:HIS229 4.4 13.0 1.0
N D:TYR227 4.4 11.8 1.0
CD1 C:TYR93 4.5 20.3 1.0
CE2 C:TYR318 4.6 24.1 1.0
O C:HOH1373 4.6 16.2 1.0
CB D:TYR227 4.6 13.8 1.0
O D:HOH1551 4.8 44.3 1.0
CG D:TYR227 4.9 22.5 1.0

Reference:

E.S.Burgie, J.B.Thoden, H.M.Holden. Molecular Architecture of Desv From Streptomyces Venezuelae: A Plp-Dependent Transaminase Involved in the Biosynthesis of the Unusual Sugar Desosamine. Protein Sci. V. 16 887 2007.
ISSN: ISSN 0961-8368
PubMed: 17456741
DOI: 10.1110/PS.062711007
Page generated: Sat Jul 20 09:31:29 2024

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