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Chlorine in PDB 4urm: Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin

Enzymatic activity of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin

All present enzymatic activity of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin, PDB code: 4urm was solved by J.Lu, S.Patel, N.Sharma, S.Soisson, R.Kishii, M.Takei, Y.Fukuda, K.J.Lumb, S.B.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.44 / 2.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.280, 75.550, 90.450, 90.00, 90.04, 90.00
R / Rfree (%) 19.53 / 25.63

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin (pdb code 4urm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin, PDB code: 4urm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4urm

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Chlorine binding site 1 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2000

b:41.6
occ:1.00
 CLW A:XAM2000 0.0 41.6 1.0
CAS A:XAM2000 1.7 33.1 1.0
CAT A:XAM2000 2.8 31.5 1.0
CAR A:XAM2000 2.8 27.5 1.0
OD1 A:ASN54 3.2 34.7 1.0
NAO A:XAM2000 3.2 34.9 1.0
CLX A:XAM2000 3.3 32.6 1.0
CAP A:XAM2000 3.5 31.5 1.0
CG A:ASN54 3.6 35.2 1.0
CD1 A:ILE86 3.6 36.7 1.0
CB A:ASN54 3.7 34.4 1.0
NAV A:XAM2000 3.9 25.0 1.0
CAU A:XAM2000 3.9 25.4 1.0
CG1 A:ILE86 4.0 35.9 1.0
CCF A:XAM2000 4.4 33.9 1.0
CAM A:XAM2000 4.5 35.0 1.0
ND2 A:ASN54 4.5 34.5 1.0
OAQ A:XAM2000 4.7 34.2 1.0
CA A:ASN54 4.7 31.3 1.0
CAN A:XAM2000 4.8 35.0 1.0
OG A:SER128 4.9 45.1 1.0
CD1 A:ILE102 4.9 44.7 1.0
O A:ASN54 5.0 31.3 1.0
CCE A:XAM2000 5.0 34.7 1.0

Chlorine binding site 2 out of 8 in 4urm

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Chlorine binding site 2 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2000

b:32.6
occ:1.00
 CLX A:XAM2000 0.0 32.6 1.0
CAT A:XAM2000 1.7 31.5 1.0
CAS A:XAM2000 2.8 33.1 1.0
CAU A:XAM2000 2.9 25.4 1.0
CLW A:XAM2000 3.3 41.6 1.0
CD1 A:ILE175 3.5 31.0 1.0
CAY A:XAM2000 3.5 19.1 1.0
CAR A:XAM2000 3.9 27.5 1.0
NAV A:XAM2000 3.9 25.0 1.0
CB A:SER128 3.9 45.1 1.0
CB A:ASN54 4.0 34.4 1.0
CG2 A:ILE51 4.0 26.3 1.0
CG A:ASN54 4.2 35.2 1.0
CD1 A:ILE86 4.2 36.7 1.0
CG1 A:ILE175 4.2 29.3 1.0
CD1 A:ILE51 4.3 23.4 1.0
ND2 A:ASN54 4.4 34.5 1.0
OG A:SER128 4.4 45.1 1.0
O A:ILE51 4.6 28.7 1.0
OD1 A:ASN54 4.7 34.7 1.0
CA A:ILE51 4.8 27.3 1.0
CB A:ILE51 4.8 27.2 1.0
CB A:ILE175 4.9 29.8 1.0
CG2 A:THR173 5.0 25.0 1.0

Chlorine binding site 3 out of 8 in 4urm

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Chlorine binding site 3 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2000

b:43.3
occ:1.00
 CLW B:XAM2000 0.0 43.3 1.0
CAS B:XAM2000 1.7 36.0 1.0
CAT B:XAM2000 2.8 31.3 1.0
CAR B:XAM2000 2.8 32.8 1.0
NAO B:XAM2000 3.2 37.4 1.0
CLX B:XAM2000 3.4 32.9 1.0
OD1 B:ASN54 3.4 31.7 1.0
CAP B:XAM2000 3.5 33.1 1.0
CG B:ASN54 3.6 32.5 1.0
CB B:ASN54 3.7 31.3 1.0
CD1 B:ILE86 3.8 38.0 1.0
NAV B:XAM2000 3.9 31.6 1.0
CAU B:XAM2000 3.9 26.1 1.0
CG1 B:ILE86 4.1 38.8 1.0
CCF B:XAM2000 4.4 30.9 1.0
ND2 B:ASN54 4.5 33.5 1.0
CAM B:XAM2000 4.5 34.4 1.0
CD1 B:ILE102 4.6 49.2 1.0
OG B:SER128 4.7 46.9 1.0
OAQ B:XAM2000 4.7 30.4 1.0
CA B:ASN54 4.9 32.8 1.0
CCE B:XAM2000 4.9 33.5 1.0
OCK B:XAM2000 5.0 35.8 1.0
CAN B:XAM2000 5.0 32.1 1.0

Chlorine binding site 4 out of 8 in 4urm

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Chlorine binding site 4 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2000

b:32.9
occ:1.00
 CLX B:XAM2000 0.0 32.9 1.0
CAT B:XAM2000 1.7 31.3 1.0
CAS B:XAM2000 2.8 36.0 1.0
CAU B:XAM2000 2.8 26.1 1.0
CLW B:XAM2000 3.4 43.3 1.0
CAY B:XAM2000 3.5 19.0 1.0
CG1 B:ILE175 3.8 21.9 1.0
CG2 B:ILE51 3.9 33.4 1.0
NAV B:XAM2000 3.9 31.6 1.0
CAR B:XAM2000 3.9 32.8 1.0
CD1 B:ILE175 4.0 21.3 1.0
CB B:SER128 4.0 46.5 1.0
CB B:ASN54 4.1 31.3 1.0
CD1 B:ILE51 4.2 31.4 1.0
CG B:ASN54 4.3 32.5 1.0
ND2 B:ASN54 4.3 33.5 1.0
CD1 B:ILE86 4.3 38.0 1.0
OG B:SER128 4.4 46.9 1.0
O B:ILE51 4.6 34.2 1.0
CB B:ILE51 4.8 34.2 1.0
CB B:ILE175 4.8 22.8 1.0
CA B:ILE51 4.8 33.7 1.0
OD1 B:ASN54 4.9 31.7 1.0

Chlorine binding site 5 out of 8 in 4urm

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Chlorine binding site 5 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2000

b:68.3
occ:1.00
 CLW C:XAM2000 0.0 68.3 1.0
CAS C:XAM2000 1.7 60.9 1.0
CAT C:XAM2000 2.7 56.9 1.0
CAR C:XAM2000 2.8 58.4 1.0
NAO C:XAM2000 3.1 61.9 1.0
CLX C:XAM2000 3.2 58.0 1.0
CAP C:XAM2000 3.4 59.5 1.0
CD1 C:ILE86 3.6 81.9 1.0
CG1 C:ILE86 3.7 81.5 1.0
CB C:ASN54 3.8 51.9 1.0
CAU C:XAM2000 3.9 54.5 1.0
NAV C:XAM2000 3.9 56.3 1.0
OD1 C:ASN54 4.0 54.2 1.0
CG C:ASN54 4.0 52.3 1.0
CD1 C:ILE102 4.1 76.0 1.0
CCF C:XAM2000 4.2 68.0 1.0
CAM C:XAM2000 4.4 65.5 1.0
OCK C:XAM2000 4.5 66.0 1.0
OAQ C:XAM2000 4.7 58.6 1.0
CCE C:XAM2000 4.7 67.4 1.0
ND2 C:ASN54 4.8 50.6 1.0
CA C:ASN54 4.9 54.2 1.0

Chlorine binding site 6 out of 8 in 4urm

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Chlorine binding site 6 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2000

b:58.0
occ:1.00
 CLX C:XAM2000 0.0 58.0 1.0
CAT C:XAM2000 1.7 56.9 1.0
CAS C:XAM2000 2.7 60.9 1.0
CAU C:XAM2000 2.8 54.5 1.0
CD1 C:ILE175 3.0 47.4 1.0
CLW C:XAM2000 3.2 68.3 1.0
CAY C:XAM2000 3.5 52.4 1.0
CB C:ASN54 3.8 51.9 1.0
NAV C:XAM2000 3.9 56.3 1.0
CAR C:XAM2000 3.9 58.4 1.0
CD1 C:ILE86 4.0 81.9 1.0
CB C:SER128 4.0 55.9 1.0
CG C:ASN54 4.2 52.3 1.0
ND2 C:ASN54 4.2 50.6 1.0
CG1 C:ILE175 4.3 48.0 1.0
OG C:SER128 4.3 56.5 1.0
CD1 C:ILE51 4.3 51.5 1.0
CG2 C:ILE51 4.5 52.7 1.0
O C:ILE51 4.8 52.1 1.0
OD1 C:ASN54 4.9 54.2 1.0
CB C:ILE175 5.0 47.9 1.0

Chlorine binding site 7 out of 8 in 4urm

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Chlorine binding site 7 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2000

b:72.1
occ:1.00
 CLW D:XAM2000 0.0 72.1 1.0
CAS D:XAM2000 1.7 63.7 1.0
CAR D:XAM2000 2.8 62.0 1.0
CAT D:XAM2000 2.8 58.1 1.0
NAO D:XAM2000 3.0 67.0 1.0
CLX D:XAM2000 3.4 57.0 1.0
CAP D:XAM2000 3.4 64.6 1.0
OD1 D:ASN54 3.5 60.7 1.0
CG D:ASN54 3.7 59.5 1.0
CD1 D:ILE86 3.8 80.4 1.0
CB D:ASN54 3.8 58.9 1.0
NAV D:XAM2000 3.9 59.5 1.0
CAU D:XAM2000 3.9 57.3 1.0
CG1 D:ILE86 4.1 79.9 1.0
CCF D:XAM2000 4.1 76.8 1.0
CG2 D:ILE86 4.1 80.0 1.0
CAM D:XAM2000 4.3 71.8 1.0
ND2 D:ASN54 4.6 59.2 1.0
OAQ D:XAM2000 4.6 65.9 1.0
CCE D:XAM2000 4.7 75.8 1.0
CB D:ILE86 4.8 79.8 1.0
CAN D:XAM2000 4.8 72.0 1.0
O D:ASN54 4.8 56.7 1.0
OCK D:XAM2000 4.8 76.5 1.0
CA D:ASN54 4.9 56.5 1.0

Chlorine binding site 8 out of 8 in 4urm

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Chlorine binding site 8 out of 8 in the Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Staph Gyraseb 24KDA in Complex with Kibdelomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl2000

b:57.0
occ:1.00
 CLX D:XAM2000 0.0 57.0 1.0
CAT D:XAM2000 1.7 58.1 1.0
CAS D:XAM2000 2.8 63.7 1.0
CAU D:XAM2000 2.8 57.3 1.0
CD1 D:ILE175 3.2 49.9 1.0
CLW D:XAM2000 3.4 72.1 1.0
CAY D:XAM2000 3.4 56.4 1.0
CB D:ASN54 3.8 58.9 1.0
NAV D:XAM2000 3.9 59.5 1.0
CAR D:XAM2000 3.9 62.0 1.0
CB D:SER128 4.0 59.8 1.0
CG D:ASN54 4.0 59.5 1.0
ND2 D:ASN54 4.1 59.2 1.0
CD1 D:ILE86 4.2 80.4 1.0
CD1 D:ILE51 4.2 49.9 1.0
CG1 D:ILE175 4.3 50.7 1.0
CG2 D:ILE51 4.4 50.9 1.0
OG D:SER128 4.4 60.1 1.0
OD1 D:ASN54 4.7 60.7 1.0
O D:ILE51 4.8 49.7 1.0
CB D:ILE175 5.0 51.5 1.0

Reference:

J.Lu, S.Patel, N.Sharma, S.M.Soisson, R.Kishii, M.Takei, Y.Fukuda, K.J.Lumb, S.B.Singh. Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed A Novel U-Shaped Binding Mode. Acs Chem.Biol. V. 9 2023 2014.
ISSN: ISSN 1554-8929
PubMed: 24992706
DOI: 10.1021/CB5001197
Page generated: Sat Dec 12 11:16:05 2020

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