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Chlorine in PDB 2xew: Crystal Structure of K11-Linked Diubiquitin

Protein crystallography data

The structure of Crystal Structure of K11-Linked Diubiquitin, PDB code: 2xew was solved by A.Bremm, S.M.V.Freund, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.92 / 2.20
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.230, 79.960, 221.230, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of K11-Linked Diubiquitin (pdb code 2xew). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of K11-Linked Diubiquitin, PDB code: 2xew:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 2xew

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Chlorine binding site 1 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1080

b:45.4
occ:1.00
 O D:HOH2051 3.1 24.3 1.0
N A:GLU16 3.2 21.8 1.0
CE A:LYS33 3.4 31.6 1.0
CA A:LEU15 3.7 14.2 1.0
O A:GLU16 3.8 19.4 1.0
CD2 A:LEU15 3.9 21.6 1.0
CB A:GLU16 4.0 27.9 0.5
C A:LEU15 4.0 17.8 1.0
CA A:GLU16 4.1 25.7 0.5
CA A:GLU16 4.1 25.3 0.5
CB A:LEU15 4.1 14.3 1.0
NZ A:LYS29 4.3 30.4 1.0
CB A:GLU16 4.3 28.9 0.5
NZ A:LYS33 4.3 33.2 1.0
C A:GLU16 4.4 22.4 1.0
CD A:LYS29 4.4 22.7 1.0
O D:HOH2053 4.4 24.5 1.0
O A:THR14 4.5 25.7 1.0
CD A:LYS33 4.6 25.7 1.0
CG A:LEU15 4.7 19.2 1.0
CG A:LYS29 4.7 14.7 1.0
O A:HOH2041 4.7 37.7 1.0
CB A:LYS29 4.8 6.2 1.0
CB D:ASP52 4.8 17.7 1.0
O A:HOH2015 4.9 48.4 1.0
N A:LEU15 4.9 19.3 1.0
CE A:LYS29 5.0 25.3 1.0

Chlorine binding site 2 out of 7 in 2xew

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Chlorine binding site 2 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1076

b:42.9
occ:1.00
 N C:GLN2 3.2 20.4 1.0
CB C:LYS63 3.6 25.9 1.0
CB C:GLN2 3.7 26.2 1.0
CD C:LYS63 3.9 41.9 1.0
CA C:GLN2 4.0 23.4 1.0
CA C:MET1 4.0 27.3 1.0
OE2 C:GLU64 4.0 45.4 1.0
C C:MET1 4.1 29.4 1.0
CG C:LYS63 4.2 29.1 1.0
CB C:MET1 4.2 25.1 1.0
O C:GLN2 4.3 21.4 1.0
CD C:GLU64 4.5 43.6 1.0
OE1 C:GLU64 4.6 44.5 1.0
CA C:LYS63 4.6 20.0 1.0
C C:GLN2 4.7 24.6 1.0
N C:GLU64 4.7 20.3 1.0
C C:LYS63 5.0 22.4 1.0

Chlorine binding site 3 out of 7 in 2xew

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Chlorine binding site 3 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1078

b:38.2
occ:1.00
 N D:GLU16 3.1 15.7 1.0
O C:HOH2045 3.3 30.0 1.0
CE D:LYS33 3.7 29.3 1.0
CA D:LEU15 3.7 12.4 1.0
NZ D:LYS29 3.8 23.8 1.0
O D:GLU16 3.8 22.6 1.0
NZ D:LYS33 3.8 31.0 1.0
C D:LEU15 3.9 15.8 1.0
CD2 D:LEU15 4.0 19.8 1.0
CA D:GLU16 4.0 22.2 1.0
CB D:GLU16 4.1 25.9 1.0
CB D:LEU15 4.2 11.4 1.0
O C:HOH2046 4.2 36.3 1.0
O D:HOH2029 4.3 31.5 1.0
C D:GLU16 4.4 25.7 1.0
CD D:LYS29 4.4 23.7 1.0
O D:THR14 4.4 25.4 1.0
CB C:ASP52 4.6 22.0 1.0
CG D:LYS29 4.7 19.6 1.0
CD D:LYS33 4.7 30.5 1.0
CE D:LYS29 4.7 22.7 1.0
CG D:LEU15 4.7 17.2 1.0
N C:GLY53 4.9 24.7 1.0
N D:LEU15 4.9 16.0 1.0
CB D:LYS29 4.9 17.6 1.0

Chlorine binding site 4 out of 7 in 2xew

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Chlorine binding site 4 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1078

b:51.5
occ:1.00
 O I:HOH2050 2.9 11.7 1.0
NE I:ARG42 3.4 43.5 1.0
CG I:ARG42 3.8 32.6 1.0
CB I:ARG42 3.9 25.3 1.0
CD I:ARG72 3.9 27.1 0.6
O I:HOH2027 4.0 48.7 1.0
NH2 I:ARG72 4.0 30.6 0.6
CA I:ARG42 4.1 20.5 1.0
OE1 I:GLN49 4.1 52.0 1.0
NE I:ARG72 4.1 30.4 0.6
CD I:ARG42 4.2 37.7 1.0
CZ I:ARG72 4.2 28.2 0.6
NH1 I:ARG42 4.3 45.3 1.0
CD I:ARG72 4.3 28.7 0.5
CZ I:ARG42 4.3 46.7 1.0
NE I:ARG72 4.4 29.6 0.5
CB I:GLN49 4.4 30.9 1.0
NZ I:LYS27 4.5 16.4 1.0
O I:LEU50 4.6 22.0 1.0
CD I:GLN49 4.6 50.2 1.0
O I:GLN41 4.7 18.1 1.0
CG I:GLN49 4.8 40.1 1.0
O I:HOH2052 4.8 26.3 1.0
N I:LEU43 4.9 22.1 1.0
NH1 I:ARG72 5.0 28.3 0.6
C I:ARG42 5.0 22.2 1.0

Chlorine binding site 5 out of 7 in 2xew

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Chlorine binding site 5 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1078

b:38.2
occ:1.00
 OD1 L:ASN25 3.0 40.2 1.0
O L:HOH2017 3.2 35.6 1.0
CB L:ALA28 3.7 15.0 1.0
CA L:ASN25 3.7 14.8 1.0
N L:ASN25 3.8 15.6 1.0
CG L:GLU24 3.9 17.7 1.0
O L:GLU24 3.9 15.4 1.0
C L:GLU24 3.9 13.9 1.0
CG L:ASN25 4.1 35.3 1.0
CB L:ASN25 4.5 25.8 1.0
O L:HOH2018 4.5 28.6 1.0
CB L:GLU24 4.5 9.3 1.0
C L:ASN25 4.8 13.8 1.0
O L:HOH2015 4.8 28.4 1.0
OE2 L:GLU24 4.9 20.5 1.0
CA L:GLU24 4.9 14.3 1.0
CD L:GLU24 4.9 23.1 1.0
O L:ASN25 5.0 21.3 1.0

Chlorine binding site 6 out of 7 in 2xew

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Chlorine binding site 6 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1079

b:40.5
occ:1.00
 O K:HOH2059 3.2 40.0 1.0
N L:THR14 3.4 20.8 1.0
O L:THR14 3.7 24.0 1.0
NZ L:LYS33 3.8 42.3 1.0
CA L:ILE13 3.9 24.6 1.0
CG2 L:ILE13 4.0 23.5 1.0
CD L:LYS33 4.0 32.6 1.0
C L:ILE13 4.2 25.6 1.0
CA L:THR14 4.3 18.5 1.0
CB L:THR14 4.4 22.6 1.0
C L:THR14 4.4 20.0 1.0
CE L:LYS33 4.5 38.2 1.0
O L:THR12 4.5 35.5 1.0
CB L:ILE13 4.6 22.8 1.0
OG1 L:THR14 4.6 25.2 1.0
O L:HOH2029 4.6 28.7 1.0
OE2 L:GLU34 4.7 23.1 1.0

Chlorine binding site 7 out of 7 in 2xew

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Chlorine binding site 7 out of 7 in the Crystal Structure of K11-Linked Diubiquitin


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 K11-Linked Diubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1080

b:42.9
occ:1.00
 O L:HOH2043 2.9 33.8 1.0
O L:HOH2042 3.2 37.5 1.0
CB L:ASP52 4.3 20.4 1.0
N L:GLY53 4.5 21.3 1.0
CA L:GLY53 4.8 23.1 1.0

Reference:

A.Bremm, S.M.V.Freund, D.Komander. LYS11-Linked Ubiquitin Chains Adopt Compact Conformations and Are Preferentially Hydrolyzed By the Deubiquitinase Cezanne Nat.Struct.Mol.Biol. V. 17 939 2010.
ISSN: ISSN 1545-9993
PubMed: 20622874
DOI: 10.1038/NSMB.1873
Page generated: Sat Jul 20 13:48:38 2024

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