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Zinc in PDB 1ylk: Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate

Protein crystallography data

The structure of Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate, PDB code: 1ylk was solved by A.S.Covarrubias, A.M.Larsson, M.Hogbom, J.Lindberg, T.Bergfors, C.Bjorkelid, S.L.Mowbray, T.Unge, T.A.Jones, Structural Proteomics Ineurope (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.26 / 2.00
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.164, 154.074, 156.943, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate (pdb code 1ylk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate, PDB code: 1ylk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ylk

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Zinc binding site 1 out of 4 in the Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:32.0
occ:1.00
NE2 A:HIS88 2.0 25.6 1.0
O A:HOH506 2.2 36.5 1.0
SG A:CYS91 2.3 27.6 1.0
SG A:CYS35 2.3 25.4 1.0
CE1 A:HIS88 3.0 26.9 1.0
CD2 A:HIS88 3.0 25.0 1.0
CB A:CYS35 3.3 20.1 1.0
CB A:CYS91 3.4 27.1 1.0
CA A:CYS91 3.7 26.9 1.0
C B:SCN501 3.8 34.4 1.0
CB A:ASP37 3.8 21.1 1.0
OD2 A:ASP37 3.9 23.8 1.0
N A:GLY92 4.0 26.9 1.0
S B:SCN501 4.1 34.2 1.0
ND1 A:HIS88 4.1 26.3 1.0
N B:SCN501 4.1 34.7 1.0
CG A:HIS88 4.1 24.7 1.0
O A:HOH554 4.3 32.3 1.0
CG A:ASP37 4.3 21.1 1.0
C A:CYS91 4.3 26.6 1.0
N A:GLY60 4.4 21.3 1.0
CA A:GLY60 4.4 21.6 1.0
N A:ASP37 4.7 20.1 1.0
CA A:ASP37 4.8 20.7 1.0
CA A:CYS35 4.8 20.5 1.0
N A:CYS91 4.9 27.2 1.0

Zinc binding site 2 out of 4 in 1ylk

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Zinc binding site 2 out of 4 in the Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:33.3
occ:1.00
NE2 B:HIS88 2.0 24.1 1.0
O B:HOH502 2.2 33.5 1.0
SG B:CYS91 2.3 29.7 1.0
SG B:CYS35 2.4 25.0 1.0
CE1 B:HIS88 3.0 25.1 1.0
CD2 B:HIS88 3.0 24.4 1.0
CB B:CYS35 3.2 21.1 1.0
CB B:CYS91 3.4 28.3 1.0
CA B:CYS91 3.7 28.0 1.0
CB B:ASP37 3.8 20.5 1.0
C A:SCN502 3.9 39.4 1.0
OD2 B:ASP37 4.0 24.2 1.0
N B:GLY92 4.0 27.4 1.0
S A:SCN502 4.0 39.7 1.0
ND1 B:HIS88 4.1 24.3 1.0
CG B:HIS88 4.1 24.3 1.0
N A:SCN502 4.2 39.6 1.0
CA B:GLY60 4.3 21.1 1.0
CG B:ASP37 4.4 21.7 1.0
O B:HOH537 4.4 33.2 1.0
C B:CYS91 4.4 27.7 1.0
N B:GLY60 4.4 19.5 1.0
CA B:CYS35 4.7 21.5 1.0
N B:ASP37 4.7 19.6 1.0
CA B:ASP37 4.8 20.3 1.0
N B:CYS91 4.9 27.7 1.0

Zinc binding site 3 out of 4 in 1ylk

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Zinc binding site 3 out of 4 in the Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:31.2
occ:1.00
NE2 C:HIS88 2.0 24.2 1.0
SG C:CYS35 2.3 23.5 1.0
SG C:CYS91 2.3 29.9 1.0
CE1 C:HIS88 3.0 24.1 1.0
CD2 C:HIS88 3.0 24.4 1.0
CB C:CYS35 3.2 19.3 1.0
CB C:CYS91 3.3 29.1 1.0
CA C:CYS91 3.7 29.0 1.0
C C:SCN503 3.8 35.6 1.0
CB C:ASP37 3.8 20.4 1.0
OD2 C:ASP37 4.0 25.0 1.0
S C:SCN503 4.0 36.1 1.0
N C:SCN503 4.1 35.9 1.0
ND1 C:HIS88 4.1 25.0 1.0
N C:GLY92 4.1 29.1 1.0
CG C:HIS88 4.1 24.6 1.0
O C:HOH505 4.3 38.7 1.0
CA C:GLY60 4.4 22.4 1.0
CG C:ASP37 4.4 21.6 1.0
N C:GLY60 4.4 20.6 1.0
C C:CYS91 4.4 29.2 1.0
CA C:CYS35 4.7 19.9 1.0
N C:ASP37 4.7 19.8 1.0
CA C:ASP37 4.7 20.0 1.0
N C:CYS91 4.9 28.5 1.0

Zinc binding site 4 out of 4 in 1ylk

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Zinc binding site 4 out of 4 in the Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of RV1284 From Mycobacterium Tuberculosis in Complex with Thiocyanate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn404

b:31.3
occ:1.00
NE2 D:HIS88 2.1 21.0 1.0
O D:HOH405 2.3 27.6 1.0
SG D:CYS35 2.3 23.6 1.0
SG D:CYS91 2.3 27.8 1.0
CE1 D:HIS88 3.0 23.1 1.0
CD2 D:HIS88 3.1 22.0 1.0
CB D:CYS35 3.3 20.0 1.0
CB D:CYS91 3.4 27.4 1.0
CA D:CYS91 3.8 27.4 1.0
C C:SCN504 3.9 36.8 1.0
CB D:ASP37 3.9 20.5 1.0
OD2 D:ASP37 4.0 24.2 1.0
S C:SCN504 4.0 37.1 1.0
N D:GLY92 4.1 28.4 1.0
ND1 D:HIS88 4.1 22.9 1.0
O D:HOH464 4.2 31.3 1.0
CG D:HIS88 4.2 23.8 1.0
N C:SCN504 4.2 37.1 1.0
CA D:GLY60 4.3 21.7 1.0
CG D:ASP37 4.4 20.3 1.0
N D:GLY60 4.4 20.8 1.0
C D:CYS91 4.4 27.7 1.0
CA D:CYS35 4.7 20.5 1.0
N D:ASP37 4.8 19.9 1.0
CA D:ASP37 4.8 19.9 1.0
N D:CYS91 5.0 27.1 1.0

Reference:

A.Suarez Covarrubias, A.M.Larsson, M.Hogbom, J.Lindberg, T.Bergfors, C.Bjorkelid, S.L.Mowbray, T.Unge, T.A.Jones. Structure and Function of Carbonic Anhydrases From Mycobacterium Tuberculosis. J.Biol.Chem. V. 280 18782 2005.
ISSN: ISSN 0021-9258
PubMed: 15753099
DOI: 10.1074/JBC.M414348200
Page generated: Thu Oct 29 07:42:30 2020
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