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Zinc in PDB 4yf4: Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH

Enzymatic activity of Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH

All present enzymatic activity of Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH:
4.2.1.1;

Protein crystallography data

The structure of Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH, PDB code: 4yf4 was solved by A.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.88 / 1.80
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.142, 154.345, 157.732, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 4yf4:

The structure of Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH (pdb code 4yf4). 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 in the Presence of Polycarpine at Mildly Acidic pH, PDB code: 4yf4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4yf4

Go back to Zinc Binding Sites List in 4yf4
Zinc binding site 1 out of 4 in the Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH


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 in the Presence of Polycarpine at Mildly Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:22.0
occ:0.59
NE2 A:HIS88 2.3 33.0 1.0
O A:HOH328 2.4 7.6 0.3
SG A:CYS91 2.5 28.2 1.0
SG A:CYS35 2.6 29.6 0.7
O A:HOH329 2.8 52.7 1.0
CD2 A:HIS88 3.2 28.7 1.0
CB A:CYS91 3.3 29.2 1.0
CE1 A:HIS88 3.3 34.4 1.0
CA A:CYS91 3.7 25.6 1.0
CB A:CYS35 3.7 20.3 0.3
CB A:CYS35 3.7 20.1 0.7
O A:HOH331 3.7 49.0 1.0
N A:GLY92 3.9 34.2 1.0
OD2 A:ASP37 3.9 22.7 1.0
CB A:ASP37 3.9 15.0 1.0
C A:CYS91 4.3 28.5 1.0
ND1 A:HIS88 4.4 34.5 1.0
CG A:HIS88 4.4 27.2 1.0
CA A:GLY60 4.4 17.1 1.0
N A:GLY60 4.4 18.7 1.0
CG A:ASP37 4.4 14.3 1.0
SG A:CYS35 4.5 17.1 0.3
O A:HOH364 4.6 32.0 1.0
N A:ASP37 4.8 15.9 1.0
CA A:ASP37 4.8 15.2 1.0
SG A:CYS61 4.9 24.3 0.3
N A:CYS91 5.0 26.2 1.0
CA A:GLY92 5.0 29.6 1.0

Zinc binding site 2 out of 4 in 4yf4

Go back to Zinc Binding Sites List in 4yf4
Zinc binding site 2 out of 4 in the Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH


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 in the Presence of Polycarpine at Mildly Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:24.4
occ:0.55
NE2 B:HIS88 2.3 38.7 1.0
O B:HOH329 2.4 8.1 0.4
SG B:CYS35 2.5 74.4 0.6
SG B:CYS91 2.6 35.4 1.0
O B:HOH362 2.6 38.6 1.0
CD2 B:HIS88 3.0 35.1 1.0
CE1 B:HIS88 3.4 37.3 1.0
CB B:CYS91 3.6 38.7 1.0
CB B:ASP37 3.8 16.6 1.0
CA B:CYS91 3.8 39.1 1.0
CB B:CYS35 3.8 20.5 0.6
OD2 B:ASP37 3.8 29.0 1.0
CB B:CYS35 3.9 21.2 0.4
N B:GLY92 3.9 43.2 1.0
CG B:ASP37 4.2 25.8 1.0
CG B:HIS88 4.3 33.1 1.0
C B:CYS91 4.4 42.5 1.0
ND1 B:HIS88 4.4 39.0 1.0
CA B:GLY60 4.4 17.9 1.0
N B:GLY60 4.4 15.2 1.0
O B:HOH349 4.5 35.9 1.0
SG B:CYS35 4.6 14.1 0.4
CA B:ASP37 4.8 14.9 1.0
N B:ASP37 4.8 14.2 1.0
SG B:CYS61 4.9 21.1 0.4

Zinc binding site 3 out of 4 in 4yf4

Go back to Zinc Binding Sites List in 4yf4
Zinc binding site 3 out of 4 in the Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH


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 in the Presence of Polycarpine at Mildly Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:25.8
occ:0.60
O C:HOH323 2.2 6.8 0.4
NE2 C:HIS88 2.3 26.2 1.0
SG C:CYS35 2.5 39.7 0.6
SG C:CYS91 2.6 36.3 1.0
CE1 C:HIS88 3.0 29.2 1.0
O C:HOH374 3.4 41.5 1.0
CD2 C:HIS88 3.4 20.6 1.0
CB C:CYS91 3.5 40.1 1.0
CA C:CYS91 3.7 38.3 1.0
CB C:CYS35 3.8 32.8 0.6
CB C:ASP37 3.8 23.1 1.0
N C:GLY92 3.9 40.8 1.0
CB C:CYS35 3.9 33.9 0.4
OD2 C:ASP37 4.0 31.3 1.0
ND1 C:HIS88 4.2 28.7 1.0
C C:CYS91 4.3 39.6 1.0
CG C:ASP37 4.4 29.5 1.0
CG C:HIS88 4.4 23.1 1.0
CA C:GLY60 4.4 22.2 1.0
N C:GLY60 4.4 20.7 1.0
O C:HOH360 4.7 32.0 1.0
SG C:CYS35 4.7 19.3 0.4
CA C:ASP37 4.7 15.2 1.0
N C:ASP37 4.7 13.6 1.0
CG C:MET93 4.9 33.2 1.0
SG C:CYS61 4.9 21.4 0.4
CA C:GLY92 5.0 39.5 1.0
N C:MET93 5.0 32.9 1.0
N C:CYS91 5.0 34.8 1.0

Zinc binding site 4 out of 4 in 4yf4

Go back to Zinc Binding Sites List in 4yf4
Zinc binding site 4 out of 4 in the Crystal Structure of RV1284 in the Presence of Polycarpine at Mildly Acidic pH


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 in the Presence of Polycarpine at Mildly Acidic pH within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:26.6
occ:0.58
NE2 D:HIS88 2.3 28.5 1.0
O D:HOH331 2.4 5.6 0.5
O D:HOH344 2.6 41.1 1.0
SG D:CYS91 2.6 36.3 1.0
SG D:CYS35 2.7 43.1 0.5
CE1 D:HIS88 3.2 31.2 1.0
CD2 D:HIS88 3.3 20.9 1.0
O D:HOH383 3.4 47.5 1.0
CB D:CYS91 3.6 37.8 1.0
N D:GLY92 3.8 40.8 1.0
CA D:CYS91 3.9 33.7 1.0
CB D:ASP37 3.9 19.1 1.0
CB D:CYS35 3.9 31.9 0.5
CB D:CYS35 4.0 28.7 0.5
OD2 D:ASP37 4.1 29.1 1.0
O D:HOH373 4.1 36.4 1.0
N D:GLY60 4.2 14.9 1.0
CA D:GLY60 4.3 21.8 1.0
ND1 D:HIS88 4.3 36.4 1.0
CG D:HIS88 4.4 28.8 1.0
C D:CYS91 4.4 36.0 1.0
CG D:ASP37 4.5 20.1 1.0
SG D:CYS35 4.6 23.0 0.5
N D:ASP37 4.7 12.2 1.0
SG D:CYS61 4.7 24.4 0.5
CA D:ASP37 4.8 18.2 1.0
CA D:GLY92 4.9 40.0 1.0

Reference:

L.Nienaber, E.Cave-Freeman, M.Cross, L.Mason, U.M.Bailey, P.Amani, R.Davis, P.Taylor, A.Hofmann. Chemical Probing Suggests Redox-Regulation of the Carbonic Anhydrase Activity of Mycobacterial RV1284. Febs J. 2015.
ISSN: ISSN 1742-464X
PubMed: 25929542
DOI: 10.1111/FEBS.13313
Page generated: Wed Dec 16 05:56:35 2020

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