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Zinc in PDB 5e0y: Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B

Enzymatic activity of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B

All present enzymatic activity of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B, PDB code: 5e0y was solved by D.M.Prigozhin, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.61 / 2.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 41.658, 41.658, 122.517, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B (pdb code 5e0y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B, PDB code: 5e0y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5e0y

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Zinc binding site 1 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


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 Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:27.4
occ:0.50
 ND1 A:HIS600 2.1 15.1 1.0
OXT A:GLN626 2.2 13.0 1.0
O A:GLN626 2.6 16.6 1.0
C A:GLN626 2.8 21.5 1.0
CE1 A:HIS600 3.0 16.9 1.0
CG A:HIS600 3.2 9.8 1.0
CB A:HIS600 3.6 18.1 1.0
NE2 A:HIS600 4.1 15.2 1.0
CA A:HIS600 4.2 13.1 1.0
CA A:GLN626 4.2 16.9 1.0
CD2 A:HIS600 4.3 14.6 1.0
O A:HOH819 4.6 16.3 1.0
CB A:GLN626 4.8 20.6 1.0
CG A:GLN626 4.8 22.2 1.0
O A:GLY625 5.0 17.4 1.0
N A:GLN626 5.0 12.2 1.0

Zinc binding site 2 out of 9 in 5e0y

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Zinc binding site 2 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


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 Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:39.9
occ:0.50
 OE2 A:GLU575 2.0 32.8 1.0
O A:HOH837 2.1 40.6 1.0
CD A:GLU575 2.7 43.1 1.0
OE1 A:GLU575 2.8 41.5 1.0
O A:HOH841 2.8 23.8 1.0
O A:HOH843 3.6 29.1 1.0
CG A:GLU575 4.1 42.6 1.0
NH2 A:ARG579 4.2 28.0 1.0
CZ2 A:TRP571 4.5 45.4 1.0
NE A:ARG579 4.5 25.4 1.0
CZ A:ARG579 4.8 30.7 1.0

Zinc binding site 3 out of 9 in 5e0y

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Zinc binding site 3 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


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 Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:46.9
occ:0.61
 OD1 A:ASP573 2.2 23.0 1.0
CG A:ASP573 3.2 26.5 1.0
OD2 A:ASP573 3.5 24.6 1.0
CG1 A:VAL572 4.2 22.6 0.4
CB A:ASP573 4.6 18.2 1.0
CG2 A:VAL572 4.7 16.7 0.6
O A:VAL572 4.7 35.4 0.6
O A:VAL572 5.0 33.2 0.4

Zinc binding site 4 out of 9 in 5e0y

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Zinc binding site 4 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


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 Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:35.1
occ:0.44
 OD1 A:ASP594 2.1 31.4 1.0
OD2 A:ASP594 2.2 50.4 1.0
CG A:ASP594 2.4 37.7 1.0
O A:HOH844 2.6 29.2 1.0
CB A:ASP594 3.9 28.8 1.0
CA A:ASP594 4.7 13.7 1.0
N A:GLY596 4.8 16.8 1.0
NE2 A:GLN626 4.8 30.6 1.0
C A:ASP594 4.9 16.7 1.0

Zinc binding site 5 out of 9 in 5e0y

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Zinc binding site 5 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn705

b:14.8
occ:0.49
 CD2 A:HIS600 3.5 14.6 1.0
NE2 A:HIS600 3.8 15.2 1.0
ND2 A:ASN601 3.8 43.6 1.0
CB A:ASN601 3.9 25.7 1.0
CE1 A:PHE570 4.1 37.0 1.0
CG A:ASN601 4.4 38.8 1.0
O A:HIS600 4.4 12.2 1.0
CD1 A:PHE570 4.6 34.3 1.0
CG A:HIS600 4.8 9.8 1.0

Zinc binding site 6 out of 9 in 5e0y

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Zinc binding site 6 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:

Zinc binding site 7 out of 9 in 5e0y

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Zinc binding site 7 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn706

b:37.8
occ:0.68
 O A:HOH820 2.9 24.6 1.0
N A:GLY597 3.6 13.6 1.0
CA A:GLY597 3.9 14.1 1.0
C A:GLY596 4.7 18.0 1.0
CA A:GLY596 5.0 25.1 1.0

Zinc binding site 8 out of 9 in 5e0y

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Zinc binding site 8 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn707

b:60.1
occ:0.53
 O A:HOH810 2.1 43.1 1.0
NZ A:LYS589 2.5 44.4 1.0
OD1 A:ASP592 3.0 25.2 1.0
OD2 A:ASP592 3.1 39.1 1.0
CE A:LYS589 3.1 41.8 1.0
ZN A:ZN708 3.1 53.8 0.5
CG A:ASP592 3.4 25.9 1.0
O A:HOH804 4.5 14.7 1.0
CD A:LYS589 4.5 28.2 1.0
CB A:ASP592 4.9 26.4 1.0

Zinc binding site 9 out of 9 in 5e0y

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Zinc binding site 9 out of 9 in the Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Pasta Domain 4 of Mycobacterium Tuberculosis Protein Kinase B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn708

b:53.8
occ:0.49
 O A:HOH810 2.1 43.1 1.0
ZN A:ZN707 3.1 60.1 0.5
OD2 A:ASP592 3.3 39.1 1.0
OD1 A:ASN601 3.5 53.1 1.0
O A:GLY625 3.6 17.4 1.0
OD1 A:ASP592 3.7 25.2 1.0
CG A:ASP592 3.8 25.9 1.0
CG A:ASN601 4.1 38.8 1.0
O A:GLN626 4.2 16.6 1.0
CA A:ASN601 4.3 17.2 1.0
CB A:ASN601 4.4 25.7 1.0
CB A:PHE624 4.5 14.6 1.0
C A:GLY625 4.5 13.7 1.0
N A:ASN601 4.6 13.3 1.0
CA A:GLN626 4.6 16.9 1.0
C A:GLN626 4.7 21.5 1.0

Reference:

D.M.Prigozhin, K.G.Papavinasasundaram, C.E.Baer, K.C.Murphy, A.Moskaleva, T.Y.Chen, T.Alber, C.M.Sassetti. Structural and Genetic Analyses of the Mycobacterium Tuberculosis Protein Kinase B Sensor Domain Identify A Potential Ligand-Binding Site. J.Biol.Chem. V. 291 22961 2016.
ISSN: ESSN 1083-351X
PubMed: 27601474
DOI: 10.1074/JBC.M116.731760
Page generated: Sun Oct 27 14:56:48 2024

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