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Zinc in PDB 4jiw: C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Enzymatic activity of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

All present enzymatic activity of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5:
3.2.1.17;

Protein crystallography data

The structure of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiw was solved by S.A.Buth, P.G.Leiman, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 3.40
Space group P 61 2 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.157, 184.157, 238.893, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 24.3

Other elements in 4jiw:

The structure of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 (pdb code 4jiw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4jiw

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Zinc binding site 1 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:0.6
occ:1.00
 NE2 D:HIS54 1.9 0.7 1.0
CE1 D:HIS54 2.0 0.3 1.0
NE2 D:HIS46 2.0 0.9 1.0
NE2 D:HIS14 2.0 0.3 1.0
SG D:CYS81 2.4 0.2 1.0
CE1 D:HIS46 2.4 0.5 1.0
CD2 D:HIS14 2.9 0.8 1.0
CE1 D:HIS14 3.1 0.6 1.0
O D:CYS81 3.2 0.2 1.0
CD2 D:HIS54 3.3 0.8 1.0
ND1 D:HIS54 3.3 0.6 1.0
CD2 D:HIS46 3.3 0.8 1.0
CB D:CYS81 3.4 0.5 1.0
ND1 D:HIS46 3.7 0.3 1.0
C D:CYS81 3.9 0.6 1.0
CG D:HIS54 4.0 0.7 1.0
NE D:ARG56 4.0 0.7 1.0
CG D:HIS14 4.1 0.7 1.0
ND1 D:HIS14 4.2 0.6 1.0
CG D:HIS46 4.2 0.8 1.0
CA D:CYS81 4.3 0.8 1.0
CD D:ARG56 4.3 0.2 1.0
CG D:ARG56 4.3 96.1 1.0
CB D:TYR17 4.6 0.3 1.0
CZ D:ARG56 4.6 0.9 1.0
CG D:TYR17 4.6 0.3 1.0
O D:GLY82 4.6 0.2 1.0
CD2 D:TYR17 4.8 0.9 1.0
NH2 D:ARG56 4.9 0.3 1.0
N D:GLY82 4.9 0.7 1.0

Zinc binding site 2 out of 4 in 4jiw

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Zinc binding site 2 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn101

b:0.3
occ:1.00
 NE2 H:HIS14 2.0 0.3 1.0
NE2 H:HIS46 2.0 0.4 1.0
NE2 H:HIS54 2.0 0.0 1.0
SG H:CYS81 2.3 0.1 1.0
CE1 H:HIS46 2.6 0.4 1.0
CE1 H:HIS54 2.8 0.2 1.0
CE1 H:HIS14 2.9 0.6 1.0
CD2 H:HIS14 3.1 0.3 1.0
CD2 H:HIS54 3.2 0.6 1.0
CD2 H:HIS46 3.3 0.5 1.0
O H:CYS81 3.4 0.3 1.0
CB H:CYS81 3.4 0.2 1.0
ND1 H:HIS46 3.9 0.2 1.0
NE H:ARG56 3.9 0.6 1.0
ND1 H:HIS54 4.0 0.4 1.0
C H:CYS81 4.0 0.7 1.0
ND1 H:HIS14 4.0 0.6 1.0
CG H:ARG56 4.2 0.9 1.0
CG H:HIS14 4.2 0.6 1.0
CG H:HIS54 4.2 0.5 1.0
CD H:ARG56 4.2 0.1 1.0
CG H:HIS46 4.2 0.9 1.0
CA H:CYS81 4.4 0.1 1.0
O H:GLY82 4.4 0.6 1.0
CZ H:ARG56 4.4 0.0 1.0
CB H:TYR17 4.6 0.1 1.0
CG H:TYR17 4.7 0.2 1.0
NH2 H:ARG56 4.8 0.2 1.0
N H:GLY82 4.8 0.1 1.0
CD2 H:TYR17 4.9 0.4 1.0

Zinc binding site 3 out of 4 in 4jiw

Go back to Zinc Binding Sites List in 4jiw
Zinc binding site 3 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.1
occ:1.00
 NE2 L:HIS46 2.0 87.4 1.0
NE2 L:HIS54 2.0 0.2 1.0
NE2 L:HIS14 2.0 0.5 1.0
SG L:CYS81 2.3 0.3 1.0
CE1 L:HIS46 2.7 92.7 1.0
CE1 L:HIS54 2.8 0.6 1.0
CD2 L:HIS14 3.0 0.3 1.0
CE1 L:HIS14 3.0 0.3 1.0
CD2 L:HIS54 3.1 0.8 1.0
CD2 L:HIS46 3.2 93.7 1.0
CB L:CYS81 3.3 0.4 1.0
O L:CYS81 3.4 0.8 1.0
ND1 L:HIS46 3.9 0.6 1.0
ND1 L:HIS54 4.0 0.2 1.0
C L:CYS81 4.0 0.6 1.0
NE L:ARG56 4.0 0.4 1.0
ND1 L:HIS14 4.1 0.4 1.0
CG L:HIS14 4.1 0.8 1.0
CG L:HIS54 4.2 0.8 1.0
CG L:HIS46 4.2 0.3 1.0
CA L:CYS81 4.3 0.2 1.0
CD L:ARG56 4.4 0.4 1.0
CG L:ARG56 4.5 0.0 1.0
CZ L:ARG56 4.5 0.1 1.0
CB L:TYR17 4.6 0.6 1.0
CG L:TYR17 4.7 0.7 1.0
NH2 L:ARG56 4.8 0.9 1.0
O L:GLY82 4.8 0.1 1.0
CD2 L:TYR17 4.9 0.5 1.0
O L:HIS54 5.0 0.2 1.0

Zinc binding site 4 out of 4 in 4jiw

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Zinc binding site 4 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:0.6
occ:1.00
 NE2 P:HIS14 2.0 0.3 1.0
NE2 P:HIS46 2.0 0.0 1.0
NE2 P:HIS54 2.0 0.5 1.0
SG P:CYS81 2.3 0.3 1.0
CE1 P:HIS54 2.9 0.4 1.0
CE1 P:HIS46 2.9 0.2 1.0
CD2 P:HIS14 2.9 0.6 1.0
CE1 P:HIS14 3.1 0.2 1.0
CD2 P:HIS54 3.1 0.7 1.0
CD2 P:HIS46 3.2 0.9 1.0
CB P:CYS81 3.5 1.0 1.0
O P:CYS81 3.8 0.1 1.0
NE P:ARG56 3.9 0.9 1.0
ND1 P:HIS54 4.0 0.9 1.0
ND1 P:HIS46 4.0 0.6 1.0
C P:CYS81 4.1 0.8 1.0
CG P:HIS14 4.1 0.8 1.0
ND1 P:HIS14 4.1 0.7 1.0
CG P:HIS54 4.2 0.6 1.0
CD P:ARG56 4.2 0.1 1.0
CG P:ARG56 4.2 0.2 1.0
CG P:HIS46 4.2 0.1 1.0
CB P:TYR17 4.4 0.1 1.0
CA P:CYS81 4.4 0.4 1.0
CZ P:ARG56 4.5 0.2 1.0
CG P:TYR17 4.6 0.5 1.0
O P:GLY82 4.6 0.2 1.0
N P:GLY82 4.7 0.6 1.0
NH2 P:ARG56 4.8 1.0 1.0
CD2 P:TYR17 4.9 0.5 1.0
O P:HIS54 5.0 0.5 1.0
CD1 P:TYR17 5.0 0.5 1.0

Reference:

M.M.Shneider, S.A.Buth, B.T.Ho, M.Basler, J.J.Mekalanos, P.G.Leiman. Paar-Repeat Proteins Sharpen and Diversify the Type VI Secretion System Spike. Nature V. 500 350 2013.
ISSN: ISSN 0028-0836
PubMed: 23925114
DOI: 10.1038/NATURE12453
Page generated: Wed Dec 16 05:26:27 2020

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