Zinc in PDB 5a0v: Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family

Protein crystallography data

The structure of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family, PDB code: 5a0v was solved by X.Y.Pei, P.Bralley, G.H.Jones, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.719 / 2.80
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 184.130, 184.130, 112.680, 90.00, 90.00, 90.00
R / Rfree (%) 15.42 / 20.84

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family (pdb code 5a0v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family, PDB code: 5a0v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5a0v

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Zinc binding site 1 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1456

b:0.9
occ:1.00
OD2 A:ASP173 2.4 33.4 0.5
OD2 A:ASP88 2.4 41.1 0.0
NE2 A:HIS399 2.5 42.1 0.5
OP2 E:G1 2.7 79.8 0.0
NE2 A:HIS89 2.9 38.8 0.7
CD2 A:HIS89 2.9 42.6 1.0
CG A:ASP88 3.3 39.8 0.9
OD1 A:ASP88 3.4 39.8 0.6
CE1 A:HIS399 3.4 49.1 1.0
CD2 A:HIS399 3.4 35.5 0.8
CG A:ASP173 3.5 37.8 1.0
ZN A:ZN1457 3.6 85.5 1.0
P E:G1 3.6 84.9 1.0
OP1 E:G1 3.6 90.0 1.0
ND2 A:ASN33 3.9 39.3 1.0
OD1 A:ASP173 4.0 36.7 0.4
CE1 A:HIS89 4.1 39.0 0.6
O2' E:C0 4.2 44.9 0.3
CG A:HIS89 4.2 45.1 1.0
NE2 A:HIS84 4.4 31.3 0.4
ND1 A:HIS399 4.5 41.8 0.7
CG A:HIS399 4.6 36.9 0.8
CB A:ASP88 4.7 43.1 0.5
NE2 A:HIS377 4.7 31.1 0.7
CE1 A:HIS84 4.7 32.4 1.0
O3' E:C0 4.7 66.7 0.4
O5' E:G1 4.7 59.8 0.2
CB A:ASP173 4.8 33.4 1.0
ND1 A:HIS89 4.8 44.7 0.4
O A:ASP88 4.8 43.2 0.8
CG A:ASN33 4.9 40.0 0.6

Zinc binding site 2 out of 4 in 5a0v

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Zinc binding site 2 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1457

b:85.5
occ:1.00
OP1 E:G1 2.5 90.0 1.0
NE2 A:HIS84 2.6 31.3 0.4
ND1 A:HIS86 2.7 31.9 0.6
NE2 A:HIS151 2.8 29.6 0.8
OD2 A:ASP173 3.0 33.4 0.5
CD2 A:HIS84 3.3 30.6 1.0
CE1 A:HIS84 3.5 32.4 1.0
CD2 A:HIS151 3.5 29.3 1.0
CE1 A:HIS86 3.5 32.5 1.0
CG A:HIS86 3.6 36.2 0.9
ZN A:ZN1456 3.6 0.9 1.0
P E:G1 3.8 84.9 1.0
CG A:ASP173 3.8 37.8 1.0
CB A:HIS86 3.8 42.6 1.0
CB A:ASP173 3.8 33.4 1.0
CE1 A:HIS151 3.8 43.4 1.0
OP2 E:G1 4.3 79.8 0.0
CG A:HIS84 4.4 34.5 0.6
ND1 A:HIS84 4.4 39.4 1.0
C5' E:G1 4.4 61.5 1.0
OG A:SER152 4.5 34.1 0.7
O5' E:G1 4.6 59.8 0.2
NE2 A:HIS377 4.6 31.1 0.7
NE2 A:HIS86 4.6 31.8 0.6
CD2 A:HIS86 4.7 34.4 0.3
O3' E:C0 4.7 66.7 0.4
CG A:HIS151 4.8 29.0 1.0
CD2 A:HIS89 4.8 42.6 1.0
OD1 A:ASP88 4.8 39.8 0.6
ND1 A:HIS151 4.9 35.3 0.3
NE2 A:HIS89 4.9 38.8 0.7
CE1 A:HIS377 4.9 30.7 0.8
OD1 A:ASP173 5.0 36.7 0.4

Zinc binding site 3 out of 4 in 5a0v

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Zinc binding site 3 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1453

b:83.5
occ:1.00
OP2 F:G1 2.2 0.4 0.5
ND1 B:HIS86 2.4 43.9 1.0
NE2 B:HIS84 2.4 46.8 0.3
OD2 B:ASP173 2.5 43.0 0.2
NE2 B:HIS151 2.5 49.8 1.0
P F:G1 2.9 79.7 0.5
OP1 F:G1 3.0 72.7 0.5
CD2 B:HIS84 3.1 40.3 1.0
CG B:ASP173 3.2 36.8 1.0
CE1 B:HIS86 3.3 40.3 0.7
CD2 B:HIS151 3.3 46.5 0.9
ZN B:ZN1454 3.4 0.1 1.0
CB B:ASP173 3.4 42.0 0.6
CG B:HIS86 3.5 41.4 0.2
CE1 B:HIS84 3.5 39.4 1.0
CE1 B:HIS151 3.6 42.5 1.0
O5' F:G1 3.8 54.1 0.5
CB B:HIS86 3.8 43.3 1.0
O3' F:C0 4.1 62.6 1.0
CG B:HIS84 4.2 47.6 1.0
OD1 B:ASP173 4.3 38.8 0.7
ND1 B:HIS84 4.4 47.2 0.6
NE2 B:HIS86 4.4 41.4 0.8
CD2 B:HIS89 4.4 51.8 1.0
CG B:HIS151 4.5 39.9 1.0
CD2 B:HIS86 4.6 45.3 1.0
NE2 B:HIS89 4.6 43.9 0.6
CE1 B:HIS377 4.6 35.3 0.8
ND1 B:HIS151 4.6 43.0 0.6
NE2 B:HIS377 4.7 35.4 0.7
OD1 B:ASP88 4.8 58.0 0.8
C5' F:G1 4.9 53.1 0.5
OG B:SER152 5.0 38.4 0.7
CA B:ASP173 5.0 42.2 1.0

Zinc binding site 4 out of 4 in 5a0v

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Zinc binding site 4 out of 4 in the Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalysis and 5' End Sensing By Ribonuclease Rnase J of the Metallo-Beta-Lactamase Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1454

b:0.1
occ:1.00
OD2 B:ASP88 2.3 46.8 0.2
OP2 F:G1 2.4 0.4 0.5
OD2 B:ASP173 2.4 43.0 0.2
NE2 B:HIS399 2.6 44.1 0.3
NE2 B:HIS89 2.6 43.9 0.6
CD2 B:HIS89 3.0 51.8 1.0
CG B:ASP173 3.2 36.8 1.0
CG B:ASP88 3.3 47.0 0.6
ZN B:ZN1453 3.4 83.5 1.0
OD1 B:ASP173 3.4 38.8 0.7
CE1 B:HIS399 3.5 40.3 1.0
CD2 B:HIS399 3.5 45.4 1.0
OD1 B:ASP88 3.6 58.0 0.8
P F:G1 3.8 79.7 0.5
ND2 B:ASN33 3.8 43.2 1.0
CE1 B:HIS89 3.9 45.4 0.6
O3' F:C0 4.0 62.6 1.0
NE2 B:HIS84 4.1 46.8 0.3
CG B:HIS89 4.3 51.7 1.0
O2' B:C5P1458 4.4 76.1 0.5
CE1 B:HIS377 4.4 35.3 0.8
ND1 B:HIS399 4.5 44.6 0.5
CE1 B:HIS84 4.5 39.4 1.0
CB B:ASP173 4.5 42.0 0.6
CG B:HIS399 4.6 44.6 0.7
CB B:ASP88 4.6 46.6 0.7
O5' F:G1 4.6 54.1 0.5
ND1 B:HIS89 4.7 51.4 0.7
OP1 F:G1 4.8 72.7 0.5
CG B:ASN33 4.9 43.4 0.8
NE2 B:HIS377 4.9 35.4 0.7

Reference:

X.Y.Pei, P.Bralley, G.H.Jones, B.F.Luisi. Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J Nucleic Acids Res. V. 43 8066 2015.
ISSN: ISSN 0305-1048
PubMed: 26253740
DOI: 10.1093/NAR/GKV732
Page generated: Wed Dec 16 06:01:14 2020

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