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Zinc in PDB 4n0o: Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna

Enzymatic activity of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna

All present enzymatic activity of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna:
2.7.7.48; 3.4.19.12; 3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna, PDB code: 4n0o was solved by Z.Deng, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.628, 88.838, 128.781, 81.74, 90.01, 71.42
R / Rfree (%) 24.6 / 26.4

Other elements in 4n0o:

The structure of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna (pdb code 4n0o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna, PDB code: 4n0o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 4n0o

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Zinc binding site 1 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:53.5
occ:1.00
 ND1 A:HIS32 2.0 44.8 1.0
SG A:CYS17 2.4 48.0 1.0
SG A:CYS33 2.4 49.0 1.0
NE2 A:HIS29 2.5 56.4 1.0
CE1 A:HIS29 2.6 56.4 1.0
CE1 A:HIS32 2.7 43.8 1.0
CG A:HIS32 3.2 45.0 1.0
CB A:CYS17 3.3 53.7 1.0
CB A:CYS33 3.5 49.6 1.0
CD2 A:HIS29 3.8 51.9 1.0
CB A:HIS32 3.8 43.8 1.0
ND1 A:HIS29 3.8 55.2 1.0
NE2 A:HIS32 3.9 43.2 1.0
N A:CYS17 4.1 56.9 1.0
N A:CYS33 4.1 46.4 1.0
CD2 A:HIS32 4.2 44.0 1.0
CA A:CYS33 4.3 48.1 1.0
CA A:CYS17 4.4 53.9 1.0
CG A:HIS29 4.4 52.5 1.0
C A:HIS32 4.5 44.5 1.0
CB A:SER15 4.6 48.5 1.0
O A:CYS33 4.6 45.4 1.0
CA A:HIS32 4.8 42.9 1.0
C A:CYS33 4.8 48.0 1.0
CD2 A:LEU76 4.9 40.2 1.0
N A:ALA16 4.9 52.9 1.0

Zinc binding site 2 out of 12 in 4n0o

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Zinc binding site 2 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:73.7
occ:0.99
 ND1 A:HIS44 2.4 60.4 1.0
SG A:CYS53 2.4 56.5 1.0
SG A:CYS42 2.4 67.3 1.0
SG A:CYS56 2.6 75.7 1.0
OE1 A:GLU57 3.2 68.5 1.0
CE1 A:HIS44 3.3 64.0 1.0
CG A:HIS44 3.4 65.6 1.0
CB A:CYS53 3.7 57.6 1.0
CB A:HIS44 3.7 61.9 1.0
CD A:GLU57 3.7 70.6 1.0
CG A:GLU57 4.0 71.5 1.0
CB A:CYS42 4.0 62.4 1.0
CB A:CYS56 4.4 74.8 1.0
CA A:CYS42 4.4 63.3 1.0
NE2 A:HIS44 4.4 68.8 1.0
OE2 A:GLU57 4.5 63.1 1.0
O A:CYS56 4.5 79.3 1.0
N A:HIS44 4.5 61.2 1.0
CD2 A:HIS44 4.5 65.7 1.0
CA A:HIS44 4.6 58.5 1.0
C A:CYS56 4.8 73.3 1.0
C A:CYS42 4.9 61.2 1.0
CA A:CYS53 5.0 54.2 1.0
CB A:GLU57 5.0 72.5 1.0

Zinc binding site 3 out of 12 in 4n0o

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Zinc binding site 3 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:46.1
occ:1.00
 SG A:CYS7 2.0 44.3 1.0
SG A:CYS25 2.2 39.4 1.0
SG A:CYS4 2.5 43.3 1.0
SG A:CYS22 2.6 44.2 1.0
CB A:CYS7 3.1 42.3 1.0
CB A:CYS4 3.3 43.7 1.0
CB A:CYS25 3.3 47.0 1.0
N A:CYS7 3.7 40.4 1.0
CB A:CYS22 3.7 45.5 1.0
CA A:CYS7 3.9 39.0 1.0
O A:HOH733 4.2 37.4 1.0
C A:VAL6 4.5 40.6 1.0
N A:CYS22 4.5 48.9 1.0
CA A:CYS22 4.5 47.8 1.0
CA A:CYS25 4.6 49.9 1.0
CB A:VAL6 4.7 37.2 1.0
N A:CYS25 4.7 53.3 1.0
C A:CYS7 4.7 38.9 1.0
N A:GLY8 4.7 36.6 1.0
CA A:CYS4 4.8 43.0 1.0
C A:CYS22 4.8 50.6 1.0
N A:VAL6 4.8 41.7 1.0
CA A:VAL6 4.8 38.8 1.0
CB A:ALA9 4.9 43.4 1.0
N A:ALA9 4.9 40.5 1.0
O A:CYS22 5.0 52.9 1.0

Zinc binding site 4 out of 12 in 4n0o

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Zinc binding site 4 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:43.0
occ:1.00
 NE2 C:HIS29 2.1 65.3 1.0
SG C:CYS17 2.1 35.0 1.0
ND1 C:HIS32 2.2 50.4 1.0
SG C:CYS33 2.6 67.0 1.0
CE1 C:HIS32 2.8 52.5 1.0
CB C:CYS17 2.9 35.2 1.0
CE1 C:HIS29 2.9 64.2 1.0
CD2 C:HIS29 3.2 63.8 1.0
CG C:HIS32 3.4 50.8 1.0
N C:CYS17 3.8 37.4 1.0
CA C:CYS17 3.9 35.7 1.0
CB C:HIS32 4.0 53.0 1.0
NE2 C:HIS32 4.1 50.7 1.0
ND1 C:HIS29 4.1 63.6 1.0
CB C:SER15 4.1 41.7 1.0
CB C:CYS33 4.2 58.4 1.0
CG C:HIS29 4.3 62.9 1.0
CD2 C:HIS32 4.4 51.3 1.0
N C:CYS33 4.4 53.6 1.0
CD2 C:LEU76 4.4 32.0 1.0
OG C:SER15 4.5 41.0 1.0
C C:ALA16 4.7 39.2 1.0
N C:ALA16 4.7 41.4 1.0
CA C:CYS33 4.8 56.5 1.0
C C:HIS32 4.9 50.9 1.0
CE2 C:PHE21 4.9 46.6 1.0
C C:CYS17 4.9 35.0 1.0

Zinc binding site 5 out of 12 in 4n0o

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Zinc binding site 5 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:83.1
occ:0.99
 SG C:CYS42 2.0 61.7 1.0
ND1 C:HIS44 2.7 64.7 1.0
CB C:HIS44 2.8 59.9 1.0
SG C:CYS56 2.9 71.3 1.0
CG C:HIS44 3.1 64.5 1.0
SG C:CYS53 3.1 69.6 1.0
CB C:CYS53 3.7 63.4 1.0
CB C:CYS42 3.7 59.0 1.0
CE1 C:HIS44 3.9 65.5 1.0
CA C:HIS44 4.2 59.0 1.0
CD2 C:HIS44 4.4 64.1 1.0
CB C:CYS56 4.5 69.5 1.0
N C:HIS44 4.6 58.5 1.0
CA C:CYS42 4.6 61.7 1.0
NE2 C:HIS44 4.7 65.2 1.0

Zinc binding site 6 out of 12 in 4n0o

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Zinc binding site 6 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:41.2
occ:1.00
 SG C:CYS25 2.1 41.2 1.0
SG C:CYS7 2.1 45.0 1.0
SG C:CYS4 2.5 43.8 1.0
CB C:CYS7 2.9 49.1 1.0
SG C:CYS22 3.1 63.5 1.0
CB C:CYS25 3.1 49.4 1.0
N C:CYS7 3.4 46.1 1.0
CA C:CYS7 3.7 46.1 1.0
CB C:CYS4 3.8 42.5 1.0
CB C:CYS22 4.1 57.1 1.0
C C:VAL6 4.3 47.8 1.0
CB C:VAL6 4.3 44.6 1.0
CG1 C:VAL6 4.4 45.1 1.0
CA C:CYS25 4.4 51.2 1.0
N C:CYS25 4.5 56.1 1.0
C C:CYS7 4.7 46.3 1.0
CA C:VAL6 4.7 43.2 1.0
N C:VAL6 4.8 42.8 1.0
N C:GLY8 4.8 46.2 1.0
N C:CYS22 4.9 55.0 1.0

Zinc binding site 7 out of 12 in 4n0o

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Zinc binding site 7 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:57.7
occ:1.00
 ND1 E:HIS32 2.2 53.6 1.0
NE2 E:HIS29 2.3 44.9 1.0
SG E:CYS33 2.4 51.7 1.0
SG E:CYS17 3.0 54.6 1.0
CD2 E:HIS29 3.0 44.8 1.0
CB E:CYS33 3.1 50.7 1.0
CG E:HIS32 3.1 54.6 1.0
CE1 E:HIS32 3.1 55.0 1.0
N E:CYS33 3.3 55.2 1.0
CB E:HIS32 3.4 53.2 1.0
CE1 E:HIS29 3.4 43.9 1.0
CA E:CYS33 3.7 54.8 1.0
CB E:CYS17 3.7 50.8 1.0
C E:HIS32 4.0 52.3 1.0
O E:CYS33 4.1 60.4 1.0
C E:CYS33 4.2 57.3 1.0
NE2 E:HIS32 4.3 57.4 1.0
CD2 E:HIS32 4.3 55.7 1.0
CG E:HIS29 4.3 45.5 1.0
CA E:HIS32 4.3 51.9 1.0
ND1 E:HIS29 4.4 41.4 1.0
OG E:SER15 4.6 54.0 1.0
CD2 E:LEU76 4.6 32.1 1.0
CB E:SER15 4.6 54.3 1.0
O E:HIS32 4.8 43.3 1.0
N E:CYS17 4.9 49.0 1.0
CA E:CYS17 5.0 49.5 1.0

Zinc binding site 8 out of 12 in 4n0o

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Zinc binding site 8 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:69.7
occ:0.99
 SG E:CYS42 2.2 62.7 1.0
SG E:CYS56 2.5 52.8 1.0
SG E:CYS53 2.6 65.6 1.0
ND1 E:HIS44 2.7 65.0 1.0
CB E:CYS42 2.8 65.3 1.0
CB E:CYS53 3.3 65.0 1.0
CE1 E:HIS44 3.4 65.1 1.0
CG E:HIS44 3.6 68.8 1.0
N E:CYS56 3.8 70.2 1.0
CB E:MET55 3.9 82.8 1.0
CB E:CYS56 4.0 63.3 1.0
CB E:HIS44 4.1 68.7 1.0
CA E:CYS42 4.3 65.8 1.0
C E:MET55 4.3 77.1 1.0
NE2 E:HIS44 4.4 69.5 1.0
CA E:CYS56 4.4 65.9 1.0
CA E:MET55 4.5 82.0 1.0
N E:MET55 4.5 84.0 1.0
CD2 E:HIS44 4.6 69.8 1.0
N E:HIS44 4.7 68.4 1.0
C E:CYS42 4.7 69.4 1.0
CA E:CYS53 4.7 67.6 1.0
O E:HOH743 4.7 37.6 1.0
N E:GLY43 4.9 69.0 1.0
N E:CYS42 5.0 64.8 1.0

Zinc binding site 9 out of 12 in 4n0o

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Zinc binding site 9 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:62.6
occ:1.00
 SG E:CYS7 2.0 48.3 1.0
SG E:CYS22 2.0 59.8 1.0
SG E:CYS4 2.5 56.1 1.0
SG E:CYS25 3.1 47.3 1.0
CB E:CYS22 3.3 56.1 1.0
CB E:CYS25 3.3 49.4 1.0
CB E:CYS7 3.6 49.6 1.0
CB E:CYS4 3.7 53.8 1.0
N E:CYS7 3.9 47.3 1.0
N E:CYS22 4.1 55.6 1.0
CA E:CYS22 4.2 55.8 1.0
CA E:CYS7 4.3 46.5 1.0
N E:CYS25 4.3 56.3 1.0
CB E:ALA9 4.4 46.0 1.0
CA E:CYS25 4.4 51.2 1.0
N E:ALA9 4.7 44.6 1.0
C E:CYS22 4.7 58.7 1.0
CB E:VAL6 4.8 53.2 1.0
N E:GLY8 4.8 45.6 1.0
C E:CYS7 4.8 46.2 1.0
C E:VAL6 4.9 48.7 1.0
N E:GLY23 5.0 59.4 1.0

Zinc binding site 10 out of 12 in 4n0o

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Zinc binding site 10 out of 12 in the Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Complex Structure of Arterivirus Nonstructural Protein 10 (Helicase) with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn501

b:52.2
occ:1.00
 NE2 G:HIS29 2.1 53.0 1.0
ND1 G:HIS32 2.1 44.7 1.0
SG G:CYS33 2.4 53.5 1.0
CE1 G:HIS29 2.4 52.4 1.0
SG G:CYS17 2.6 43.2 1.0
CE1 G:HIS32 3.0 47.4 1.0
CB G:CYS17 3.2 44.8 1.0
CG G:HIS32 3.2 44.3 1.0
CB G:CYS33 3.4 44.3 1.0
CD2 G:HIS29 3.4 54.3 1.0
CB G:HIS32 3.7 43.3 1.0
N G:CYS33 3.7 41.7 1.0
ND1 G:HIS29 3.7 51.1 1.0
CA G:CYS33 4.1 42.0 1.0
C G:HIS32 4.1 41.5 1.0
N G:CYS17 4.1 44.6 1.0
NE2 G:HIS32 4.2 46.0 1.0
OG G:SER15 4.2 47.1 1.0
CG G:HIS29 4.2 52.7 1.0
CA G:CYS17 4.3 42.6 1.0
CD2 G:HIS32 4.3 44.7 1.0
CB G:SER15 4.4 49.8 1.0
CA G:HIS32 4.5 41.5 1.0
O G:HIS32 4.6 42.3 1.0
CD2 G:LEU76 4.7 39.9 1.0
C G:CYS33 4.7 40.1 1.0
O G:CYS33 4.8 37.3 1.0

Reference:

Z.Deng, K.C.Lehmann, X.Li, C.Feng, G.Wang, Q.Zhang, X.Qi, L.Yu, X.Zhang, W.Feng, W.Wu, P.Gong, Y.Tao, C.C.Posthuma, E.J.Snijder, A.E.Gorbalenya, Z.Chen. Structural Basis For the Regulatory Function of A Complex Zinc-Binding Domain in A Replicative Arterivirus Helicase Resembling A Nonsense-Mediated Mrna Decay Helicase. Nucleic Acids Res. V. 42 3464 2014.
ISSN: ISSN 0305-1048
PubMed: 24369429
DOI: 10.1093/NAR/GKT1310
Page generated: Sun Oct 27 02:55:29 2024

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