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Zinc in PDB 3tht: Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B

Protein crystallography data

The structure of Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B, PDB code: 3tht was solved by C.Pastore, I.Topalidou, F.Forouhar, A.C.Yan, M.Levy, J.F.Hunt, Northeaststructural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.06 / 3.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.166, 73.279, 149.814, 90.00, 112.73, 90.00
R / Rfree (%) 22 / 27.7

Other elements in 3tht:

The structure of Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B (pdb code 3tht). 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 and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B, PDB code: 3tht:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3tht

Go back to Zinc Binding Sites List in 3tht
Zinc binding site 1 out of 4 in the Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:37.6
occ:1.00
SG A:CYS343 2.3 39.2 1.0
ND1 A:HIS242 2.3 47.7 1.0
SG A:CYS349 2.4 37.4 1.0
SG A:CYS341 2.6 44.5 1.0
CB A:CYS349 2.8 38.5 1.0
CG A:HIS242 2.9 46.8 1.0
CE1 A:HIS242 3.1 48.1 1.0
CB A:HIS242 3.2 43.7 1.0
CA A:CYS349 3.6 38.7 1.0
CB A:CYS343 3.7 42.7 1.0
CD2 A:HIS242 3.8 48.5 1.0
CB A:CYS341 3.9 47.5 1.0
NE2 A:HIS242 3.9 48.3 1.0
N A:CYS343 4.1 44.6 1.0
OE1 A:GLN352 4.2 35.5 1.0
N A:CYS349 4.5 38.7 1.0
CA A:CYS343 4.5 43.5 1.0
CA A:HIS242 4.6 41.3 1.0
CD1 A:TYR288 4.7 33.5 1.0
C A:CYS349 4.7 39.9 1.0
C A:CYS341 4.9 47.5 1.0
N A:ASN342 4.9 47.0 1.0
CE1 A:TYR288 4.9 35.1 1.0
O A:TYR345 4.9 39.2 1.0
CG A:TYR288 4.9 31.8 1.0

Zinc binding site 2 out of 4 in 3tht

Go back to Zinc Binding Sites List in 3tht
Zinc binding site 2 out of 4 in the Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:30.9
occ:1.00
SG B:CYS343 2.2 34.8 1.0
ND1 B:HIS242 2.3 36.0 1.0
SG B:CYS349 2.3 39.8 1.0
SG B:CYS341 2.4 31.3 1.0
CG B:HIS242 3.0 36.3 1.0
CB B:CYS349 3.0 36.3 1.0
CB B:HIS242 3.0 35.0 1.0
CE1 B:HIS242 3.4 35.3 1.0
CA B:CYS349 3.6 35.5 1.0
CB B:CYS341 3.6 34.9 1.0
CB B:CYS343 3.7 37.2 1.0
N B:CYS343 4.0 37.3 1.0
NE2 B:GLN352 4.2 36.0 1.0
CD2 B:HIS242 4.2 37.0 1.0
CD1 B:TYR288 4.2 28.1 1.0
CE1 B:TYR288 4.3 30.6 1.0
NE2 B:HIS242 4.4 36.2 1.0
O B:CYS341 4.4 37.0 1.0
C B:CYS341 4.4 36.8 1.0
CA B:HIS242 4.4 34.3 1.0
CA B:CYS343 4.4 37.2 1.0
N B:CYS349 4.6 34.0 1.0
CA B:CYS341 4.7 36.1 1.0
N B:ASN342 4.7 36.5 1.0
C B:CYS349 4.7 36.1 1.0
C B:HIS242 4.9 33.5 1.0
O B:HIS242 4.9 34.7 1.0
O B:CYS343 5.0 37.9 1.0

Zinc binding site 3 out of 4 in 3tht

Go back to Zinc Binding Sites List in 3tht
Zinc binding site 3 out of 4 in the Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.0
occ:1.00
ND1 C:HIS242 2.2 54.4 1.0
SG C:CYS343 2.3 49.2 1.0
SG C:CYS341 2.4 51.4 1.0
SG C:CYS349 2.5 66.7 1.0
CB C:CYS349 2.8 63.4 1.0
CB C:CYS341 3.1 54.1 1.0
CG C:HIS242 3.1 55.3 1.0
CE1 C:HIS242 3.2 56.0 1.0
CB C:HIS242 3.4 53.1 1.0
CB C:CYS343 3.8 54.4 1.0
CA C:CYS349 3.8 62.9 1.0
N C:CYS343 3.9 57.3 1.0
NE2 C:GLN352 4.2 59.8 1.0
C C:CYS341 4.2 55.8 1.0
CA C:CYS341 4.3 55.2 1.0
CD2 C:HIS242 4.3 57.3 1.0
NE2 C:HIS242 4.3 58.0 1.0
N C:ASN342 4.3 56.9 1.0
CE1 C:TYR288 4.4 47.2 1.0
CA C:CYS343 4.4 56.4 1.0
CD1 C:TYR288 4.5 46.7 1.0
O C:TYR345 4.6 49.3 1.0
O C:CYS341 4.6 55.1 1.0
N C:CYS349 4.7 61.3 1.0
C C:ASN342 4.8 57.7 1.0
CA C:HIS242 4.9 51.7 1.0
C C:CYS349 4.9 63.2 1.0
OG C:SER351 4.9 58.7 1.0
O C:CYS343 4.9 56.2 1.0
CA C:ASN342 4.9 58.2 1.0

Zinc binding site 4 out of 4 in 3tht

Go back to Zinc Binding Sites List in 3tht
Zinc binding site 4 out of 4 in the Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure and Rna Binding Properties of the Rrm/Alkb Domains in Human ABH8, An Enzyme Catalyzing Trna Hypermodification, Northeast Structural Genomics Consortium Target HR5601B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:40.8
occ:1.00
SG D:CYS343 2.2 34.1 1.0
ND1 D:HIS242 2.2 30.3 1.0
SG D:CYS349 2.3 32.6 1.0
SG D:CYS341 2.4 33.7 1.0
CB D:CYS349 2.9 34.5 1.0
CE1 D:HIS242 3.0 29.7 1.0
CG D:HIS242 3.2 30.6 1.0
CB D:CYS343 3.4 39.7 1.0
CB D:HIS242 3.6 30.8 1.0
CB D:CYS341 3.6 39.9 1.0
CA D:CYS349 3.9 35.2 1.0
N D:CYS343 3.9 44.7 1.0
NE2 D:HIS242 4.1 30.4 1.0
CD2 D:HIS242 4.2 30.8 1.0
CA D:CYS343 4.3 41.6 1.0
CE1 D:TYR288 4.3 26.8 1.0
CD1 D:TYR288 4.3 27.4 1.0
OE1 D:GLN352 4.5 46.4 1.0
C D:CYS341 4.5 42.9 1.0
O D:CYS341 4.7 44.3 1.0
CA D:CYS341 4.7 41.5 1.0
N D:ASN342 4.8 43.0 1.0
N D:CYS349 4.8 34.6 1.0
C D:CYS349 4.9 35.6 1.0
O D:TYR345 4.9 32.9 1.0
CA D:HIS242 5.0 31.3 1.0
CZ D:TYR288 5.0 25.9 1.0
CG D:TYR288 5.0 28.7 1.0

Reference:

C.Pastore, I.Topalidou, F.Forouhar, A.C.Yan, M.Levy, J.F.Hunt. Crystal Structure and Rna Binding Properties of the Rna Recognition Motif (Rrm) and Alkb Domains in Human Alkb Homolog 8 (ABH8), An Enzyme Catalyzing Trna Hypermodification. J.Biol.Chem. V. 287 2130 2012.
ISSN: ISSN 0021-9258
PubMed: 22065580
DOI: 10.1074/JBC.M111.286187
Page generated: Wed Dec 16 04:52:22 2020

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