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Zinc in PDB 4i2i: Binary Complex of Mouse Tdt with AP5A

Enzymatic activity of Binary Complex of Mouse Tdt with AP5A

All present enzymatic activity of Binary Complex of Mouse Tdt with AP5A:
2.7.7.31;

Protein crystallography data

The structure of Binary Complex of Mouse Tdt with AP5A, PDB code: 4i2i was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.10 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.750, 84.100, 103.890, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24

Other elements in 4i2i:

The structure of Binary Complex of Mouse Tdt with AP5A also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Binary Complex of Mouse Tdt with AP5A (pdb code 4i2i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Binary Complex of Mouse Tdt with AP5A, PDB code: 4i2i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4i2i

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Zinc binding site 1 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:44.7
occ:1.00
 OD1 A:ASP345 2.1 38.4 1.0
N7B A:AP5601 2.1 85.2 1.0
OD2 A:ASP434 2.1 45.2 1.0
OD2 A:ASP343 2.3 46.6 1.0
C8B A:AP5601 2.9 85.2 1.0
O1D A:AP5601 3.0 87.8 1.0
CG A:ASP345 3.0 32.8 1.0
CG A:ASP343 3.1 41.2 1.0
CG A:ASP434 3.2 43.2 1.0
OD1 A:ASP343 3.2 45.4 1.0
C5B A:AP5601 3.2 86.6 1.0
OD2 A:ASP345 3.3 37.1 1.0
MG A:MG609 3.4 62.2 1.0
N6B A:AP5601 3.8 87.9 1.0
CB A:ASP434 3.8 32.8 1.0
C6B A:AP5601 4.0 87.7 1.0
PD A:AP5601 4.0 88.8 1.0
N9B A:AP5601 4.1 86.1 1.0
OD1 A:ASP434 4.2 45.9 1.0
C4B A:AP5601 4.3 86.6 1.0
O3D A:AP5601 4.3 79.9 1.0
CB A:ASP345 4.4 25.0 1.0
CZ3 A:TRP450 4.4 41.3 1.0
CB A:ASP343 4.5 33.6 1.0
O3G A:AP5601 4.5 94.8 1.0
O A:HOH747 4.6 46.5 1.0
NH2 A:ARG432 4.8 44.1 1.0

Zinc binding site 2 out of 7 in 4i2i

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Zinc binding site 2 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:51.7
occ:1.00
 O A:HOH803 2.2 29.8 1.0
ND1 A:HIS416 2.2 45.3 1.0
O A:HOH804 2.2 36.1 1.0
O A:HOH802 2.4 26.6 1.0
CG A:HIS416 3.2 41.5 1.0
CE1 A:HIS416 3.2 45.5 1.0
CB A:HIS416 3.4 37.4 1.0
CA A:HIS416 4.0 36.1 1.0
CD2 A:HIS416 4.3 42.6 1.0
NE2 A:HIS416 4.4 44.3 1.0
C A:HIS416 4.9 43.2 1.0

Zinc binding site 3 out of 7 in 4i2i

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Zinc binding site 3 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:61.9
occ:1.00
 NE2 A:HIS412 1.9 33.5 0.5
CE1 A:HIS412 2.1 34.1 0.5
OE2 A:GLU307 2.1 43.5 1.0
O A:HOH798 2.3 24.9 1.0
O A:HOH863 2.9 30.0 1.0
CD A:GLU307 3.1 52.6 1.0
CD2 A:HIS412 3.2 34.8 0.5
ND1 A:HIS412 3.4 36.4 0.5
CG A:GLU307 3.5 28.9 1.0
CG A:HIS412 3.9 35.4 0.5
O A:HOH799 4.1 45.6 1.0
OE1 A:GLU307 4.2 45.2 1.0
ND2 A:ASN304 4.3 32.7 1.0
OD1 A:ASN304 4.4 31.6 1.0
CG1 A:VAL415 4.7 38.2 1.0
CG A:ASN304 4.8 36.5 1.0
CD A:LYS429 4.8 27.4 1.0
NZ A:LYS429 4.9 53.7 1.0
CB A:GLU307 5.0 25.4 1.0

Zinc binding site 4 out of 7 in 4i2i

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Zinc binding site 4 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:77.8
occ:1.00
 NE2 A:HIS466 2.1 54.8 1.0
O A:HOH807 2.1 35.2 1.0
CE1 A:HIS466 3.0 55.8 1.0
CD2 A:HIS466 3.1 53.2 1.0
O A:HOH806 3.1 71.7 1.0
ND1 A:HIS466 4.2 55.5 1.0
CG A:HIS466 4.2 51.4 1.0
CG A:ARG462 4.5 52.5 1.0
CG2 A:THR465 4.9 34.8 1.0

Zinc binding site 5 out of 7 in 4i2i

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Zinc binding site 5 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:79.2
occ:1.00
 OE2 A:GLU264 2.2 0.7 1.0
O A:HOH796 2.3 29.5 1.0
CD A:GLU264 3.2 97.4 1.0
O A:HOH808 3.2 54.6 1.0
OE1 A:GLU264 3.6 90.9 1.0
CG A:GLU264 4.5 63.7 1.0
O A:HOH820 4.6 54.7 1.0

Zinc binding site 6 out of 7 in 4i2i

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Zinc binding site 6 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:67.7
occ:1.00
 OD2 A:ASP473 2.0 55.4 1.0
ND1 A:HIS475 2.1 44.8 1.0
O A:HOH775 2.1 28.9 1.0
CG A:ASP473 2.8 47.2 1.0
CE1 A:HIS475 2.9 45.0 1.0
OD1 A:ASP473 3.0 48.5 1.0
CG A:HIS475 3.2 42.4 1.0
CB A:HIS475 3.6 37.0 1.0
NE2 A:HIS475 4.1 45.3 1.0
CD2 A:HIS475 4.2 44.7 1.0
CB A:ASP473 4.2 30.6 1.0
O A:HOH777 4.5 41.7 1.0
N A:HIS475 4.6 32.7 1.0
CA A:HIS475 4.6 33.8 1.0
O A:HOH720 4.8 49.4 1.0
N A:ALA476 4.9 31.4 1.0

Zinc binding site 7 out of 7 in 4i2i

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Zinc binding site 7 out of 7 in the Binary Complex of Mouse Tdt with AP5A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Binary Complex of Mouse Tdt with AP5A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn608

b:71.7
occ:1.00
 OD2 A:ASP179 1.9 64.5 1.0
SG A:CYS188 2.4 64.9 1.0
CG A:ASP179 3.0 63.6 1.0
CB A:CYS188 3.3 58.8 1.0
OD1 A:ASP179 3.5 62.9 1.0
N A:CYS188 3.8 59.1 1.0
CA A:CYS188 4.1 57.3 1.0
CB A:ASP179 4.2 55.4 1.0
NH1 A:ARG182 4.9 52.3 1.0
C A:SER187 5.0 61.2 1.0

Reference:

J.Gouge, S.Rosario, F.Romain, P.Beguin, M.Delarue. Structures of Intermediates Along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism. J.Mol.Biol. V. 425 4334 2013.
ISSN: ISSN 0022-2836
PubMed: 23856622
DOI: 10.1016/J.JMB.2013.07.009
Page generated: Sun Oct 27 00:29:14 2024

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