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Zinc in PDB 1pp7: Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr

Protein crystallography data

The structure of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr, PDB code: 1pp7 was solved by M.A.Schumacher, A.O.T.Lau, P.J.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.43 / 2.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.340, 41.430, 58.390, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr (pdb code 1pp7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr, PDB code: 1pp7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1pp7

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Zinc binding site 1 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn74

b:80.0
occ:1.00
N7 E:DG26 2.2 39.3 1.0
C8 E:DG26 3.0 38.6 1.0
C5 E:DG26 3.3 40.1 1.0
O6 E:DG26 3.9 39.1 1.0
C6 E:DG26 4.0 39.5 1.0
N9 E:DG26 4.2 39.6 1.0
C4 E:DG26 4.4 41.7 1.0
O4 E:DT27 4.9 32.8 1.0

Zinc binding site 2 out of 7 in 1pp7

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Zinc binding site 2 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn72

b:84.8
occ:1.00
N7 F:DG8 2.1 45.9 1.0
C8 F:DG8 3.0 43.9 1.0
C5 F:DG8 3.2 44.3 1.0
O E:HOH77 3.5 33.4 1.0
O6 F:DG8 3.6 44.3 1.0
C6 F:DG8 3.8 47.1 1.0
N6 F:DA9 4.0 43.4 1.0
N9 F:DG8 4.2 45.2 1.0
C6 F:DT7 4.3 35.8 1.0
C4 F:DG8 4.3 41.3 1.0
C2' F:DT7 4.4 43.1 1.0
C5 F:DT7 4.6 36.8 1.0
N1 F:DT7 4.7 40.4 1.0
C7 F:DT7 4.8 31.5 1.0
C6 F:DA9 4.8 44.4 1.0
N7 F:DA9 4.9 42.2 1.0

Zinc binding site 3 out of 7 in 1pp7

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Zinc binding site 3 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn73

b:77.4
occ:1.00
N7 F:DG11 2.3 39.0 1.0
C8 F:DG11 3.2 46.2 1.0
C5 F:DG11 3.3 37.6 1.0
O6 F:DG11 3.7 27.6 1.0
C6 F:DG11 3.9 31.9 1.0
ZN F:ZN77 4.0 0.4 1.0
O4 F:DT12 4.2 36.1 1.0
C7 F:DT12 4.3 25.3 1.0
N9 F:DG11 4.3 49.4 1.0
C4 F:DG11 4.4 41.6 1.0
N7 F:DA10 4.6 49.0 1.0
C5 F:DA10 4.8 47.5 1.0
C8 F:DA10 4.9 53.9 1.0
C4 F:DT12 5.0 36.4 1.0

Zinc binding site 4 out of 7 in 1pp7

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Zinc binding site 4 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn76

b:93.1
occ:1.00
C5 F:DC3 2.6 36.7 1.0
C6 F:DC3 3.2 32.3 1.0
C4 F:DC3 3.8 33.1 1.0
O4 E:DT37 3.8 39.4 1.0
N4 F:DC3 4.0 31.0 1.0
N6 F:DA4 4.5 39.6 1.0
N1 F:DC3 4.6 36.9 1.0
C4 E:DT37 4.7 40.5 1.0
N3 F:DC3 5.0 28.3 1.0
C7 E:DT37 5.0 37.6 1.0

Zinc binding site 5 out of 7 in 1pp7

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Zinc binding site 5 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn77

b:0.4
occ:1.00
N7 F:DA10 2.6 49.0 1.0
C8 F:DA10 3.4 53.9 1.0
C5 F:DA10 3.7 47.5 1.0
N6 F:DA10 3.9 39.0 1.0
ZN F:ZN73 4.0 77.4 1.0
C6 F:DA10 4.2 40.8 1.0
N7 F:DA9 4.5 42.2 1.0
N9 F:DA10 4.6 56.5 1.0
C8 F:DA9 4.6 45.4 1.0
N7 F:DG11 4.7 39.0 1.0
O6 F:DG11 4.8 27.6 1.0
C4 F:DA10 4.8 51.9 1.0
C5 F:DA9 5.0 44.2 1.0

Zinc binding site 6 out of 7 in 1pp7

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Zinc binding site 6 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn132

b:39.6
occ:1.00
ND1 U:HIS39 2.1 26.3 1.0
O U:HOH144 2.3 23.4 1.0
CE1 U:HIS39 2.9 29.5 1.0
CG U:HIS39 3.1 27.0 1.0
CB U:HIS39 3.6 29.0 1.0
CG2 U:VAL115 3.8 28.1 1.0
OG1 U:THR43 3.9 36.7 1.0
NE2 U:HIS39 4.1 27.0 1.0
C U:HIS39 4.1 27.0 1.0
O U:HIS39 4.2 27.7 1.0
CD2 U:HIS39 4.2 26.8 1.0
N U:MET40 4.3 28.0 1.0
CA U:HIS39 4.5 24.8 1.0
CA U:MET40 4.7 27.9 1.0
CG U:MET40 4.8 53.8 1.0
CB U:THR43 4.9 31.9 1.0

Zinc binding site 7 out of 7 in 1pp7

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Zinc binding site 7 out of 7 in the Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the T. Vaginalis Initiator Binding Protein Bound to the Ferredoxin Inr within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn133

b:0.6
occ:1.00
OE2 U:GLU7 2.5 97.6 1.0
OE1 U:GLU7 2.9 98.5 1.0
CD U:GLU7 3.0 95.0 1.0
O U:HOH160 3.3 49.0 1.0
CG U:GLU7 4.5 90.4 1.0
CA U:GLY77 4.9 37.7 1.0

Reference:

M.A.Schumacher, A.O.T.Lau, P.J.Johnson. Structural Basis of Core Promoter Recognition in A Primitive Eukaryote Cell(Cambridge,Mass.) V. 115 413 2003.
ISSN: ISSN 0092-8674
PubMed: 14622596
DOI: 10.1016/S0092-8674(03)00887-0
Page generated: Mon Jan 25 16:11:32 2021

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